Hepetieties Virus

1
Introduction
Bioinformatics is an interdisciplinary research area at the interface between
computer science and biological science. It involves the technology that uses
computers for storage, retrieval, manipulation and distribution of
information related to biological macromolecules such as DNA, RNA and
proteins. Bioinformatics is limited to seuence, structural, and functional
analysis of genes and genomes and their corresponding products and is often
considered computational molecular biology. It consists of two subfields! the
development of computational tools and databases and the application of
these tools and databases in generating biological "nowledge to better
understand living systems. #hese tools are used in three areas of genomic
and molecular biological research! molecular seuence analysis, molecular
structural analysis and molecular functional analysis. #he areas of seuence
analysis include seuence alignment, seuence database searching, motif
and pattern discovery, gene and promoter finding, reconstruction of
evolutionary relationships, and genome assembly and comparison.
$tructural analyses include protein and nucleic acid structure analysis,
comparison, %lassification and prediction. #he functional analysis includes
gene e&pression profiling, protein' protein interaction prediction, protein sub
cellular locali(ation prediction, metabolic pathway reconstruction, and
simulation. #he three aspects of bioinformatics analysis are not isolated but
often interact to produce integrated results. )or e&ample, protein structure
prediction depends on seuence alignment data* clustering of gene
e&pression profiles reuires the use of phylogenetic tree construction
methods derived In seuence analysis. $euence' based prediction is related
functional analysis of co e&pressed genes. #he first ma+or bioinformatics
,
pro+ect was underta"en by -argaret Day off in 1./0, who developed a first
protein seuence database called Atlas of 1rotein $euence and $tructure.
$ubseuently, in the early 1.23s, the Broo"haven national laboratory
established the 1rotein Data Ban" for archiving three'dimensional protein
structures. At its onset, the database stored less than a do(en protein
structures, compared to more than 43,333 structures today. #he first
seuence alignment algorithm was developed by Needleman and 5unsch in
1.23. #his was a fundamental step in the development of the field of
bioinformatics, which paved the way for the routine seuence comparisons
and database searching practiced by modern biologists.
13 #he recent advance of Bioinformatics is molecular modeling which is
aimed at understanding structure'function and structure property relationship
in physic'chemical processes and pharmaceuticals 6 thus has become
increasingly important for finding and designing new drugs. In fact
computers are playing an important role in new drug discovery and drug
design.
HEPATITIS:-
4
Hepatitis 7plural hepatitides8 implies in+ury
to liver characteri(ed by presence of inflammatory cells in the
liver tissue. 9tymologically from ancient :ree" hepar or hepato' meaning
;liver,; and suffi& -itis, denoting ;inflammation<. #he condition can be self
limiting, healing on its own, or can progress to scarring of the liver
. Hepatitis is acute when it lasts less than 6 months
and chronic when it persists longer. A group of
viruses known as the hepatitis viruses cause most cases of
liver damage worldwide. Hepatitis can also be due to toxins
(notably alcohol), other infections or
from autoimmune process.
t may run a sub
clinical course when the a!ected person may not feel ill.
"he patient becomes unwell and symptomatic when the
disease impairs liver functions that include, among other
things, screening of harmful substances, regulation of blood
composition, and production of bile to help digestion.
=
Causes
Acute hepatitis
#iral Hepatitis$ Hepatitis A to % (more than &'( of viral
cause), Herpes simplex, )ytomegalovirus, %pstein*
+arr, ,ellow fever virus, Adenoviruses.
-on viral infection$ "oxoplasma, .eptospira, /
fever, 0ocky mountain spotted fever
Alcohol
"oxins$ Amanita toxin in mushrooms, )arbon
tetrachloride, Asafetida
1rugs$ 2aracetamol, Amoxicillin, Antituberculosis
medicines, 3inocycline and many others.
schemic hepatitis (circulatory insu4ciency)(5)
2regnancy
Auto immune conditions, e.g. 6ystemic .upus
%rythematosus (6.%)
3etabolic diseases, e.g. 7ilson8s disease
Chronic hepatitis
#iral hepatitis$ Hepatitis + with or without hepatitis 1,
hepatitis ) (Hepatitis A and % do not lead to chronic
disease)
0
Autoimmune$ Autoimmune hepatitis
Alcohol
1rugs$ 3ethyl*dopa, -itrofurantoin,isonia9ide, :etocon
a9ole
-on*alcoholic steatohepatitis
Heredity$ 7ilson8s disease, alpha 5*antitrypsin
de;ciency
2rimary biliary cirrhosis and primary sclerosing
cholangitis occasionally mimic chronic hepatitis

Viral hepatitis
A virus is a particle which is smaller than bacteria, and contains comple&
genetic information called DNA or RNA. #his genetic material allows the
virus to infect bacteria or living cells, set up the machinery to reproduce
itself, leading to destruction of the cell in which it resides. #o date, five
viruses, labeled A through 9, have been identified which appear to cause
viral hepatitis. >iruses A and 9 can be contracted from contaminated water
or food 7by mouth8, while viruses B, % and D are transmitted by direct
in+ection into the bloodstream 7through any method of in+ection under the
s"in8. #he term viral hepatitis describes any one of the illnesses caused by
the five viruses mentioned, and consists of an infection of liver cells which
leads to damage of the liver over days in some cases, but over many years in
others. #hirty years ago, none of the hepatitis viruses had been identified. In
the 1./3;s, transfusion'related viral hepatitis was e&tremely common, with
43? of patients receiving blood products becoming infected. By 1.23, a
/
blood test called the Australia antigen, was developed which appeared to
identify those infected with one hepatitis virus which we now call hepatitis
B. #he investigator who discovered the Australia antigen, the protein which
ma"es up the coat of the virus and which is now called the hepatitis B
surface antigen 7@BsAg8, was awarded the Nobel pri(e. Aur understanding
of viral hepatitis has grown tremendously since the discovery of the
Australia antigen.
%urrently 11 viruses are recogni(ed as causing hepatitis,
#wo are herpes viruses 7cytomegalovirus virus B%->C and 9pstein' Barr
virusB9B>C8 and . are hepatotropic viruses 9B> and %-> cause mild ,self'
resolving forms of hepatitis with no permanent hepatic damage. Both viruses
causes the typical infectious mononucleosis of fatigue ,nausea , and malaise.
Af the nine human hepatotrofic viruses ,only five are well
characteri(ed* hepatitis : and ##>7transfusion transmitted virus8 are newly
discovered viruses .hepatitis A 7sometimes called infectious hepatitis8, and
hepatic 9 7formally called enteric Dtransmitted NANB hepatitis8 ,are
transmitted by fecal'oral contamination .#he most important type include
hepatitis B7sometime called serum hepatitis8, hepatitis % 7formally called
formally non'A ,non'B hepatic8, and hepatitis D 7formally called delta
hepatitis8.
Hepatitis A
Incubation period 4'0 wee"s 7mean ,E days8
-ilder disease than @epatitis B* asymptomatic infections are very common,
especially in children.
2
Adults, especially pregnant women, may develop more severe disease.
Although convalescence may be prolonged, there is no chronic form of the
disease. )ulminant hepatitis is rare! 3.1? of cases >irus enters via the gut*
replicates in the alimentary tract and spreads to infect the liver, where it
multiplies in hepatocytes.
>iraemia is transient. Virus is excreted in the stools for two weeks
preceding the onset of symptoms.

5orld'wide distribution* endemic in most countries. #he incidence in first
world countries is declining. #here is an especially high incidence in
developing countries and rural areas. In rural areas of $outh Africa , the
seroprevalence is 133?.
Hepatitis E
Incubation period 43'=3 days
Acute, self limiting hepatitis, no chronic carrier state
Age! predominantly young adults, 10'=3 years .)ulminate hepatitis in
pregnant women. -ortality rate is high 7up to =3?8.$imilar to hepatitis A*
virus replicates in the gut initially, before invading the liver, and virus is
shed in the stool prior to the onset of symptoms. >iraemia is transient. A
large inoculum of virus is needed to establish infection.Fittle is "nown yet.
#he incidence of infection appears to be low in first world countries.
E
Hepatitis C
1utative Togavirus related to the )lavi and 1esti viruses.
#hus probably enveloped. @as a ssRNA genome
Does not grow in cell culture, but can infect %himpan(ees Incubation period
/'E wee"s
%auses a milder form of acute hepatitis than does hepatitis B
But 03? individuals develop chronic infection, following e&posure.
18 %hronic liver disease
,8 @epatocellular carcinoma
Incidence endemic world'wide* high incidence in Gapan, Italy and $pain
In $outh Africa, 1? blood donors have antibodies
Hepatitis D
Defective virus which reuires @epatitis B as a helper virus in order to
replicate. Infection therefore only occurs in patients who are already
infected with Hepatitis B.Increased severity of liver disease in @epatitis B
carriers. virus particle 4/ nm in diameter encapsulated with @BsAg, derived
from @B> delta antigen is associated with virus particles ssRNA genome
Identified in intra'venous drug abusers
Hepatitis
A virus originally cloned from the serum of a surgeon with non'A, non'B,
non'% hepatitis, has been called @epatitis : virus. It was implicated as a
.
cause of parenterally transmitted hepatitis, but is no longer believed to be a
ma+or agent of liver disease. It has been classified as a )lavivirus

Hepatitis !
"hat is the Hepatitis ! Virus#
#he hepatitis B virus 7@B>8 is a DNA'containing virus which is capable of
infecting human liver cells and other cells in the body, once it gains access to
the blood stream. Ane of the most interesting features of the hepatitis B virus
is that the virus itself does not damage the liver, the damage being caused by
the individual;s own immune system attac"ing the virus'infected cells. $ince
liver damage from the virus may be very little, many patients are called
healthy carriers. #his means that although they may transmit the disease to
others, they have normal'appearing livers and normal liver function tests.
5hile many individuals remain healthy for many years or a lifetime, others
develop chronic hepatitis, cirrhosis, and occasionally liver cell cancer. #hese
outcomes are lin"ed to the virus and its effects, although it is unli"ely that
the virus directly causes cancer. #hose patients who develop hepatitis
7damage to liver cells with inflammation8, do so on account of the body;s
normal inclination to attac" the foreign proteins contained in viruses, and in
the cells in which the viruses are found. #his process, called the immune
response, determines the pace and the severity of the liver cell in+ury in this
condition, and will be described in more detail below.
$ince the identification of the hepatitis B virus, several other viruses which
are nearly identical, have been identified in 9astern woodchuc"s, ground
suirrels and 1e"ing duc"s. #he members of this virus family, termed the
13
;@epadna; viruses, have similar life cycles to that observed in man and can
serve as animal models, allowing further study of these uniue disease'
causing agents.

