Vol. 22 no. 2 2006, pages 195–201
The SWISS-MODEL workspace: a web-based environment
for protein structure homology modelling
Konstantin Arnold1,2, Lorenza Bordoli1,2, Ju ¨rgen Kopp1,2and Torsten Schwede1,2,?
1Biozentrum Basel, University of Basel, Switzerland and2Swiss Institute of Bioinformatics, Basel, Switzerland
Received on August 25, 2005; revised and accepted on November 7, 2005
Advance Access publication November 13, 2005
Associate Editor: Dmitrij Frishman
dimensional structures are available. Building homology models
requiresspecialized programsand up-to-datesequenceand structural
single web-based workspace facilitates access to homology modelling
from a computer with web connection without the need of downloading
and installing large program packages and databases.
the user in building protein homology models at different levels of com-
several modelling projects can be carried out in parallel. Protein
ible from the workspace and are updated in regular intervals. Tools for
template selection, model building and structure quality evaluation can
be invoked from within the workspace. Workflow and usage of the
workspace are illustrated by modelling human Cyclin A1 and human
Transmembrane Protease 3.
Availability: The SWISS-MODEL workspace can be accessed freely
Supplementary information: Supplementary data are available at
Three-dimensional (3D) protein structures are of great interest for
the rational design of many different types of biological experi-
ments, such as site-directed mutagenesis or structure-based discov-
ery of specific inhibitors. However, the number of structurally
characterized proteins is small compared with the number of
known protein sequences: as of November 2005, more than
33000 experimentally determined protein structures were deposited
protein knowledge database (Bairoch et al., 2005) held more than
2.3 million sequences. Various computational methods for model-
ling 3D structures of proteins have been developed to overcome this
limited (Chothia, 1992) and the 3D structure of proteins is better
conserved than their sequences, it is often possible to identify a
homologous protein with a known structure (template) for a given
protein sequence (target). In these cases, homology modelling has
proven tobethe methodofchoicetogenerate a reliable 3Dmodelof
a protein from its amino acid sequence as impressively shown in
several meetings of the bi-annual CASP experiment (Tramontano
and Morea, 2003; Moult, 2005). Homology modelling is routinely
the effects of sequence variations (Marti-Renom et al., 2000; Kopp
and Schwede, 2004a; Hillisch et al., 2004). Building a homology
model comprises four main steps: (1) identification of structural
template(s), (2) alignment of target sequence and template struc-
ture(s), (3) model building and (4) model quality evaluation. These
steps can be repeated until a satisfying modelling result is achieved.
Eachofthe foursteps requiresspecialized softwareaswell asaccess
to up-to-date protein sequence and structure databases.
Selection of the most suitable template structure and the align-
ment between target and template are still the predominant sources
of errors in comparative models (Tramontano and Morea, 2003). In
our own experience and that of others (Bates et al., 2001), manual
intervention at different steps of model building can significantly
improve the accuracy of the results. We havedeveloped the SWISS-
MODEL workspace to address this aspect by providing a range of
tools that allow the user to validate and to modify the different
modelling steps manually. The SWISS-MODEL workspace integ-
rates programs and databases required for homology modelling in
an easy-to-use web-based modelling workbench. It allows the user
to construct comparative protein models from a computer with web
connection without the need of downloading and installing large
program packages and databases.
Depending on the difficulty of the individual modelling task, the
workspace assists the user in building and evaluating protein homo-
logy models at different levels of complexity. For models that can
be built based on sufficiently similar templates, we provide a highly
automated modelling procedure with a minimum of user interven-
tion. On the other hand, for more difficult modelling scenarios with
less target–template sequence similarity, the user is given control
over individual steps of model building: functional domains in
multi-domain proteins can be detected, secondary structure and
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disordered regions can be predicted for the target sequence, suitable
template structures identified by searching the SWISS-MODEL
Template Library (SMTL), and target–template alignments can
be manually adjusted. As quality evaluation is indispensable for
a predictive method like homology modelling, every model is
accompanied by several quality checks. All relevant data of a mod-
elling project are presented in graphical synopsis.