Classification and general features$
%amily $ hepadnaviridae
enera ! orthohepadnavirus7e.g.hepatitis B B@B>C of human 8
,Avihepadnavirus 7e.g. Duc" hepatitis B virus8
&i'e =,nm >irions 7also "nown as HDane particlesH8 contain a circular
dsDNA genome.
11
Fig.hepatitis B virus structure

HBV Antigens
H!sAg I surface 7coat8 protein produced in e&cess as spheres 6 tubules
H!cAg I inner core protein
H!eAg I secreted protein* function un"nown.
Clinical Features Incubation period , ' 0 months

Insidious onset of symptoms. #ends to cause a more severe disease than
@epatitis A.
Asymptomatic infections occur freuently.
Pathogenesis
Infection is parenterally transmitted. #he virus replicates in the liver and
virus particles, as well as e&cess viral surface protein, are shed in large
amounts into the blood. >iraemia is prolonged and the (lood of infected
individuals is highly infectious.
Complications
18 1ersistant infection!'
)ollowing acute infection, appro&imately 0? of infected individuals fail to
eliminate the virus completely and become persistantly infected.
1,
#hose who are at particular ris" include!
babies, young children
immunocompromised patients
males J females
#he virus persists in the hepatocytes and on)going liver damage occurs
because of the host immune response against the infected liver cells.
Chronic infection may ta"e one of two forms!
Chronic persistent Hepatitis ' the virus persists, but there is minimal liver
damage
Chronic Active Hepatitis ' #here is aggressive destruction of liver tissue and
rapid progression to cirrhosis or liver failure. 1atients who become
persistently infected are at ris" of developing hepatocellular carcinoma
*HCC+,
@B> is thought to play a role in the development of this malignancy
because!
a8 E3? of patients with @%% are carriers of hepatitis B.
b8 >irus DNA can be identified in hepatocellular carcinoma cells.
c8 >irus DNA can integrate into the host chromosome.
-+ %ulminant Hepatitis
Rare* accounts for 1? of infections.
Epidemiology
.revalence of disease in Africa
5orld'wide there are =03 million persistant carriers of hepatitis B, 03
14
million of which are in Africa. %arriage rates vary mar"edly in different
areas. In $outh Africa, infection is much more common in rural communities
than in the cities. Hepatitis B is parenterally transmitted
18 !lood$
Blood transfusions, serum products,
sharing of needles, ra(ors
#attooing, acupuncture
Renal dialysis
Argan donation
,8 &exual intercourse
48 Hori'ontal transmission in children, families, ;close personal contact;.
#his is the ma+or mode of transmission in $outh Africa where the ma+ority
of individuals become infected at between three and nine years of age.
@ori(ontal transmission also occurs in children;s institutions and mental
homes.
=8 Vertical transmission ' perinatal transmission from a carrier mother to
her baby
1=
#ran placental 7rare8
during delivery
1ost natal , KK breast feeding , KKclose contact
(This is the major mode of transmission in South East Asia)
Diagnosis! &erology
Acute infection with resolution Viral antigens
18 &urface antigen *H!sAg+ is secreted in e&cess into the blood as ,, nm
spheres and tubules. Its presence in serum indicates that virus replication is
occurring in the liver
,8 /e/ antigen *H!eAg+ secreted protein is shed in small amounts into the
blood. Its presence in serum indicates that a high level of viral replication is
48 core antigen 7@BcAg8 core protein is not found in blood
Anti(ody response$
18 &urface anti(ody 7anti'@Bs8 becomes detectable late in convalescence,
10
and indicates immunity following infection. It remains detectable for life
and is not found in chronic carriers 7see below8.
,8 e anti(ody 7anti'@Be8 becomes detectable as viral replication falls. It
indicates low infectivity in a carrier.
48 Core Ig0 rises early in infection and indicates recent infection
=8 Core Ig rises soon after Ig-, and remains present for life in both
chronic carriers as well as those who clear the infection. Its presence
indicates e&posure to @B>.of the chronic carrier

%ig,Hepatitis ! virus in serum.
Prevention
1+ Active Immuni'ation
#wo types of vaccine are available!
1/
&erum derived ' prepared from @BsAg purified from the serum of
@B> carriers
2ecom(inant @BsAg ' made by genetic engineering in yeasts
Both vaccines are eually safe and effective. #he administration of three
doses induces protective levels of antibodies in .0? of vaccine recipients.
Lniversal immuni(ation of infants was introduced in April 1..0. Infants
receive 4 doses at /, 13 and 1= wee"s of age.
>accine should be administered to people at high ris" of infection with
@B>!
18 @ealth care wor"ers
,8 $e&ual partners of chronic carriers
48 Infants of @B> carrier mothers
3+ .assive Anti(ody
@epatitis B immune globulin should be administered to non immune
individuals following single episode e&posure to @B>'infected blood. )or
e&ample! needle stic" in+uries.
5hat is @epatitis B Infection Fi"eK
5hen most individuals become infected with the hepatitis B virus, they are
not aware of the infection for several wee"s, until they develop symptoms of
acute hepatitis, such as nausea, fatigue and +aundice 7yellowing of the eyes8.
#he acute hepatitis phase may last for several wee"s and occasionally leads
to hospitali(ation, but acute hepatitis B resolves completely in .0? of those
infected.
12
Athers who do not develop significant symptoms
following e&posure may not be aware of the infection. #hese individuals
may also overcome the infection completely and develop immunity, but
freuently become chronic carriers.
#he outcome of hepatitis B infection depends to a great
e&tent on the status of the person;s immune system at the time of e&posure.
-ost chronic carriers or those with chronic hepatitis B are not aware of their
on'going infection, although some have persistent fatigue.
0olecular virology
:enome ! circular and 4.,"b in si(e, double stranded. It has compact
1E
%ig, hepatitis ! virus genome
organi(ation, with four overlapping reading frames running in one direction
and no noncoding regions. #he minus strand is unit length and has a protein
covalently attached to the 0; end. #he other strand, the plus strand, is
variable in length, but has less than unit length, and has an
RNA oligonulceotide at its 0; end. #hus neither DNA strand is closed and
circularity is maintained by cohesive ends 7$trauss, ,33,8. #he four
overlapping open reading frames 7AR)s8 in the genome are responsible for
the transcription and e&pression of seven different hepatitis B proteins. #he
transcription and translation of these proteins is through the used of multiple
in'frame start codons. #he @B> genome also contains parts that regulate
transcription, determine the site of polyadenylation and a specific transcript
for encapsidation into the nucleocapsid.

4ife cycle
In order to reproduce, the hepatitis B virus, must first attach onto a cell which is
capable of supporting its replication. Although hepatocytes are "nown to be the most
effective cell type for replicating @B>, other types of cells in the human body have
be found to be able to support replication to a lesser degree.
#he initial steps following @B> entry are not clearly defined
although it is "nown that the virion initially attaches to a susceptible hepatocyte
through recognition of cell surface receptor that has yet to be indified 7:arces,
1.
@B>18. #he DNA is then enters into the nucleus, where it is "nown to form a
convalently close circular form called cccDNA
. #he 7'8 strand of cccDNA is the template for
transcription by RNA polII of a longer than genome length RNA called the
pregenome and shorter subgenomic transcripts, all of which serve as mRNAs. #he
shorter viral mRNAs are translated by ribosomes attached to the cell;s endoplasmic
reticulum and the proteins that are destined to become @B> surface antigens in the
viral envelope are assembled.
#he pregenome RNA is translated to produce a polymerase protein, 1,
which then binds to a specific site at the 4; end of its own transcript, where viral
DNA synthesis eventually occurs. Accuring at the same time as capsid formation,
the RNA'1 protein comple& is pac"aged and reverse transcription begins.
At early times after the infection, the DNA is recirculated
to the nucleus, where the process is repeated, resulting in the the accumulation of 13
to 43 molecules of %%% DNA and an increase in viral mRNA concentrations
7)lint etal., 2/08.
,3
)ig. @B> life cycle
#he hepatitis B virion, also "nown as the Dane particle, is the one infectious
particle found within the body of an infected patient. #his virion has a
diameter of =,nm and its outer envelope contains a high uantity of hepatitis
b surface proteins. #he envelope surrounds the inner nucleocapsid which is
made up of 1E3 hepatitis B core proteins arranged in an icosahedral
arrangement. #he nucleocapsid also contains at least one hepatitis b
ploymerase protein 718 along with the @B> genome.

,1
In infected people, virions actually compose a small minority of @B>'
derived particles. Farge numbers of smaller subviral particles are also
present,that usually outnumber the virions in the ratio of 133!1.#hese two
subviral particles the hepatitis B filament and a hepatitis B sphere,are often
referred to as a group named surface antigen particles.#he sphere contains
both middle and small surface proteins whereas the filament also includes
large hepatitis B surface protein lso includes large hepatitis B surface
protein. #he absence of the hepatitis B core, polymerase, and genome causes
these particles to have a non'infectious nature. @igh levels of these non'
infectious particles can be found during the acute phase of the infection.
$ince the non'infectious particles present the same sites as the virion, they
induce a significant immune response and are thought to be non'
advantagous for the virus. @owever, it is also believed that the presence of
high levels of non'infectious particles may allow the infectious viral
particles to travel undetected by antibodies through the blood stream
7:arces, @B>1

Hepatitis ! Antigens$
#here are three different types of hepatitis b antigens encoded by the @B>
genome'
.@epatitis B $urface antigen 7@BsAg8' #here are three different types of
hepatitis B surface antigens* small hepatitis B surface antigen 7@BsAg or
$@BsAg8, middle hepatitis B surface antigen 7-@BsAg8, and large hepatitis
B surface Antigen 7F@BsAg8. @BsAg is the smallest protein of the hepatitis
,,
B surface proteins and has historically been "nown as the Australia antigen
7Au antigen8. It is very hydrophobic, containing four'transmembrane
spanning regions. #his protein is the prime constituent of all hepatitis b
particle forms and appears to be manufactured by the virus in high
uantities. It also contains a highly antigenic epitope which may be
responsible for triggering immune response. Regardless of the high
Antigenicity and prevalence of these particles,the immune system appears
basically oblivious to their presence.
@epatitis B %ore Antigen 7@BcAg8' #he only @B> antigen that can not be
detected directly by blood test, this antigen can only be isolated by analy(ing
an infected hepatocyte. A 1E0 amino acid protein is e&pressed in the
cytoplasm of infected cells, they are highly associated with nucleocapsid
assembly 7$trauss, ,33,8.
@epatitis B e Antigen 7@BeAg8' #he e antigen is named due to its HearlyH
appearance during an acute @B> infection. #hought to be located in the core
structure of the virus molecule, this antigen can be detected by blood test. If
found its usually indicative of complete virus particles in circulation.
7$trauss, ,33,8
,4

2EVIE" 5% 4ITE2AT62E
Appro&imately 0? of the world population is infected by the hepatitis B
virus 7@B>8 that causes a necroinflammatory liver disease of variable
duration and severity. %hronically infected patients with active liver disease
carry a high ris" of developing cirrhosis and hepatocellular carcinoma.
,=
@epatitis B is caused by hepatitis B 7@B> 8,double Dstranded circular DNA
virus of %omple& structure . @B> is classified as orthohepadnavirus within
the family @eadnaviridae $erum of individuals infected with hepatitis B
contains 4 distinct antigen particle! a spherical ,, nm particle a =, nm
7containing DNA and DNA polymerase8 called Dane particle, and tubular or
filamentous that vary in length. #hese are infective form of virus.#he
hepatitis B is normally transmitted by blood transfusion, contaminated
euipment, drug users< unsterile needle ,or any body secretion.
#he immune response to @B>'encoded antigens is responsible both for viral
clearance and for disease pathogenesis during this infection. 5hile the
humoral antibody response to viral envelope antigens contributes to the
clearance of circulating virus particles, the cellular immune response to the
envelope, nucleocapsid, and polymerase antigens eliminates infected cells.
#he dominant cause of viral persistence during @B> infection is the
development of a wea" antiviral immune response to the viral antigens.
5hile neonatal tolerance probably plays an important role in viral
persistence in patients infected at birth, the basis for poor responsiveness in
adult'onset infection is not well understood and reuires further analysis.
>iral evasion by epitope inactivation and # cell receptor antagonism may
contribute to the worsening of viral persistence in the setting of an
ineffective immune response, as can the incomplete down regulation of viral
gene e&pression and the infection of immunologically privileged tissues.
%hronic liver cell in+ury and the attendant inflammatory and regenerative
responses create the mutagenic and mutagenic stimuli for the development
of DNA damage that can cause hepatocellular carcinoma. 9lucidation of the
,0
immunological and virological basis for @B> persistence may yield
immunotherapeutic and antiviral strategies to terminate chronic @B>
infection and reduce the ris" of its life'threatening seuellae.
@epadnaviruses 7hepatitis B viruses8 cause transient and chronic infections
of the liver. #ransient infections run a course of several months, and chronic
infections are often lifelong. %hronic infections can lead to liver failure with
cirrhosis and hepatocellular carcinoma. #he replication strategy of these
viruses has been described in great detail, but virus'host interactions leading
to acute and chronic disease are still poorly understood. $tudies on how the
virus evades the immune response to cause prolonged transient infections
with high'titer viremia and lifelong infections with an ongoing inflammation
of the liver are still at an early stage, and the role of the virus in liver cancer
is still elusive. #he state of "nowledge in this very active field is therefore
reviewed with an emphasis on past accomplishments as well as goals for the
future.
718&urface antigen *H!sAg+ is secreted in e&cess into the blood as ,, nm
spheres and tubules. Its presence in serum indicates that virus replication is
,8 /e/ antigen *H!eAg+ secreted protein is shed in small amounts into the
blood. Its presence in serum indicates that a high level of viral replication is
48 core antigen 7@BcAg8 core protein is not found in blood
,/
Anti(ody
18 &urface anti(ody 7anti'@Bs8 becomes detectable late in convalescence,
and indicates immunity following infection. It remains detectable for life
and is not found in chronic carriers.
,8 e anti(ody 7anti'@Be8 becomes detectable as viral replication falls. It
indicates low infectivity in a carrier.
48 Core Ig0 rises early in infection and indicates recent infection
=8 Core Ig rises soon after Ig-, and remains present for life in both
chronic carriers as well as those who clear the infection. Its presence
indicates e&posure to @B>. of the chronic carrier.

@omology or comparative modeling involves the prediction of the structure
of a uery seuence from the structures of one or more structural templates.
#he procedure involves the identification of possible templates that have a
clear seuence relationship to the uery, the assembly of the model, the
prediction of regions of the structure that are li"ely to have different
conformations than the templates 7e.g., loops8, and ultimately, the refinement
of the structure in an attempt to account for inherent differences between the
template and uery structures. As mentioned above, homology modeling
,2
figures heavily as a rationale for structural genomics initiatives under the
stated assumption that accurate models can be built for uery seuences that
have a greater than 43? seuence identity with their best template.
#he uality of the alignment of the uery to the template seuence is a ma+or
factor in determining the uality of homology models. #his is one of the
sources of the 43? rule, because alignment uality usually decreases
dramatically below about 43? seuence identity. 7A structural e&planation
for this observation has been offered by %hung and $ubbiah, 1../8.
Advances in the accuracy of seuence alignments using structure'based
profile methods such as those described above should result in continuing
improvements in the uality of homology models.
5ith the number of protein'ligand comple&es available in the 1rotein Data
Ban" constantly growing, structure'based approaches to drug design and
screening have become increasingly important. Alongside this e&plosion of
structural information, a number of molecular doc"ing methods have been
developed over the last years with the aim of ma&imally e&ploiting all
available structural and chemical information that can be derived from
proteins, from ligands, and from protein'ligand comple&es. In this respect,
the term ;guided doc"ing; is introduced to refer to doc"ing approaches that
incorporate some degree of chemical information to actively guide the
orientation of the ligand into the binding site. #o reflect the focus on the use
of chemical information, a classification scheme for guided doc"ing
approaches is proposed. In general terms, guided doc"ing approaches can be
divided into indirect and direct approaches. Indirect approaches incorporate
chemical information implicitly, having an effect on scoring but not on
orienting the ligand during sampling. In contrast, direct approaches
,E
incorporate chemical information e&plicitly, thus actively guiding the
orientation of the ligand during sampling. Direct approaches can be further
divided into protein'based, mapping'based, and ligand'based approaches to
reflect the source used to derive the features capturing the chemical
information inside the protein cavity. 5ithin each category, a representative
list of doc"ing approaches is discussed. In view of the limitations of current
scoring functions, it was generally found that ma"ing optimal use of
chemical information represents an efficient "nowledge'based strategy for
improving binding affinity estimations, ligand binding'mode predictions,
and virtual screening enrichments obtained from protein'ligand doc"ing.
#his review gives an introduction into ligand ' receptor doc"ing and
illustrates the basic underlying concepts. An overview of different
approaches and algorithms is provided. Although the application of doc"ing
and scoring has led to some remar"able successes, there are still some ma+or
challenges ahead, which are outlined here as well. Approaches to address
some of these challenges and the latest developments in the area are
presented. $ome aspects of the assessment of doc"ing program performance
are discussed. A number of successful applications of structure'based virtual
screening are described.
,.
43
0aterial and methods
Bioinformatics is an interdisciplinary research area at the interface between
computer science and biological science. It involves the technology that uses
computers for storage, retrieval, manipulation and distribution of
information related to biological macromolecules such as DNA, RNA and
proteins.
Bioinformatics is limited to seuence, structural, and functional analysis of
genes and genomes and their corresponding products and is often considered
41
computational molecular biology. It consists of two subfields! the
development of computational tools and databases and the application of
these tools and databases in generating biological "nowledge to better
understand living systems. #hese tools are used in three areas of genomic
and molecular biological research! molecular seuence analysis, molecular
structural analysis and molecular functional analysis.
1, 7C!I)
9stablished in 1.EE as a national resource for molecular biology
information, N%BI creates public databases, conducts research in
computational biology, develops software tools for analy(ing genome
data, and disseminates biomedical information ' all for the better
understanding of molecular processes affecting human health and disease
&wiss)prot)
$ a curated protein se<uence database which strives to
provide a high level of annotation (such as the description
of the function of a protein, its domains structure, post*
translational modi;cations, variants, etc.), a minimal level
of redundancy and high level of integration with other
databases
3. .rotein se8uence) of :lycerate "inase 7@BeAg'binding protein
=81rimary Accession number'MEI>$E , 9% ,.2.1.41,from human. sabcelular
location Dcytoplasm %atalytic activity 'A#1 N 7R8'glycerate I AD1 N 4'
phospho'7R8'glycerate etc .
4,

-, %A&TA

%A&TA is a DNA and 1rotein seuence alignment software pac"age first
described 7as )A$#18 by David G. Fipman and 5illiam R. 1earson in 1.E0
in the article Rapid and sensitive protein similarity searches. #he original
)A$#1 program was designed for protein seuence similarity searching.
)A$#A, described in 1.EE 7Improved #ools for Biological $euence
%omparison8 added the ability to do DNA!DNA searches, translated
protein!DNA searches, and also provided a more sophisticated shuffling
program for evaluating statistical significance. #here are several programs in
this pac"age that allow the alignment of protein seuences and DNA
seuences. )A$#A is pronounced H)A$#'AyeH, and stands for H)A$#'AllH,
because it wor"s with any alphabet, an e&tension of H)A$#'1H 7protein8 and
H)A$#'NH 7nucleotide8 alignment.
#he current )A$#A pac"age contains programs for protein!protein,
DNA!DNA, protein!translated DNA 7with frameshifts8, and ordered or
unordered peptide searches. Recent versions of the )A$#A pac"age include
special translated search algorithms that correctly handle frameshift errors
7which si&'frame'translated searches do not handle very well8 when
comparing nucleotide to protein seuence data.
In addition to rapid heuristic search methods, the )A$#A pac"age provides
$$9AR%@, an implementation of the optimal $mith'5aterman algorithm. A
ma+or focus of the pac"age is the calculation of accurate similarity statistics,
so that biologists can +udge whether an alignment is li"ely to have occurred
44
by chance, or whether it can be used to infer homology. #he )A$#A pac"age
is available fromfasta.bioch.virginia.edu
9,!4A&T
In bioinformatics, !asic 4ocal Alignment &earch Tool, or !4A&T, is
an algorithm for comparing primary biological seuence information, such
as the amino'acid seuences of different proteins or the nucleotides of DNA
seuences. A BAST search enables a researcher to compare a uery
seuence with a library or database of seuences, and identify library
seuences that resemble the uery seuence above a certain threshold.
:, .rimary ; secondary structure analysis
Using Prot Param - for primary structure
1rot1aram computes various physico'chemical properties that can be
deduced from a protein seuence. No additional information is reuired
about the protein under consideration. #he protein can either be specified as
a $wiss'1rotO#r9-BF accession number or ID, or in form of a raw
seuence. 5hite space and numbers are ignored. If you provide the
accession number of a $wiss'1rotO#r9-BF entry, you will be prompted with
an intermediary page that allows you to select the portion of the seuence on
which you would li"e to perform the analysis. #he choice includes a
selection of mature chains or peptides and domains from the $wiss'1rot
feature table 7which can be chosen by clic"ing on the positions8, as well as
the possibility to enter start and end position in two bo&es. By default 7i.e. if
you leave the two bo&es empty8 the complete seuence will be analy(ed.
4=
It calculate following parameter ''
extinction coefficient
half-life
instability index
aliphatic index
Using SOPMA for secondary structure analysis
Recently a new method called the self'optimi(ed prediction method

7$A1-8
has been described to improve the success rate in the

prediction of the
secondary structure of proteins. In this paper

we report improvements
brought about by predicting all the seuences

of a set of aligned proteins
belonging to the same family. #his

improved $A1- method 7&5.0A8
correctly predicts /..0? of amino

acids for a three'state description of the
secondary structure

7 'heli&, P'sheet and coil8 in a whole database containing
1,/ chains of non'homologous 7less than ,0? identity8 proteins.

Goint
prediction with &5.0A and a neural networ"s method 71@D8

correctly
predicts E,.,? of residues for 2=? of co'predicted

amino acids. 1redictions
40
are available by 9mail to deleageQibcp.fr or on a 5eb page
7http!OOwww.ibcp.frOpredict.html 8
.25T5C54 %5445"ED
Abtained the Receptor 7#arget 1rotein8 from the literature references and
available +ournals available online and .u(med literature for @B> strain

Retrieved the %A&TA seuence of the protein @BeAg from the database
&wiss) .rot,

Retrieved the 1DB'ID for template structure using !4A&T$ 1DBID
,BEN and found the similarity search.