The accuracy, stability and reliability of the automated SWISS-
MODEL server pipeline (Peitsch, 1995; Guex and Peitsch, 1997;
Schwede et al., 2003) has been continuously validated by the EVA-
CM evaluation project (Koh et al., 2003). The workspace extends
the web-based SWISS-MODEL system by assisting manual user
intervention in model building and evaluation. Here, we will illus-
trate the application of SWISS-MODEL workspace in two model-
ling projects of different complexity: human Cyclin A1 and
Transmembrane Protease 3.
2 SYSTEMS AND METHODS
2.1Modelling modes in SWISS-MODEL workspace
Depending on the difficulty of the modelling task, three different
types of modelling modes are provided, which differ in the amount
of user intervention: automated mode, alignment mode and project
mode. Modelling requests are directly computed by the SWISS-
MODEL server homology modelling pipeline (Schwede et al.,
2003). The ‘automated mode’ has been developed for cases
where the target–template similarity is sufficiently high to allow
for fully automated modelling. As a rule of thumb, automated
sequence alignments are sufficiently reliable when target and tem-
plate share >50% identical residues (Rost, 1999). ‘Automated
mode’ submissions require only the amino acid sequence or the
UniProt accession code of the target protein as input data. The
modelling pipeline automatically selects suitable templates based
on a Blast E-value limit, which can be adjusted upon submission.
The automated template selection will favour high-resolution
template structures with reasonable stereochemical properties as
assessed by ANOLEA mean force potential (Melo and Feytmans,
Multiple sequence alignments are a common tool in many
molecular biology projects, and are often the result of extensive
theoretical and experimental exploration of a certain family of
proteins. If a 3D structure for at least one of the members is
known, a given alignment can be used as starting point for com-
parative modelling using the ‘alignment mode’. In order to facilitate
the use of alignments, the submission is implemented as a three-step
procedure: The input alignment, which can be provided in several
different formats (FASTA, MSF, ClustalW, PFAM, SELEX), is
converted into a standard ClustalW format in the first step. The
user indicates which sequence in the alignment corresponds to the
target protein, and which corresponds to a protein with an experi-
mentally determined structure deposited in the PDB database
(Westbrook et al., 2003). Commonly, protein sequences used for
multiple sequence alignments are not identical to their correspond-
ing PDB entries, e.g. due to missing atom coordinates, mutations or
sequence tags introduced for easier purification and crystallization.
Therefore, in the subsequent step the submitted alignment is
matched against the sequence of the template structure coordinates
extracted from the SWISS-MODEL template library. Since most
modelling programs depend on a perfect match between the
template sequence in the input alignment and the residues present
in the coordinate file, this step relieves the user from the obligation
to deliver ‘perfect’ alignments to PDB entries. Instead one can
actually work with sequences directly retrieved from sequence data-
bases. The server pipeline will build the model based on this align-
ment. During the modelling process, implemented as rigid fragment
assembly in the SWISS-MODEL pipeline, the modelling engine
might introduce minor heuristic modifications to improve the place-
ment of insertions and deletions based on the structural context
(Schwede et al., 2003).