Foaded the target seuence in pd( format in &"I&& 05DE4 as a raw
seuence and modeled the receptor.
4/
>alidated modeled receptor using $tructure Analysis >alidation $erver
*&AV&+,
>erified our model through different parameter li"e 2anachandran plot and
other which is available in $A>$

$elected the best Figand from the Database <E for @B> disease.
Run the HE= and found the structure of drug molecule.
42
4E
conserved, which may in turn lead to e&periments to test those hypotheses.
)or e&ample, the spatial arrangement of conserved residues may suggest
whether a particular residue is conserved to stabili(e the folding, to
participate in binding some small molecule, or to foster association with
another protein or nucleic acid.
%igure $ %irst> the known> template -D structures are aligned with the
target se8uence to (e modelled, &econd> spatial features> such as C? )
C? distances> hydrogen (onds> and main chain and side chain dihedral
angles> are transferred from the templates to the target, Thus> a num(er
4.
of spatial restraints on its structure are o(tained, Third> the -D model is
o(tained (y satisfying all the restraints as well as possi(le,
@omology modeling can produce high'uality structural models when the
target and template are closely related, which has inspired the formation of a
structural genomics consortium dedicated to the production of representative
e&perimental structures for all classes of protein folds. #he chief
inaccuracies in homology modeling, which worsen with lower seuence
identity, derive from errors in the initial seuence alignment and from
improper template selection Fi"e other methods of structure prediction,
current practice in homology modeling is assessed in a biannual large'scale
e&periment "nown as the %ritical Assessment of #echniues for 1rotein
$tructure 1rediction, or %A$1.
Template selection and sequence alignment
#he critical first step in homology modeling is the identification of the best
template structure, if indeed any are available. #he simplest method of
template identification relies on serial pairwise seuence alignments aided
by database search techniues such as )A$#A and BFA$#. -ore sensitive
methods based on multiple seuence alignment ' of which 1$I'BFA$# is
the most common e&ample ' iteratively update their position'specific scoring
matri& to successively idenfity more distantly related homologs. #his family
of methods has been shown to produce a larger number of potential
templates and to identify better templates for seuences that have only
distant relationships to any solved structure. 1rotein threading, also "nown
=3
as fold recognition or 4D'1D alignment, can also be used as a search
techniue for identifying templates to be used in traditional homology
modeling methods. 5hen performing a BFA$# search, a reliable first
approach is to identify hits with a sufficiently low E'value, which are
considered sufficiently close in evolution to ma"e a reliable homology
model. Ather factors may tip the balance in marginal cases* for e&ample, the
template may have a function similar to that of the uery seuence, or it may
belong to a homologous operon. @owever, a template with a poor E'value
should generally not be chosen, even if it is the only one available, since it
may well have a wrong structure, leading to the production of a misguided
model. A better approach is to submit the primary seuence to fold'
recognition servers or, better still, consensus meta'servers which improve
upon individual fold'recognition servers by identifying similarities
7consensus8 among independent predictions.
Aften several candidate template structures are identified by these
approaches. Although some methods can generate hybrid models from
multiple templates, most methods rely on a single template. #herefore,
choosing the best template from among the candidates is a "ey step, and can
affect the final accuracy of the structure significantly. #his choice is guided
by several factors, such as the similarity of the uery and template
seuences, of their functions, and of the predicted uery and observed
template secondary structures. 1erhaps most importantly, the covera!e of the
aligned regions! the fraction of the uery seuence structure that can be
predicted from the template, and the plausibility of the resulting model.
#hus, sometimes several homology models are produced for a single uery
seuence, with the most li"ely candidate chosen only in the final step.
=1
It is possible to use the seuence alignment generated by the database search
techniue as the basis for the subseuent model production* however, more
sophisticated approaches have also been e&plored.
@, 0olecular Docking
Introduction to Docking
Doc"ing studies are molecular modelling studies aiming at finding a proper
fit between a ligand and its binding site.
#here are two classes of protein doc"ing!
181rotein'protein doc"ing
,81rotein Receptor'Figand
.rotein).rotein Docking interactions
1rotein'protein interactions occur between two proteins that are similar in
si(e. #he interface between the two molecules tend to be flatter and
smoother than those in protein'ligand interactions. 1rotein'protein
interactions are usually more rigid* the interfaces of these interactions do not
have the ability to alter their conformation in order to improve binding and
ease movement. %onformational changes are limited by steric constraint and
thus are said to be rigid.
=,
)ig! 1rotein'1rotein doc"ing.
.rotein 2eceptorA4igand docking
1rotein receptor'ligand motifs fit together tightly, and are often referred to as
a loc" and "ey mechanism. #here is both high specificity and induced fit
within these interfaces with specificity increasing with rigidity. 1rotein
receptor'ligand can either have a rigid ligand and a fle&ible receptor, or a
fle&ible ligand with a rigid receptor.
)ig!1rotein Figand'Receptor Doc"ing
2igid 4igand with a %lexi(le 2eceptor
#he native structure of the rigid ligand fle&ible receptor often ma&imi(es the
interface area between the molecules. #hey move within respect to one
another in a perpendicular direction in respect to the interface. #his allows
for binding of a receptor with a larger than usual ligand. Normally when
there is ligand overlap in the doc"ing interface, energy penalties incur. If the
van der 5aals forces can be decreased, energy loss in the system will be
=4
minimili(ed. #his can be accomplished by allowing fle&ibility in the
receptor. )le&ibility receptors allow for doc"ing of a larger ligand than
would be allowed for with a rigid receptor.
%lexi(le 4igand with a 2igid 2eceptor
5hen the fit between the ligand and receptor does not need to be induced,
the receptor can retain its rigidity while maintaing the free energy of the
system. )or successful doc"ing, the parameters of the ligand need to be
maintained and the ligand must be slightly smaller in si(e than that of the
receptor interface. No doc"ing is completely rigid though* there is intrinsic
movement which allows for small conformational adaptation for ligand
binding. 5hen the si& degrees of freedom for protein movement are ta"en
into consideration 7three rotational, three translational8, the amount of
inherent fle&ibility allowed the receptor is even greater. #his further offsets
any energy penalty between the receptor and ligand, allowing for easier,
more enegetically favorable binding between the two.
Aim of docking
#he aim of doc"ing is to find out the new drugs target, it will open new
vistas for further drug development .#he finding of our doc"ing will be
useful in finding a cure for the infectious disease bird flu, also it will open
new avenues for finding other possible drug targets in influen(a A virus. #he
doc"ing results can be used to design new lead compounds and hence can
aid in the new drug discovery process.

==
2eceptor
A residue on the surface of the cell that serves as a recognition or binding
site for antigens,antibody or other cellular or immunological components.It
is a molecule with in a cell suface to which a substance 7such as harmones or
a drug 8,selectively bind causing a change in the activity of the cell.
4igand
#he molecule which binds to a protein molecule 7eg, receptor8. As a ligand
binds through the interaction of many wea", noncovalent bonds formed to
the binding site of a protein, the tight binding of a ligand depends upon a
precise fit to the surface'e&posed amino acid residues on the protein.
Active &ite
#he active site of a proteinOen(yme is the region that binds the substrates
7and the cofactor, if any8. It also contains the residues that directly
participate in the ma"ing and brea"ing of bonds. #hese residues are called
the catal"tic !roups. In essence, the interaction of the en(yme and substrate
at the active site promotes the formation of the transition state. #he active
site is the region of the en(yme that most directly lowers the Delta # of the
reaction, which results in the rate enhancement characteristic of en(yme
action.
Amino acids in protein active sites$
It is difficult to generali(e which amino acids are li"ely to be in a protein
activeOfunctional site as this greatly depends on the type of function. 5ith
that in mind, below are preferences for the ,3 amino acids to lie within
=0
functional regions on proteins #hese were wor"ed out by considering how
often particular amino acids were in contact with bound non'protein atoms
in protein three'dimensional structures. 1ostive values mean that the amino
acid ma"es more contacts than one would e&pect by chance* negative values
mean that it ma"es fewer. #he below does not include protein'protein, or
protein'peptide interactions, where many of the amino acids with negative
values 7e.g. tryptophan or proline8 can play critical roles.
@is 3.4/3 #yr '3.3=3 Asp 3.3=0 :ly '3.323
#rp '3.1=3 -et 3.3,0 >al '3.3/3 Asn 3.3E3
Feu '3.1E3 1he '3.1,3 :ln 3.303 %ys 3.,13
Ile '3.330
Ala 3.3,0 :lu 3.303 Arg 3.300
1ro '3.,33
Fys 3.133 #hr 3.133 $er 3.143
2A0ACHA7D2A7 .45T
A Ramachandran 1lot 7also "nown as Ramachandran -ap or a
Ramachandran diagram 8, developed by :opalasamudram Narayana
Ramachandran, is a way to visuali(e dihedral angles phi against 7sai 8 of
amino acid residues in protein structure. It shows the possible conformation
of phi and shi angles for a polypeptide. In a polypeptide, the main
chain N'%R and %R' %R bonds relatively are free to rotate. #his plot is
drawn between torsion angles phi and psi. Ramachandran used computer
models of small polypeptides to systematically vary and with the ob+ective
of finding stable conformations. )or each conformation, the structure was
e&amined for close contacts between atoms. Atoms were treated as hard
spheres with
=/
dimensions corresponding to their >ander 5aals radii. And the angles, which
cause spheres to collide, correspond to sterically disallowed conformations
of the polypeptide bac"bone.
$A>$ 7$tructure analysis and validation server8
$A>$ is a server for analy(ing protein structures for validity and assessing
how correct they are. Depending on how many programs one select to use,
the server can ta"e several minutes to run. It also depends on how many
residues there are in the protein that is submitted.
1RA%@9%S
#he aim of 1RA%@9%S is to assess how normal, or conversely how
unusual, the
geometry of the residues in a given protein structure is ,as compared with
stereo chemical parameters derived from well'refined, high resolution
structure. #he chec"s also ma"e use of Tideal< bond lengths and bond angles,
as derived from a recent and comprehensive analysis of small molecule
structures in the %ambridge $tructural Database 7%$D8.
I7.6T
#he input to 1RA%@9%S is a single file containing the coordinates of the
protein structure. Ane of the by'products of running 1RA%@9%S is that
coordinate file will be Ucleaned upV by the first of the programs. #he
cleaning up process corrects any mislabelled atoms and creates a new
coordinates file which has a fileDe&tension of .new. .new file will have the
atoms labelled in accordance with the IL1A% naming convention.
=2
56T.6T
#he output comprises of the plots, together with detailed residue'by'residue
listing. It generates number of output files in the default directory which
have the same name as the original 1DB file, but with different e&tensions.
#he residue'by residue listing has a, out e&tension and lists all the computed
stereo chemical properties, by residue, in a printable A$%II te&t file.
ENERGY MINIMIA!ION
9nergy is a function of the degree of freedom in a molecule 7i.e. bonds,
angels, and dihedrals8. 9nergy minimi(ation can repair distorted geometries
by moving atoms release internal constraints. 9nergy minimi(ation is good
to release local constraints for a residue, but it will not pass through high
energy barriers and stop in a local minima.
#he potential energy calculated by summing the energies of various
interactions is a numerical value for a single conformation. #his number can
be used to evaluate a particular conformation, but it may not be a useful
measure of a conformation because it can be dominated by a few bad
interactions. )or instance, a large molecule with an e&cellent conformation
fro nearly all atoms can have a large overall energy because of a single bad
interactions, for instance two atoms too near each other space and having a
huge >ander walls repulsion energy. It is often preferable to carry out energy
minimi(ation on a conformation to find the best nearby conformation.
9nergy minimi(ation is usually performed by gradient optimi(ation! atoms
=E
are moved so as to reduce the net forces on them. #he minimi(ed structure
has small forces on each atom and therefore serves as an e&cellent starting
point for molecular dynamics simulations.

=.
2esult and discussion
1,&wiss)prot entry )) .rotein seuence :lycerate "inase 7 @BeAg'binding
protein =8
Entry Information
Entry name G"#!$%&UMAN
Primary accession number '(I)S(
Name and origin of t*e protein
Protein name Glycerate +inase
Synonyms E# ,-.-/-0/
&1eAg-2inding protein 3
Gene name Name4 G"Y#!$
Synonyms: HBEBP4
!"#ames: $P%&'(
"rom Homo sapiens )Human* +,ax-.: &/(/0
,axonomy Eu1aryota2 3eta4oa2 5hordata2 5raniata2
6ertebrata2 Euteleostomi2 3ammalia2 Eutheria2
Euarchonto7lires2 Primates2 Haplorrhini2 5atarrhini2
Hominidae2 Homo.
Protein existence 8: E9idence at transcript le9el2
!lat result$)
!ist of potentially matching se"uences#
Include 5uery se5uence
03
Db AC Description Score E-
value

pdb1QGT-C Chain C,(HbcagHu!an Hepatitis " #iral
Capsid $gi%& '() )e-&*

pdb ,MIG'% %hain %, @epatitis B %apsid 1rotein 5ith An N'#ermina...
1.2 ,e'01

pdb 'G++-C CA,SD-H"#D1 Chain C,Hu!an T* Capsid,
Strain Ad... 1/' )e-&(
pdb 1TA+-" 01,1-2HEAT.. Chain ", Cr3stal Structure
45 03lanase (Gh1( 1n Co!p...
'6 ).(
pdb 1A2/-A Chain A, Structure 45 Glutathione S-
Trans5erase 1ii 1 '6 ).(

Graphical overview of the alignments
01
.rimary structure prediction
!y .rot.aram4
GLCTK_HUMAN (Q!"#$
DE Gl3cerate 7inase (EC '.6.1.+1 (H"eAg-binding
protein *.
,he computation has been carried out on the complete se:uence
)6,0 amino acids*.
.
N%m&er of amino aci's( &'+
Molec%lar weight( &&'&'.)
Theoretical p!( ).'&
Amino aci' composition(
Ala (A 6* 1*.18
Arg (9 ++ ).+8
Asn (: 11 '.18
Asp (D '1 *.(8
C3s (C & 1.(8
Gln (Q +' ).18
Glu (E '; &.*8
Gl3 (G &1 /.;8
His (H 1) +.18
1le (1 1& './8
<eu (< ;1 1&.&8
<3s (= 1( 1./8
>et (> 1' '.+8
0,
,he (? 1( 1./8
,ro (, '; &.*8
Ser (S '6 &.'8
Thr (T '' *.'8
Trp (2 * (.;8
T3r (@ & 1.(8
#al (# +; 6.+8
,3l (4 ( (.(8
Sec (A ( (.(8
(" ( (.(8
(B ( (.(8
(0 ( (.(8
#otal number of negatively charged residues 7Asp N :lu$( */
#otal number of positively charged residues 7Arg N Fys8! *+
Atomic composition(
Carbon C '*+&
H3drogen H +/)6
:itrogen : 611

4C3gen 4 61/
Sul5ur S 16
)orm%la( C
'*+&
H
+/)6
:
611
4
61/
S
16
Total n%m&er of atoms( 6;*/
*+tinction coefficients(
ECtinction coe55icients are in units o5 >
-1
c!
-1
, at
';( n! !easured in Dater.
ECt. coe55icient '/6((
Abs (.18 (E1 gFl (.&+;, assu!ing A<< C3s
residues appear as hal5 c3stines
04
ECt. coe55icient '/*&(
Abs (.18 (E1 gFl (.&++, assu!ing :4 C3s residues
appear as hal5 c3stines
&econdary structure prediction
By SOPMA result for : UNK!"#$"%
>iew $A1-A in!
1( '( +( *( &(
)( 6(
% % % % %
% %
SeGuence length H &'+
S4,>A H
Alpha heliC (Hh H '+& is **./+8
+
1(
heliC (Gg H ( is (.((8
,i heliC (1i H ( is (.((8
"eta bridge ("b H ( is (.((8
ECtended strand (Ee H ;( is 1&.+(8
"eta turn (Tt H +) is ).;;8
"end region (Ss H ( is (.((8
9ando! coil (Cc H 16' is +'.;/8
A!bigous states (I H ( is (.((8
4ther states H ( is (.((8
0=
,ara!eters H
2indoD Didth H 16
Si!ilarit3 threshold H ;
:u!ber o5 states H *
0ultiple se8uence alignment
Clustal"3 2esults
1.
Number of
sequences
13
,.
Alignment score
,E0/0
4.
Sequence format Pearson
=.
Sequence type
Aa
0.
Output fle clustalw2-20080510-
09552541.output
/.
Alignment fle clustalw2-20080510-
09552541.aln
2.
Guide tree fle clustalw2-20080510-
09552541.dnd
00
E.
Your input fle clustalw2-20080510-
09552541.input
Scores Table
SeGA :a!e <en(aa SeG" :a!e
<en(aa Score
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
EEEEEEEEEEEEEEEEEEEEEEEE
1 Q;1#S;%G<CT=-HA>A: &'+ ' Q)*;/)%
H"EAG-ASH# '16 +
1 Q;1#S;%G<CT=-HA>A: &'+ + ,(+1&*%
H"EAG-DH"#1 +(& +
1 Q;1#S;%G<CT=-HA>A: &'+ * ,(C)J/%
H"EAG-DH"#+ +(& +
1 Q;1#S;%G<CT=-HA>A: &'+ & ,(+1&+%
H"EAG-GSH# '16 +
1 Q;1#S;%G<CT=-HA>A: &'+ ) ,(C)/'%
H"EAG-H"#A' '1* +
1 Q;1#S;%G<CT=-HA>A: &'+ 6 ,(C)'&%
H"EAG-H"#A+ '1* +
1 Q;1#S;%G<CT=-HA>A: &'+ ; ,16(//%
H"EAG-H"#A* '1* +
1 Q;1#S;%G<CT=-HA>A: &'+ / Q;11(&%
H"EAG-H"#A& '1* +
1 Q;1#S;%G<CT=-HA>A: &'+ 1( Q/1C+6%
H"EAG-H"#A) '1* '
' Q)*;/)%H"EAG-ASH# '16 + ,(+1&*%
H"EAG-DH"#1 +(& '1
' Q)*;/)%H"EAG-ASH# '16 * ,(C)J/%
H"EAG-DH"#+ +(& '1
' Q)*;/)%H"EAG-ASH# '16 & ,(+1&+%
H"EAG-GSH# '16 /1
' Q)*;/)%H"EAG-ASH# '16 ) ,(C)/'%
H"EAG-H"#A' '1* ))
' Q)*;/)%H"EAG-ASH# '16 6 ,(C)'&%
H"EAG-H"#A+ '1* )&
0/
' Q)*;/)%H"EAG-ASH# '16 ; ,16(//%
H"EAG-H"#A* '1* )&
' Q)*;/)%H"EAG-ASH# '16 / Q;11(&%
H"EAG-H"#A& '1* )&
' Q)*;/)%H"EAG-ASH# '16 1( Q/1C+6%
H"EAG-H"#A) '1* )&
+ ,(+1&*%H"EAG-DH"#1 +(& * ,(C)J/%
H"EAG-DH"#+ +(& /6
+ ,(+1&*%H"EAG-DH"#1 +(& & ,(+1&+%
H"EAG-GSH# '16 '*
+ ,(+1&*%H"EAG-DH"#1 +(& ) ,(C)/'%
H"EAG-H"#A' '1* ')
+ ,(+1&*%H"EAG-DH"#1 +(& 6 ,(C)'&%
H"EAG-H"#A+ '1* '6
+ ,(+1&*%H"EAG-DH"#1 +(& ; ,16(//%
H"EAG-H"#A* '1* '&
+ ,(+1&*%H"EAG-DH"#1 +(& / Q;11(&%
H"EAG-H"#A& '1* ')
+ ,(+1&*%H"EAG-DH"#1 +(& 1( Q/1C+6%
H"EAG-H"#A) '1* ')
* ,(C)J/%H"EAG-DH"#+ +(& & ,(+1&+%
H"EAG-GSH# '16 '&
* ,(C)J/%H"EAG-DH"#+ +(& ) ,(C)/'%
H"EAG-H"#A' '1* ')
* ,(C)J/%H"EAG-DH"#+ +(& 6 ,(C)'&%
H"EAG-H"#A+ '1* '6
* ,(C)J/%H"EAG-DH"#+ +(& ; ,16(//%
H"EAG-H"#A* '1* '&
* ,(C)J/%H"EAG-DH"#+ +(& / Q;11(&%
H"EAG-H"#A& '1* ')
* ,(C)J/%H"EAG-DH"#+ +(& 1( Q/1C+6%
H"EAG-H"#A) '1* ')
& ,(+1&+%H"EAG-GSH# '16 ) ,(C)/'%
H"EAG-H"#A' '1* 6(
& ,(+1&+%H"EAG-GSH# '16 6 ,(C)'&%
H"EAG-H"#A+ '1* )/
& ,(+1&+%H"EAG-GSH# '16 ; ,16(//%
H"EAG-H"#A* '1* )/
& ,(+1&+%H"EAG-GSH# '16 / Q;11(&%
H"EAG-H"#A& '1* )/
02
& ,(+1&+%H"EAG-GSH# '16 1( Q/1C+6%
H"EAG-H"#A) '1* )/
) ,(C)/'%H"EAG-H"#A' '1* 6 ,(C)'&%
H"EAG-H"#A+ '1* /;
) ,(C)/'%H"EAG-H"#A' '1* ; ,16(//%
H"EAG-H"#A* '1* /;
) ,(C)/'%H"EAG-H"#A' '1* / Q;11(&%
H"EAG-H"#A& '1* /;
) ,(C)/'%H"EAG-H"#A' '1* 1( Q/1C+6%
H"EAG-H"#A) '1* /;
6 ,(C)'&%H"EAG-H"#A+ '1* ; ,16(//%
H"EAG-H"#A* '1* /;
6 ,(C)'&%H"EAG-H"#A+ '1* / Q;11(&%
H"EAG-H"#A& '1* /6
6 ,(C)'&%H"EAG-H"#A+ '1* 1( Q/1C+6%
H"EAG-H"#A) '1* /;
; ,16(//%H"EAG-H"#A* '1* / Q;11(&%
H"EAG-H"#A& '1* /6
; ,16(//%H"EAG-H"#A* '1* 1( Q/1C+6%
H"EAG-H"#A) '1* /;
/ Q;11(&%H"EAG-H"#A& '1* 1( Q/1C+6%
H"EAG-H"#A) '1* /6
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
IIIIIIIIIIIIIIIIIIIII
Alignment
C<ASTA< '.(.& !ultiple seGuence align!ent
,16(//%H"EAG-H"#A*
---------------------------------------------------
---------
0E
Q/1C+6%H"EAG-H"#A)
---------------------------------------------------
---------
,(C)/'%H"EAG-H"#A'
---------------------------------------------------
---------
,(C)'&%H"EAG-H"#A+
---------------------------------------------------
---------
Q;11(&%H"EAG-H"#A&
---------------------------------------------------
---------
Q)*;/)%H"EAG-ASH#
---------------------------------------------------
---------
,(+1&+%H"EAG-GSH#
---------------------------------------------------
---------
,(+1&*%H"EAG-DH"#1
---------------------------------------------------
---------
,(C)J/%H"EAG-DH"#+
---------------------------------------------------
---------
Q;1#S;%G<CT=-HA>A:
>AAA<Q#<,9<A9A,<H,<<29GS#A9<ASS>A<AEQA9Q<?ESA#GA#<,
G,><H9A<S )(

,16(//%H"EAG-H"#A*
---------------------->Q<?H<C<11SCT-
C,T#QAS=<C<G2<2G-------> +(
Q/1C+6%H"EAG-H"#A)
---------------------->Q<?H<C<11SCT-
C,T#QAS=<C<G2<2G-------> +(
,(C)/'%H"EAG-H"#A'
---------------------->Q<?H<C<11SCT-
C,T#QAS=<C<G2<2G-------> +(
0.
,(C)'&%H"EAG-H"#A+
---------------------->Q<?H<C<11SCT-
C,T#QAS=<C<G2<2G-------> +(
Q;11(&%H"EAG-H"#A&
---------------------->Q<?H<C<11SCT-
C,T?QAS=<C<G2<2G-------> +(
Q)*;/)%H"EAG-ASH#
---------------------->@<?H<C<#?AC#SC,T#QAS=<C<G2<2
D-------> +1
,(+1&+%H"EAG-GSH#
---------------------->@<?H<C<#?AC#,C,T#QAS=<C<G2<2
D-------> +1