In difficult modelling projects, where the correct alignment
between target and template cannot be clearly determined by
sequence-based methods, visual inspection and manual manipula-
tion of the alignment can significantly improve the quality of the
resulting model (Bates et al., 2001). The program DeepView—
Swiss-PdbViewer (Guex and Peitsch, 1997)—can be used to gen-
erate, display, analyse and manipulate modelling project files for
SWISS-MODEL workspace. Project files contain the superposed
template structures and the alignment between the target and the
template. In this mode the user has full control over essential mod-
elling parameters, i.e. the choice of template structures, the correct
alignment of residues, and the placement of insertions and deletions
in the context of the 3D structure. Project files can also be generated
by the workspace template selection tools and are the default output
format of the modelling pipeline. This allows analysing and iter-
atively improving the output of ‘automated mode’ and ‘alignment
mode’ modelling projects. The program DeepView can be down-
loaded freely from the ExPASy web site (http://www.expasy.org/
2.2SWISS-MODEL template library
The template structure database used by SWISS-MODEL (SMTL)
is derived from the Protein Data Bank (Westbrook et al., 2003). In
order to allow sequence-based template searches, each PDB entry
is split into individual chains. The separated template chains are
annotated with information about experimental method, resolution
(if applicable), ANOLEA mean force potential, Gromos96 energy
and PQS (Henrick and Thornton, 1998) quaternary state assignment
to allow for rapid retrieval of the relevant structural information
during template selection. Theoretical models, structures only con-
sisting of Caatoms and incorrectly formatted database entries are
In order to speed up the sequence database search step of the
template identificationalgorithms and toprovidea clear andconcise
overview of the results, templates sharing 100% sequence identity
are grouped into an SMTL100 library using the program CD-HIT,
a fast clustering method for sequences at high identity thresholds
(Li et al., 2001, 2002). Clusters of sequences having 90, 70 and
50% sequence identity are derived from the RCSB non-redundant
PDB lists. Information aboutthe members of the cluster is presented
in the detailed output of the different template search programs.
For each template, the SWISS-MODEL workspace provides a
summary showing a small ribbon representation, experimental
details, information about bound molecules, as well as links to
PDB (Westbrook et al., 2003), SCOP (Andreeva et al., 2004),
CATH (Pearl et al., 2005), PDBsum (Laskowski et al., 2005)
and MSD (Velankar et al., 2005).
K.Arnold et al.
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2.3 Domain assignment, secondary structure and
Many proteins are modular and made up of several structurally
distinct domains, which often reflect evolutionary relationships
and may correspond to units of molecular function (Andreeva
et al., 2004; Bateman et al., 2004; Pearl et al., 2005). The member
databases of InterPro (Mulder et al., 2005) allow for both the iden-
tification of protein domains and the assignment of protein function.
Using IprScan (Zdobnov and Apweiler, 2001), a PERL-based Inter-
ProScan implementation, protein domains and functional sites can
be assigned to regions of a target sequence. Splitting multi-domain
proteins into separated domains often improves the sensitivity and
performance of profile-based template search methods (see below).
Secondary structure prediction methods are provided, which are
especially useful when combined with other types of analyses:
e.g. in cases where only templates with very low sequence homo-
logy can be detected by sequence-based search methods, predicted
secondary structure may help to decide if a putative template shares
structural features of the target protein. The secondary structure
prediction program PsiPred (Jones, 1999) is accessible from the
tools section of the workspace.
some proteins have regions that are natively disordered, unstruc-
tured or have flexible regions without permanent regular secondary
structure. It has been suggested that disordered regions may possess
biological functions, and could be involved in signalling and regu-
lation processes (Dunker and Obradovic, 2001; Iakoucheva et al.,
2002).The proteindisorderprediction program Disopred(Jones and
Ward, 2003) estimates the propensity of protein sequences to be
disordered. The result of secondary structure, disorder and domain
boundary prediction (Fig. 1) can aid the selection of modelling
templates for specific regions of the target protein.
2.4 Template identification
sequence can range from ‘trivial’ for well-characterized protein
families to ‘impossible’ for proteins with a so far unknown fold.
Consequently, the SWISS-MODEL workspace provides access to a
set of increasingly complex and computationally demanding meth-
ods to search for templates.
be identified using a gapped BLAST (Altschul et al., 1997) query
against the SWISS-MODEL template library extracted from PDB.
When no suitable templates are identified, or only parts of the target
sequence are covered, two additional approaches for more sensitive
detection of distant relationships among protein families are pro-
vided: an iterative profile Blast search and a Hidden Markov Model-
based template search.
Iterative profile blast.
In the iterative profile Blast approach
(Altschul et al., 1997) a profile for the query sequence is built
from homologue sequences found by iterative searches of the
NR database (Wheeler et al., 2005). Subsequently, this profile is
used to search for homologous structures in the template library.
This method has been initially introduced as PDB-Blast by Godzik
HMM-based template library search.
Markov Models for a non-redundant set of the sequences in the
template library was generated. Each model of the library was
Templates which are close homologues of the target can
A library of Hidden
created from a multiple sequence alignment generated by an iter-
ative search of the NR databases using SAM-T2K (Hughey and
Krogh, 1996). Model building, calibration and library searches were
performed using the SAM (v 3.4) software package (Karplus et al.,
1998). Although computationally intensive, model calibration
against a large, non-redundant database was calculated in order
to obtain more accurate E-values during the scoring step. To select
template HMM library for statistically significant matches.
2.5 Continuous evaluation of modelling accuracy
Evaluation of model quality is a crucial step in homology model-
ling. In our view, benchmarking the individual steps and compon-
ents of the comparative modelling workflow separately is not
sufficient to assess the overall performance of a modelling pipeline,
because the observed differences may not reflect critical steps in
practical application and are therefore often inconclusive in judging
the accuracy of an entire modelling workflow. The reliability of
different protein modelling methods can be assessed by evaluating
the results of blind predictions after the corresponding protein struc-
tures have been determined experimentally. During the biannual
‘Community Wide Experiment on the Critical Assessment of Tech-
niques for Protein Structure Prediction’ CASP (Moult, 2005), new
algorithmic developments are evaluated based on a number of test
cases, e.g. in the 2004 CASP6 experiment 43 homology modelling
targets were assessed (Tress et al., 2005). The continuous and auto-
mated assessment of modelling servers by the LiveBench
(Rychlewski and Fischer, 2005) or EVA (Koh et al., 2003) projects
is based on a large number of blind predictions. SWISS-MODEL
was the first comparative modelling server to join the EVA project
in May 2000, and has been continuously monitored since then.
EVA-CM has performed a comparative evaluation of the following
servers: 3D-Jigsaw (Bates et al., 2001), ESyPred3D (Lambert et al.,
2002), CPHModels (Lund et al., 1997), SDSC1 (Shindyalov and
Bourne, 2000) and SWISS-MODEL (Guex and Peitsch, 1997;
19698 protein target chains. Figure 2a (supplementary material)
gives an estimation of the overall accuracy of the different model-
ling servers displaying the Caatom RMSD after global superposi-
tion of the model and the experimental target structures versus
percentage of sequence identity between target and best template.
As expected, model RMSD is increasing with decreasing alignment
accuracy as defined by the percentage of equivalent Capositions
(within 3.5 s) between the optimally superimposed target and
model structures (Figure 2b, supplementary material). For target–
template pairs sharing sequence identities of >40%, only small
differences between the prediction servers are observed.
The cumulative evaluation of global Caatom RMSD over all
models in the test set shows that the models built by SWISS-
MODEL exhibit on average the lowest overall deviation (2.0 s
versus 2.7 s for 3DJIGSAW) from the experimental control struc-
tures (Figure 2c, supplementarymaterial). However, this is linkedto
a lower coverage of SWISS-MODEL for low homology templates.
In the EVA-CM comparison, the models built by SWISS-MODEL
appear to be on average more accurate, but shorter than the models
of the other servers in the evaluation.
In general, the modelling accuracy for different target proteins is
much more variable than the differences observed between different
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modelling methods for the same target. The EVA-CM database is
sufficiently large to allow the prediction of the expected accuracy of
the participating servers for a given protein sequence based on
previous data of similar modelling scenarios.