,(+1&*%H"EAG-DH"#1
---------------------->2:<91T,<S?GAACQG1?TST<<<SC#T
#,<#CT1#@ +;
,(C)J/%H"EAG-DH"#+
---------------------->2:<91T,<S?GAACQG1?TST<<<SC#T
#,<#CT1#@ +;
Q;1#S;%G<CT=-HA>A:
<D,GG9Q<=#9D9:?Q<9Q:<@<#G?G=A#<G>AAAAEE<<GQH<#QG#1S
#,=G19AA> 1'(

,16(//%H"EAG-H"#A*
D1D,------------------------
@=E?GAT#E<<S?------------------- *6
Q/1C+6%H"EAG-H"#A)
D1D,------------------------
@=E?GAT#E<<S?------------------- *6
,(C)/'%H"EAG-H"#A'
D1D,------------------------
@=E?GAT#E<<S?------------------- *6
,(C)'&%H"EAG-H"#A+
D1D,------------------------
@=E?GAT#E<<S?------------------- *6
/3
Q;11(&%H"EAG-H"#A&
D1D,------------------------
@=E?GAT#E<<S?------------------- *6
Q)*;/)%H"EAG-ASH#
D1D,------------------------
@=E?GSS@Q<<:?------------------- *;
,(+1&+%H"EAG-GSH#
D1D,------------------------
@=E?GSS@Q<<:?------------------- *;
,(+1&*%H"EAG-DH"#1
DSC<------------------------
@>D1:AS9A<A:#@D----------------- &6
,(C)J/%H"EAG-DH"#+
DSC<------------------------
@>D1:AS9A<A:#@D----------------- &6
Q;1#S;%G<CT=-HA>A:
E9AG=QE><<=,HS9#Q#?EGAED:<,D9DA<9AA<A1QQ<AEG<TADD<<
<#<1SGGGS 1;(

,16(//%H"EAG-H"#A*
--<,SD??,S#9D<<DTASA<@9EA<ES--------------------
,EHCS,HHTA<9 ;&
Q/1C+6%H"EAG-H"#A)
--<,SD??,S#9D<<DTASA<@9EA<ES--------------------
,EHCS,HHTA<9 ;&
,(C)/'%H"EAG-H"#A'
--<,SD??,S#9D<<DTASA<@9EA<ES--------------------
,EHCS,HHTA<9 ;&
,(C)'&%H"EAG-H"#A+
--<,SD??,S#9D<<DTASA<@9EA<ES--------------------
,EHCS,HHTA<9 ;&
Q;11(&%H"EAG-H"#A&
--<,SD??,S#9D<0DTASA<@9EA<ES--------------------
,EHCS,HHTA<9 ;&
Q)*;/)%H"EAG-ASH#
--<,<D??,E<:A<#DTATA<@EEE<TG--------------------
9EHCS,HHTA19 ;)
/1
,(+1&+%H"EAG-GSH#
--<,<D??,D<:A<#DTAAA<@EEE<TG--------------------
9EHCS,HHTA19 ;)
,(+1&*%H"EAG-DH"#1
--<,DD??,=1DD<#9DA=DA<E,@2=SDS1=-----------
=H#<1ATH?#D<1ED?2 1(*
,(C)J/%H"EAG-DH"#+
--<,DD??,=1DD<#9DA=DA<E,@29SDS1=-----------
=H#<1ATH?#D<1ED?2 1(*
Q;1#S;%G<CT=-HA>A:
A<<,A,1,,#T<EE=QT<T9<<AA9GAT1QE<:T19=A<SQ<=GGG<AQAA
@,AQ##S<1 '*(

,16(//%H"EAG-H"#A*
QA1<C2GE<>T<AT2#G::<ED,AS9D<##:@-------------------
--------- 116
Q/1C+6%H"EAG-H"#A)
ET1<C2GE<>T<AT2#G::<ED,AS9D<##:@-------------------
--------- 116
,(C)/'%H"EAG-H"#A'
QA1<C2GE<>T<AT2#G::<QD,AS9D<##:@-------------------
--------- 116

,(C)'&%H"EAG-H"#A+
QA1<C2GE<>T<AT2#G::<ED,AS9D<##:@-------------------
--------- 116
Q;11(&%H"EAG-H"#A&
QA1<C2G=<>T<AT2#G::<ED,AS9D<##:@-------------------
--------- 116
Q)*;/)%H"EAG-ASH#
QA<#C2EE<T9<1A2>SA:1:SEE#99#1#AH-------------------
--------- 11;
,(+1&+%H"EAG-GSH# QA<#C2EE<T9<1T2>SE:T-
TEE#9911#DH---------------------------- 116
,(+1&*%H"EAG-DH"#1
QTTQG>HE1AES<9A#1,,TTT,#,,G@<1QHEEAEE1,<GD<?=HQEE91
#S?Q,D@,1 1)*
/,
,(C)J/%H"EAG-DH"#+
QTTQG>HE1AEA<9A#1,,TTT,#,QG@<1QHDEAEE1,<GD<?=HQEE91
#S?Q,D@,1 1)*
Q;1#S;%G<CT=-HA>A:
<SD##GD,#E#1ASG,T#ASSH:#QDC<H1<:9@G<9AA<,9S#=T#<S9A
DSD,HG,HT +((

,16(//%H"EAG-H"#A*
-------------#:T:>G<=19Q<<2?91S@<T?G9ET#<E@<#S?G#21
9T,,A@9,, 1)*
Q/1C+6%H"EAG-H"#A)
-------------#:T:>G<=19Q<<2?H1SC<T?G9ET#<E@<#S?G#21
9T,,A@9,, 1)*
,(C)/'%H"EAG-H"#A'
-------------#:T:>G<=19Q<<2?H1SC<T?G9ET#<E@<#S?G#21
9T,,A@9,, 1)*
,(C)'&%H"EAG-H"#A+
-------------#:T:#G<=19Q<<2?H1SC<T?G9ET#<E@<#S?G#21
9T,,A@9,, 1)*
Q;11(&%H"EAG-H"#A&
-------------#:T:>G<=19Q<<2?H1SC<T?G9ET#<E@<#S?G#21
9T,,A@9,, 1)*
Q)*;/)%H"EAG-ASH#
-------------#:DT2G<=#9Q:<2?H<SC<T?GQHT#QE?<#S?G#91
9T,A,@9,, 1)&
,(+1&+%H"EAG-GSH#
-------------#::T2G<=#9QT<2?H<SC<T?GQHT#QE?<#S?G#21
9T,A,@9,, 1)*
,(+1&*%H"EAG-DH"#1
TA91HAH<=A@A=1:EES<D9A99<<22H@:C<<2GEAQ#T:@1S9<9T2<
ST,E=@9G9 ''*
,(C)J/%H"EAG-DH"#+
TA91HAH<=A@A=1:EES<D9A99<<22H@:C<<2GEA:#T:@1S9<9T2<
ST,E9@9G9 ''*
Q;1#S;%G<CT=-HA>A:
CGH#<:#11GS:#<A<AEAQ9QAEA<G@QA##<SAA>QGD#=S>AQ?@G<<
AH#A9T9<T +)(

/4
,16(//%H"EAG-H"#A*
:A,1<ST<,ETT##999D9G-----------------------------
9S,999T,S,9 1/&
Q/1C+6%H"EAG-H"#A)
:A,1<ST<,ETT##999D9G-----------------------------
9S,999T,S,9 1/&
,(C)/'%H"EAG-H"#A'
:A,1<ST<,ETT##999D9G-----------------------------
9S,999T,S,9 1/&
,(C)'&%H"EAG-H"#A+
:A,1<ST<,ETT##999D9G-----------------------------
9S,999T,S,9 1/&
Q;11(&%H"EAG-H"#A&
:A,1<ST<,ETT##999D9G-----------------------------
9S,999T,S,9 1/&
Q)*;/)%H"EAG-ASH#
:A,1<ST<,EHT#1999GSA9##--------------------------
9S,999T,S,9 1//
,(+1&+%H"EAG-GSH#
:A,1<ST<,EHT#1999GGS9AA--------------------------
9S,999T,S,9 1/;
,(+1&*%H"EAG-DH"#1
DA,T1EA1T9,1Q#AQGG9=TTTGT9=,9G<E,999=#=TT##@G999S=S
9E99A,T,Q ';*
,(C)J/%H"EAG-DH"#+
DA,T1EA1T9,1Q#AQGG9=TTSGT9=,9G<E,999=#=TT##@G999S=S
9E99A,T,Q ';*
Q;1#S;%G<CT=-HA>A:
,S>AGAS#EEDAQ<HE<AAE<Q1,D<Q<EEA<ET>A2G9G,#C<<AGGE,T
#Q<QGSG9G *'(

,16(//%H"EAG-H"#A*
999SQS,9999SQS9ESQC--------------------------------
--------- '1*
Q/1C+6%H"EAG-H"#A)
999SQS,9999SQS9ESQC--------------------------------
--------- '1*
/=
,(C)/'%H"EAG-H"#A'
999SQS,9999SQS9ESQC--------------------------------
--------- '1*
,(C)'&%H"EAG-H"#A+
999S,S,9999SQS9ESQC--------------------------------
--------- '1*
Q;11(&%H"EAG-H"#A&
999SQS,9999SQS9ESQC--------------------------------
--------- '1*
Q)*;/)%H"EAG-ASH# 999SQS,999-
,QS,AS:C-----------------------------------------
'16
,(+1&+%H"EAG-GSH#
999SQS,9999SQS,AS:C--------------------------------
--------- '16
,(+1&*%H"EAG-DH"#1
9AGS,<,9SSSSHH9S,S,9=------------------------------
--------- +(&
,(C)J/%H"EAG-DH"#+
9AGS,<,9SSSSHH9S,S,9=------------------------------
--------- +(&
Q;1#S;%G<CT=-HA>A:
G9:QE<A<9#GAE<992,<G,1D#<?<SGGTDGQDG,TEAAGA2#T,E<AS
QAAAEG<D1 *;(

,16(//%H"EAG-H"#A*
-------------------------------------------
Q/1C+6%H"EAG-H"#A)
-------------------------------------------
,(C)/'%H"EAG-H"#A'
-------------------------------------------
,(C)'&%H"EAG-H"#A+
-------------------------------------------
Q;11(&%H"EAG-H"#A&
-------------------------------------------
Q)*;/)%H"EAG-ASH#
-------------------------------------------
,(+1&+%H"EAG-GSH#
-------------------------------------------
/0
,(+1&*%H"EAG-DH"#1
-------------------------------------------
,(C)J/%H"EAG-DH"#+
-------------------------------------------
Q;1#S;%G<CT=-HA>A:
AT?<AH:DSHT??CC<QGGAH<<HTG>TGT:#>DTH<<?<9,9 &'+

Guide Tree
(
(
(
(
(
(
Q;1#S;%G<CT=-HA>A:H(.&/&1/,
(
,(+1&*%H"EAG-DH"#1H(.(116),
,(C)J/%H"EAG-DH"#+H(.(111/
H(.+)(&*
H(.'1+*1,
(
Q)*;/)%H"EAG-ASH#H(.(&;*/,
,(+1&+%H"EAG-GSH#H(.('**)
H(.1';**
H(.1*+)*,
Q;11(&%H"EAG-H"#A&H(.(11);
H(.((16&,
,(C)'&%H"EAG-H"#A+H(.((;1;