2.6 Tools for protein structure and model assessment
The quality of individual models can vary significantly from the
average accuracy expected for a given target–template similarity or
modelling method. Therefore, individual assessment of each model
is essential. SWISS-MODEL workspace provides graphical plots of
Anolea mean force potential (Melo and Feytmans, 1998), GRO-
MOS empirical force field energy (van Gunsteren et al., 1996),
Verify3D profile evaluation (Eisenberg et al., 1997), Whatcheck
(Hooft et al., 1996) and Procheck (Laskowski et al., 1993) reports
are generated to enable the user to estimate the quality of protein
models and template structures. To facilitate the description of
template and model structures, DSSP (Kabsch and Sander, 1983)
and Promotif (Hutchinson and Thornton, 1996) can be invoked to
classify structural features.
We have implemented the SWISS-MODEL workspace using stand-
ard web browsers as graphical user interface to the dynamic server
front-end based on Apache/PHP. Protein sequence and structure
databases, modelling software and user data are located on a
back-end system. Front-end server and the compute back-end
Fig. 1. Graphical output of SWISS-MODEL workspace representing typical steps of a modelling experiment. (a) Ribbon representation of three domains
modelled for the target protein human transmembraneprotease 3 (TMPRSS3): I, LDL receptor domainand II, Scavenger receptor in complex with the protease
domain. (b) IprScan of the target sequence detected three domains in the target protein. (c) Sequence-based searches of the template library identified two
segments with suitable templatestructures. (d) Secondarystructure and disorder prediction of the target protein. (e) Anolea mean force potential plot allows for
quality assessment of the final models.
K.Arnold et al.
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communicate via XML-RPC calls, separating the graphical display
from the computationally demanding tasks. Batch jobs are executed
on ahigh-performance Linuxcluster via SunGRID engine toensure
load balancing and optimal response times. Databases at the back-
end are automatically updated in regular intervals. The SWISS-
MODEL workspace provides a personal working area for each
registered user, which is not visible for other users. Email notifica-
tion is sent to indicate when the calculation of a work unit has been
completed. Users can access the workspace system anonymously
without providing an email address; however, it is then necessary to
bookmark the individual work units in the web browser to be able to
retrieve the results once the browser has been closed. The SWISS-
MODEL workspace is accessible at http://swissmodel.expasy.org/
3 RESULTS AND DISCUSSION
In the following chapter, we describe how the different modelling
modes and tools available from the SWISS-MODEL workspace
were applied to identify suitable templates and to build homology
models for two biologically relevant human proteins: Cyclin A1
(CCNA1) and Transmembrane Protease 3 (TMPRSS3).
3.1Modelling of human Cyclin A1
nuclear cell division cycles and in regulating cyclin-dependent
kinases (CDKs). Inactive CDK apoenzymes are partially activated
by complex formation with regulatory cyclin subunits and the com-
plexes are further activated by phosphorylation of a Thr residue in
CDKs. There are four classes of cyclins: A, B, D and E, which bind
cyclin family consists of two members, Cyclin A1 and Cyclin A2.
While Cyclin A2 is widely expressed in different tissues (Liu et al.,
1998), Cyclin A1 is limited to male germ cells. Cyclin A1 is essen-
tial for spermatocyte passage into the first meiotic division in male
explored and it is investigated whether it could be a novel target for
new approaches for male contraception (Wolgemuth et al., 2004).
To date no experimentally determined 3D structure of Cyclin A1
is available. Blast searches to identify suitable templates for the
modelling of Cyclin A1 lead to several highly significant matches.
These matches span the second half of the protein (starting at about
scanning the InterPro database of protein families and domains. All
detected templates belong to the Cyclin family; in particular the
Cyclin A2 proteins share the highest sequence similarity with
Cyclin A1. For Cyclin A2 several experimental structures are
known, which contain two subdomains of similar all-alpha fold
forming the Cyclin domain of the protein.
The Blast alignment between the sequences of the Cyclin domain
of Cyclin A1 and Cyclin A2 is unambiguous: the two sequences
share ?60% identity and contain only one gap. Based on these
observations, the Cyclin A1 regulatory domain can be easily mod-
elled using the automated mode of the SWISS-MODEL pipeline.
The modelling pipeline selects the structure of the humanCyclin A2
in complex with CDK2 and an inhibitor [PDB: 1h1rB (Davies et al.,
2002)] as a template. Although other structures of the same protein
have been deposited in the PDB, 1h1rB is selected by the modelling
pipeline because it has the highest resolution among the suitable
templates. Alternatively, other Cyclin A2 apo-protein structures or
complexes with other molecules could be used to model the Cyclin
A1 C-terminal domain. Exhaustive information about the individual
templates is available directly from the template selection output as
link to the SWISS-MODEL template library and external resources:
MSD (Velankar et al., 2005), PDB (Westbrook et al., 2003), PDB-
sum (Laskowski et al., 2005), SCOP (Andreeva et al., 2004) and
CATH (Pearl et al., 2005). For instance, in order to model the
Cyclin-CDK activated complex bound to ATP, the bovin template
1finB (Jeffrey et al., 1995) could be used instead of 1h1rB. In the
automated mode of the modelling pipeline, it is sufficient to specify
the SMTL code for the template to be used.
As expected from the high target–template similarity the quality
of both models (based on structures 1h1rB and 1finB) is very good.
Overall ANOLEA, GROMOS and Verify3D quality assessments do
not detect major problems in the models. Visual inspection of the
model and the template structure using DeepView shows good
sequence conservation at the interface between CDK2 and the cyc-
3.2Modelling of TMPRSS3
While the automated approach yields satisfying results for closely
related proteins, modelling of proteins based on templates with
remote homology requires more user intervention as presented
in the case of TMRSS3. Human Transmembrane Protease 3
(TMPRSS3) belongs to a family of transmembrane serine proteases
expressed in several tissues. Mutations in the protein have been
reported to cause neurosensory deafness (Masmoudi et al., 2001;
Scott et al., 2001; Wattenhofer et al., 2002; Lee et al., 2003).
In silico predictions indicate that the protein contains four domains:
a transmembrane (TM) domain, a low-density lipoprotein receptor
A (LDLRA), a scavenger receptor cystein-rich (SRCR) domain and
a protease domain. Pathogenic mutations have been described
in all three non-membrane domains. Currently, no experimentally
determined protein structure of human TMPRSS3 is available.
Therefore, homology models of the protein are valuable resources
to rationalize the functional impact of these mutations.
The boundaries of the individual domains of TMPRSS3 were
identified using IprScan. The sensitivity and performance of tem-
plate detection can often be improved when the template search is
performed on individual domains rather than the whole target
sequence. As previously reported (Masmoudi et al., 2001; Scott
et al., 2001; Wattenhofer et al., 2002; Lee et al., 2003), IprScan
reports the occurrence of LDLRA, SRCR and protease domains
in the TMPRSS3 protein. Blast, Iterative Profile Blast and HMM-
based template identification methods display several matches to
structures corresponding tothe protease domain andsome templates
spanning both SRCR and protease domain. For the LDLRA domain
only Iterative Profile Blast and HMM-based template identification
with significant scores (Fig. 1). Each template of the hit list is linked
to the SMTL and from there to other external resources, to allow for
domain classifications) of the different potential templates can be
compared with the annotations of the target sequence to avoid the
selection of non-homologous templates. This is especially relevant
when trying to increase the coverage of the model by including low
homology templates. The templates covering both SRCR and pro-
tease domain correspond to the structure of human Hepsin which
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belongs to the family of serine proteases. Crystal structures of a
protein–substrate complex [PDB: 1z8g (Herter et al., 2005)] or
the apo-protein [PDB: 1P57 (Somoza et al., 2003)] could be used
to build a model for the TMSSR3 protease and SRCR receptor
domains. The alignment between target sequence and template
1z8g contains several gaps and therefore should be checked care-
fully. Alignments with possible template structures can be directly
loaded into DeepView, where the placement of insertion and dele-
tions is examined in the structural context. Modified alignments can
be saved as project files and submitted to the Project mode of the
modelling workspace. The protein structure deposited as PDB entry
1z8g contains the cleaved activated form of the protease. To build a
model of the activated form, the two fragments of the template were
treated as individual chains within DeepView. Several alternative
alignments were submitted and the quality of the resulting models
models e.g. Ramachandran plots were analysed with Procheck
(Laskowski et al., 1993). The alignment, model building and evalu-
ation steps were iterated until a satisfactory result was obtained.