H(.((11(,
,(C)/'%H"EAG-H"#A'H(.((**&
H(.((('',
,16(//%H"EAG-H"#A*H(.((/*',
Q/1C+6%H"EAG-H"#A)H(.((/'6K
//
Phylogram
Tertiary structure prediction
pdb 1M:#'% was selected as template which showed around E0./?
identity with target seuence and the template structure was downloaded
from the 1DB.
$wiss'1db>iewer was launched and the following procedure was carried
out.
&teps involved in &.D!V$
open the template structure from file 7.pdb file8
choose icon ' /&wiss model/'/load the raw target se8uenceB
choose icon '/fit/'/fit raw se8uence/ then /magic fit/ then /iterative fit/
choose icon '/file/ ' /save/'/layer/7H.pdbH8
choose icon '/file/ ' /save/'/proCect/7H.pdbH8
choose icon ' /&wiss model/'/su(mit modeling re8uest/7A new browser
will be opened loading the pdb file and give the 9mail ID for receiving
the modeled structure8
open the new structure 7received from 9mail8 ' remove the template'by
selecting the target.
choose icon '/file/ ' /save/'/layer/7H.pdbH8

/2
Apen $wiss model and select load raw seuence option to load target
molecule.
1erform magic fit, iterative fit provided under )I# in order to fit the
two seuences.
/E

$ave the file as the pro+ect
$elect Usubmit modeling reuestV under $wiss model to submit it for
modeling.
/.
Homologous modeling$
5ptimise 0ode 2e8uest su(mission form
.lease fill these fields$
Wour 9mail
address!
Fa"shay1,3,Qgmail.com7-L$# be correctX8
Wour Name ! Fa"shay
Reuest title ! Fa"shay pro+ect
5ill be added to the results
header.
Dour &"I&&)05DE4 proCect file can (e found in$
C$EDocuments and &ettingsEuserEDesktopEproCFkumar,pd(
"orkunit$ .GGGG99 Title$HIIV&I

SWISS MODEL WORKSPACE
0odel information
modelled residue range E4 to 01=
based on template 3(InA 7,.04 Y8
23
$euence Identity B?C! 4=
9value! ,.23e'0,

click on model (ars

%ig, structure of template after modeling ,
0odel Validation$
IN#RADL%#IAN
$tructure Analysis and >alidation $erver greatly simplifies computational
analysis of the molecular structure and seuence of proteins. #he
stereochemical validation of model structures of proteins is an important part
21
of the comparative molecular modeling process. Ramachandran plot is a way
to visuali(e dihedral angles Z against [ of amino
acid residues in protein structure. It shows the possible conformations of Z
and [ angles for a polypeptide. #he Ramachandran plot displays the psi and
phi bac"bone conformational angles for each residue in a protein. #he
distance between two succession alpha carbon atoms in the bac"bone chain
and the angles between the two bonds of such atoms in desired protein can
be determined using this plot.
&oftware
&AV&$ http$JJnihserver,m(i,ucla,eduJ&AV&J
.rocedure
#he target protein structure obtained after homology modeling using deep
view and modeler is given as input for $A>$.

&AVE& results for proCFgunCan,pd(
Proc&ec' summary

2,
2A0CHA7D2A7 .54T$

Result -----
.lot statistics &C52E Kage
Residues in most favoured regions BA,B,FC ..3
E0./?
Residues in additional allowed regions Ba,b,l,pC 13=
..3?
24
Residues in generously allowed regions B\a,\b,\l,\pC 11
1.3?
Residues in disallowed regions 01
=.=?
'''' ''''
''''''''''''''''''
Number of non'glycine and non'proline residues 110/
133.3?
Number of end'residues 7e&cl. :ly and 1ro8 E
Number of glycine residues 7shown as triangles8 1,2
70.8
Number of proline residues /3
''''
#otal number of residues 1401
Based on an analysis of 11E structures o
and R'factor no greater than ,3?, a good uality model would be e&pected
to have over .3? in the most favoured regions.
Docking result )))) (y Hex software
2=
%ig,4igand ; 2eceptor *3!I7+

20
%ig , after docking
Do@e& 0.3 starting at )ri -ay 1/ 3.!1/!1. ,33E on host 5ARS'
A29240430..
Running @9]^$#AR#L1 file! %!_1rogram )iles_@e&
0.3_data_startup^v0.mac
Disc %ache enabled. Lsing directory! %!_1rogram )iles_@e& 0.3_cache
Assuming %!_1rogram )iles_@e& 0.3Oe&amples_,BEN.pdb is a 1DB file...
Apened 1DB file! %!_1rogram )iles_@e& 0.3Oe&amples_,BEN.pdb, ID I
,BEN
`5arning` %an;t add all hydrogens to incomplete residue! A ,04!FW$
`5arning` %an;t add all hydrogens to incomplete residue! A 41/!@I$
`5arning` %an;t add all hydrogens to incomplete residue! A 41E!FW$
`5arning` %an;t add all hydrogens to incomplete residue! A 4.4!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B E!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B .!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B 12!FW$
2/
`5arning` %an;t add all hydrogens to incomplete residue! B 4=!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B 4/!A$N
`5arning` %an;t add all hydrogens to incomplete residue! B /,!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B /0!AR:
`5arning` %an;t add all hydrogens to incomplete residue! B //!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B 41/!@I$
`5arning` %an;t add all hydrogens to incomplete residue! B 4E3!#WR
`5arning` %an;t add all hydrogens to incomplete residue! B =3=!#@R
1DB structure has crystal symmetry elements.
1DB structure has biological symmetry elements.
Foaded 1DB file! %!_1rogram )iles_@e& 0.3Oe&amples_,BEN.pdb, 7.,2
residues, 20.2 atoms, 1 models8
`5arning` )ractional charge 73.408 for non'terminal residue! A 0,!-$9
-$9!N Radius I 1.=3, %harge I '3.0,
-$9!%A Radius I 1.03, %harge I 3.1=
-$9!% Radius I 1.=3, %harge I 3.04
-$9!A Radius I 1.03, %harge I '3.03
-$9!%B Radius I 1.23, %harge I 3.3=
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.=18 for non'terminal residue! A E,!A$1
A$1!N Radius I 1.=3, %harge I '3.0,
A$1!%A Radius I 1.03, %harge I 3.,0
A$1!% Radius I 1.=3, %harge I 3.04
A$1!A Radius I 1.03, %harge I '3.03
A$1!%B Radius I 1.23, %harge I '3.,1
A$1!%: Radius I 1.=3, %harge I 3./,
A$1!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.408 for non'terminal residue! A ,.1!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
22
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.4=8 for non'terminal residue! A 41E!FW$
FW$!N Radius I 1.=3, %harge I '3.0,

FW$!%A Radius I 1.03, %harge I 3.,4
FW$!% Radius I 1.=3, %harge I 3.04
FW$!A Radius I 1.03, %harge I '3.03
FW$!%B Radius I 1.23, %harge I 3.3=
FW$!%: Radius I 1.23, %harge I 3.30
FW$!%D Radius I 1.23, %harge I 3.30
FW$!%9 Radius I 1.23, %harge I 3.,,
FW$!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.408 for non'terminal residue! A 420!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.1,8 for non'terminal residue! B E!FW$
`5arning` )ractional charge 73.1,8 for non'terminal residue! B .!FW$
2E
`5arning` )ractional charge 73.4=8 for non'terminal residue! B 12!FW$

`5arning` )ractional charge 73.408 for non'terminal residue! B 0,!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.1,8 for non'terminal residue! B /,!FW$
`5arning` )ractional charge 73.4=8 for non'terminal residue! B //!FW$
2.
`5arning` )ractional charge 7'3.,18 for non'terminal residue! B E1!A$1
`5arning` )ractional charge 73.408 for non'terminal residue! B ,.1!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.408 for non'terminal residue! B 420!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
E3
`5arning` )ractional charge 73.,48 for non'terminal residue! B =3=!#@R
#@R!N Radius I 1.=3, %harge I '3.0,
#@R!%A Radius I 1.03, %harge I 3.,2
#@R!% Radius I 1.=3, %harge I 3.04
#@R!A Radius I 1.03, %harge I '3.03
#@R!%B Radius I 1.03, %harge I 3.,1
#@R!@ Radius I 3.33, %harge I 3.,0
%ounted 13= Nve and 11= 've formal charged residues! Net formal charge!
'13
`5arning` Lsing 1DB %AN9%# records to define non'standard bonds.
J,BEN A
Assuming %!_1rogram )iles_@e& 0.3Oe&amples_,BEN.pdb is a 1DB file...
Apened 1DB file! %!_1rogram )iles_@e& 0.3Oe&amples_,BEN.pdb, ID I
,BEN
`5arning` %an;t add all hydrogens to incomplete residue! A ,04!FW$
`5arning` %an;t add all hydrogens to incomplete residue! A 41/!@I$
`5arning` %an;t add all hydrogens to incomplete residue! A 41E!FW$
`5arning` %an;t add all hydrogens to incomplete residue! A 4.4!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B E!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B .!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B 4=!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B 4/!A$N
`5arning` %an;t add all hydrogens to incomplete residue! B /,!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B /0!AR:
`5arning` %an;t add all hydrogens to incomplete residue! B //!FW$
`5arning` %an;t add all hydrogens to incomplete residue! B 41/!@I$
`5arning` %an;t add all hydrogens to incomplete residue! B 4E3!#WR
`5arning` %an;t add all hydrogens to incomplete residue! B =3=!#@R
1DB structure has crystal symmetry elements.
1DB structure has biological symmetry elements.
Foaded 1DB file! %!_1rogram )iles_@e& 0.3Oe&amples_,BEN.pdb, 7.,2
residues, 20.2 atoms, 1 models8
`5arning` )ractional charge 73.408 for non'terminal residue! A 0,!-$9
-$9!% Radius I 1.=3, %harge I 3.04
E1
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31

-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.=18 for non'terminal residue! A E,!A$1
A$1!%: Radius I 1.=3, %harge I 3./,
`5arning` )ractional charge 73.408 for non'terminal residue! A ,.1!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.4=8 for non'terminal residue! A 41E!FW$
`5arning` )ractional charge 73.408 for non'terminal residue! A 420!-$9
-$9!% Radius I 1.=3, %harge I 3.04
E,
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.1,8 for non'terminal residue! B E!FW$

`5arning` )ractional charge 73.1,8 for non'terminal residue! B .!FW$
`5arning` )ractional charge 73.408 for non'terminal residue! B 0,!-$9
-$9!% Radius I 1.=3, %harge I 3.04
E4
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.1,8 for non'terminal residue! B /,!FW$
`5arning` )ractional charge 73.4=8 for non'terminal residue! B //!FW$

`5arning` )ractional charge 7'3.,18 for non'terminal residue! B E1!A$1
`5arning` )ractional charge 73.408 for non'terminal residue! B ,.1!-$9
-$9!% Radius I 1.=3, %harge I 3.04
E=
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31
-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.408 for non'terminal residue! B 420!-$9
-$9!% Radius I 1.=3, %harge I 3.04
-$9!%: Radius I 1.23, %harge I 3.3.
-$9!$9 Radius I 1..3, %harge I 3.4,
-$9!%9 Radius I 1..3, %harge I 3.31

-$9!@ Radius I 3.33, %harge I 3.,0
`5arning` )ractional charge 73.,48 for non'terminal residue! B =3=!#@R
#@R!N Radius I 1.=3, %harge I '3.0,
#@R!%A Radius I 1.03, %harge I 3.,2
#@R!% Radius I 1.=3, %harge I 3.04
#@R!A Radius I 1.03, %harge I '3.03
#@R!%B Radius I 1.03, %harge I 3.,1
#@R!@ Radius I 3.33, %harge I 3.,0
%ounted 13= Nve and 11= 've formal charged residues! Net formal charge!
'13
`5arning` Lsing 1DB %AN9%# records to define non'standard bonds.
J,BEN A
)ound ,,4 -B main memory! setting N^-A]I44.
%hec" threefold I 3
E0
Doc"ing search mode I /D rotation N translation 7optimal8.
Lsing intermolecular distance R1, I 3.33, rounded to 3.33
$etting distance range I 3.33 to 1..03, with steps of 3.20
%alculating surface s"ins! :rid I 3./3A
%ontouring surface for molecule ,BEN.
1olar probe I 1.=3A, Apolar probe I 1.=3A
:aussian sampling over /1=. atoms done in ,.E/ seconds.

%ontoured 44EEEE triangles 71/.=== vertices8 in 1.43 seconds.
%ulled 1,E00. short edges in / cycles in =.4= seconds.
B21/02,4=./1,10.10,0443,/E0,11C
$urface traversal done in 3.,4 seconds ' )ound 1 surface segments.
1rimary surface! Area I ,/403../, >olume I 102.,1.2/.
%ulled 3 small segments in 3.,2 seconds.
%ulling reduced surface comple&ity by 20 per cent 7E1223 triangles, =3EE0
vertices8.
#otal contouring time! /.1= seconds.
%ontouring surface for molecule ,BEN.
1olar probe I 1.=3A, Apolar probe I 1.=3A
:aussian sampling over /1=. atoms done in ,.E1 seconds.
%ontoured 44EEEE triangles 71/.=== vertices8 in 1.43 seconds.
%ulled 1,E00. short edges in / cycles in =.4/ seconds.
B21/02,4=./1,10.10,0443,/E0,11C
$urface traversal done in 3.,, seconds ' )ound 1 surface segments.
1rimary surface! Area I ,/403../, >olume I 102.,1.2/.
vm! 03.33 -B.
%ulled 3 small segments in 3.,2 seconds.
%ulling reduced surface comple&ity by 20 per cent 7E1223 triangles, =3EE0
vertices8.
#otal contouring time! /.1= seconds.
$ampling surface and interior volumes for molecule ,BEN.
:enerated ,3131. e&terior and ,1/E=E interior s"in grid cells.
9&terior s"in volume I =4=,3.13* interior s"in volume I =/E4..12.
>olume sampling done in ,.4= seconds.
$ampling surface and interior volumes for molecule ,BEN.
E/
:enerated ,3131. e&terior and ,1/E=E interior s"in grid cells.
9&terior s"in volume I =4=,3.13* interior s"in volume I =/E4..12.
>olume sampling done in 1.4/ seconds.
%alculating s"in coefficients to N I ,0...
Integration applied to =12E/2 cells! =./= per cent of the total grid volume.
$"in integration to N I ,0 done in =4..0 seconds.
Doc"ing will output a ma&imum of 033 solutions per pair...
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
Doc"ing 1 pair of starting orientations...
Doc"ing receptor! ,BEN and ligand! ,BEN...
Receptor ,BEN! #ag I ,BEN

Figand ,BEN! #ag I ,BEN
5or"ing buffer for 1333333 orientations! 7,2-b8
#otal /D space! IterateB,2,E1,,1C & ))#B/=,,=,=EC I 1/1/=1,/2,.
Initial rotational increments 7NI1/8 Receptor! E1, 71.-b8, Figand! 1 71-b8
Foading all coefficient vectors into memory...
%oefficient rotations done in 3..1 seconds.
$tarting 4D ))#! NI1/.
Lsing Siss ))# for multi'dimensional D)#s.
4D ))# setup! 3.33 s. // -b memory.
9start I E/,1,.00 SGOmol 79shapeIE/,1,.00, 9forceI3.338
R I 3.33
R I 3.20
R I 1.03
R I ,.,0
R I 4.33
R I 4.20
R I =.03
R I 0.,0
R I /.33
R I /.20
E2
R I 2.03
R I E.,0
R I ..33
R I ..20
R I 13.03
R I 11.,0
R I 1,.33
R I 1,.20
R I 14.03
R I 1=.,0
R I 10.33
R I 10.20
R I 1/.03
R I 12.,0
R I 1E.33
R I 1E.20
R I 1..03
@e&! 04.// s, :)! 24.31 s, ))#! ,22.E2 s, $can! 10.=0 s, ))# Rate!
0E123.1Os.
9start I E/,1,.00 'J ran" 1
4D search found 3O1/1/=1,/2, within threshold but NA# including start
guess.
Done ,1.,= 4D ))#s for 1/1/=1,/2, orientations in 2 min, 3 sec
74E=E02=Os8.

Best start orientation BalphaI3C 79nergyI3.338 is at 1O1.
9nergy range! 9min I 3.33, 9ma& I 3.33
#op 1 orientations 'J 4 after distance sub'sampling.
5or"ing buffer for 4 orientations! 71-b8
$urviving rotational steps 7NI,08 Receptor! 1 71-b8, Figand! 1 71-b8
Foading all coefficient vectors into memory...
%oefficient rotations done in 3.33 seconds.
$tarting doc"ing search with NI,0, NalphaI/=O/=.
9start I 1=4031.4/ SGOmol 79shapeI1=4031.4/, 9forceI3.338
R I 3.33
R I 3.=3
R I 3.20
EE
9start I 1=4031.4/ 'J ran" 0
-ain pass found 3 minima within threshold but NA# including start guess.
-ain pass done in 3 min, 3 sec 712/1Os8.
$tarting orientation BalphaI3C 79nergyI1=4031.4/8 ran"ed 0 in the search.
Doc"ed structures ,BEN!,BEN in a total of 2 min, 0 sec.
Best start orientation BalphaI3C 79nergyI3.338 is at 1O1.
9nergy range! 9min I 3.33, 9ma& I 3.33
Doc"ing correlation summary by R-$ deviation and steric clashes
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
$oln 9total 9shape 9force 9air R-$ Bumps
'''' ''''''''' ''''''''' ''''''''' ''''''''' '''''''''''''''' '''''
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
$aving top 033 orientations.
Doc"ing done in a total of E min, 11 sec.
''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
No AIRs enabled or defined. $"ipping restraint chec"s.
%lustering found 1 clusters from 1 doc"ing solutions in 3.33 seconds.

'''' '''' ''''''' ''''''' ''''''' ''''''' ''''''' '''''' ''' '''''
%lst $oln -odels 9total 9shape 9force 9air >shape >clash Bmp R-$
'''' '''' ''''''' ''''''' ''''''' ''''''' ''''''' ''''''' '''''' ''' '''''
1 1 333!333 3.3 3.3 3.3 3.3 3.3 3.3 '1 '1.33
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
1 1 333!333 3.3 3.3 3.3 3.3 3.3 3.3 '1 '1.33
E.

.3

Conclusion
After analy(ing protein seuence of @epatitis B virus we come to
conclusion that though they all are closely related, they have an important
role in survival in different species. It is interesting to have closer loo" at the
matter by studying at the gene level. A phylogenetic analysis can be very
helpful in understanding the evolutionary pattern
.5e have noticed that same genes are present in all strains this shows that
are they evolved together.
.1
5ith the finishing of the ongoing gene seuencing
pro+ect on @B>, we hope it will be possible to draw conclusive decision
about the true picture of evolution in near future and gene responsible for
pathogenesis can also be identified.
%omplete inference can only be drawn based on a
comprehensive list of the gene products and their function.
In order to find out un"nown structure of protein
present in the different species we do homology modelling.. 5e forward
step to present a theoretical model using available online modelling tools.
As we study that @BeA: 7:lycerate "inase 8
protein that is coded by gene is one of the second reasons of pathogenicity
of @B>. $o we tried to doc" this protein with appropriate ligand, in order to
inhibit their activity on the basis of which the drugs have to be developed.

.,

%uture prospects
#he wor" presented in this report might +ust be a stepping stone for any such
discoveries. #he present wor" might be small finding of big issue.
1hylogenetics is that field of biology which deals with identifying and
understanding the relationships between the many different "inds of life on
earth. #his includes methods for collecting and analy(ing data, as well as
interpretation of those results as new biological information.
.4
.
#he purpose of modeling is to help the Drug developers and
Biotechnologists to develop the drug more efficiently and with more
effectiveness in future by analy(ing the modeled structure of protein.
As the new drugs target would be identified it will open new vistas for
further drug development .#he finding of our doc"ing will be useful in
finding a cure for the infectious disease bird flu, also it will open new
avenues for finding other possible drug targets in influen(a A virus.
#he doc"ing results can be used to design new lead compounds and hence
can aid in the new drug discovery process.

)inally, similar process can be applied on other pathogens and hence
possible therapeutic sites can be identified in them. $imilar method can also
be applied to other infectious diseases and hence we can loo" forward to a
better disease free world.
#he wor" presented is +ust a small part of big issue and lots of wor" still
needs to be done to establish a good phylogenetic relationship and full
fledged cure for bird flu. But we are hoping that these findings will go long
way and will prove fruitful to any going in a similar area.
.=
.0

!I!4I52A.HD

L1M ' Fannsing -. 1rescott,Gohn 1. @arley and Donald A. Slein
,-icrobiology /
th
edition
-c:raw@ill @igher 9ducation,@uman diseases caused by viruses
L3M ) ) > %hisari, % )errari
Department of -olecular and 9&perimental -edicine, $cripps Research
Institute, Fa Golla, %alifornia .,342, L$A.
./
L-M '% $eeger, 5 $ -ason
)o& %hase %ancer %enter, 1hiladelphia, 1ennsylvania 1.111, L$A.
c^seegerQfccc.edu
L9M) plumbed
L:M) @oward @ughes -edical Institute, Department of Biochemistry and
-olecular Biophysics, %olumbia Lniversity, New Wor", New Wor" 1334,,
L$A
Reprint reuests to! Barry @onig, @oward @ughes -edical Institute,
Department of Biochemistry and -olecular Biophysics, %olumbia
Lniversity, New Wor", NW 1334,, L$A
LNM) Al'Fa(i"ani, B., $heinerman, ).B., and @onig, B. ,331. %ombining
multiple structure and seuence alignments to improve seuence detection
and alignment! Application to the $@, domains of Ganus "inases. $roc. %atl.
Acad. Sci. OI$ 1=2./D1=E31. B1ub-edC.
Aloy, 1., Muerol, 9., Aviles, ).]., and $ternberg, -.G. ,331. Automated
structure'based prediction of functional sites in proteins! Applications to
assessing the validity of inheriting protein function from homology in
genome annotation and to protein doc"ing. &. 'ol. Biol. -11$ 4.0D=3E.
B1ub-edC.
Altschul, $.)., -adden, #.F., $chaffer, A.A., Rhang, G., Rhang, R., -iller,
5., and Fipman, D.G. 1..2. :apped BFA$# and 1$I'BFA$#! A new
.2
generation of protein database search programs. %ucleic Acids (es. 3:$
44E.D4=3,. B1ub-edC.
Apweiler, R., Attwood, #.S., Bairoch, A., Bateman, A., Birney, 9., Biswas,
-., Bucher, 1., %erutti, F., %orpet, )., %roning, -.D., et al. ,333. Inter1roa
An integrated documentation resource for protein families, domains and
functional sites. Bioinformatics
L@M) %heogenomics Faboratory, Research :roup on Biomedical Informatics,
Institut -unicipal Investigacib -edica and Lniversitat 1ompeu )abra,
1asseig -aritim de la Barceloneta, 42'=., 3E334 Barcelona 7%atalonia8,
$pain.
LIM) %omputational $ciences, Department of %hemistry, Nerviano -edical
$ciences, >iale 1asteur 13, ,331= Nerviano 7-I8, Italy.
romano."roemerQsanofi'aventis.com

.E

A((reviation
C&A$ Catalytic &ite Atlas
Em(oss$ European 0olecular !iology 5pen &oftware &uit
7C!I$ 7ational Centre for !iotechnology Information
7D!$ 7ucleic Acid Database
52%$ 5pen 2eading %rame
5T6$ 5perational Ta&onomic 6nit
..
.D!$ .rotein Data !an"
.hylip$ .hylogeny Inference .ac"age

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