The same procedure was applied to the modelling of the LDLRA
domain using the crystal structure 1jja of the human low-density
lipoprotein receptor. The LDL-receptor class A domain contains 6
disulphide-bound cysteins (Bieri et al., 1995). Particular care was
therefore taken in correctly aligning the cysteins. A highly con-
served cluster of negatively charged amino acids forms a Ca2+
coordination site (Daly et al., 1995). The LDLRA repeat has
been shown to consist of a beta-hairpin structure followed by a
series of beta turns. Based on the pattern of cystein residues, and
on the homology detected by template identification tools, the
TMPRSS3 sequence appears to contain only one occurrence of
the repeat. The quality assessment for the final models is satisfact-
ory and essential structural features such as the disulfide bridge
pattern and the Ca2+coordination site of the LDLRA domain appear
to be correctly retained. Regions with slightly positive energy value
reported for ANOLEA and GROMOS correspond to residues where
the alignment is less conserved and gaps in the alignment require
ab initio loop re-modelling.
The presented examples demonstrate the usefulness and the cap-
abilities of the integrated web-based modelling infrastructure
SWISS-MODEL workspace. In combination with DeepView
(Swiss-PdbViewer), it complements the server pipeline and repos-
itory (Kopp and Schwede, 2004b) as powerful and easy to use web-
based resources for comparative protein modelling.
We are grateful to Karol Miaskiewicz, Jack Collins and Robert W.
Lebherz (Advanced Biomedical Computing Center, NCIFCRF
Frederick, MD, USA) for excellent computational and technical
support. We are deeply indebted to Manuel C. Peitsch (Novartis
AG, Basel) and to Nicolas Guex (GSK, Raleigh, NC, USA) for
their pioneering work on large-scale protein structure modelling.
We would like to acknowledge financial support by the Swiss
National Science Foundation (SNF). Funding to pay the Open
Access publication charges for this article was provided by the
Swiss Institute of Bioinformatics (SIB).
Conflict of Interest: none declared.
Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs. Nucleic Acids Res., 25, 3389–3402.
Andreeva,A. et al. (2004) SCOP database in 2004: refinements integrate structure and
sequence family data. Nucleic Acids Res., 32, D226–D229.
Bairoch,A. et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res.,
33 (Database Issue), D154–D159.
Bateman,A. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32,
Bates,P.A. et al. (2001) Enhancement of protein modeling by human intervention in
applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins, (Suppl. 5),
Bieri,S. et al. (1995) Disulfide bridges of a cysteine-rich repeat of the LDL receptor
ligand-binding domain. Biochemistry, 34, 13059–13065.
Chothia,C. (1992) Proteins. One thousand families for the molecular biologist. Nature,
Daly,N.L. et al. (1995) Three-dimensional structure of a cysteine-rich repeat from the
low-density lipoprotein receptor. Proc. Natl Acad. Sci. USA, 92, 6334–6338.
Davies,T.G. et al. (2002) Structure-based design of a potent purine-based cyclin-
dependent kinase inhibitor. Nat. Struct. Biol., 9, 745–749.
Dunker,A.K. and Obradovic,Z. (2001) The protein trinity—linking function and
disorder. Nat. Biotechnol., 19, 805–806.
Eisenberg,D. et al. (1997) VERIFY3D: assessment of protein models with three-
dimensional profiles. Methods Enzymol., 277, 396–404.
Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer:
an environment for comparative protein modeling. Electrophoresis, 18,
Henrick,K. and Thornton,J.M. (1998) PQS: a protein quaternary structure file server.
Trends Biochem. Sci., 23, 358–361.
Herter,S. et al. (2005) Hepatocyte growth factor is a preferred in vitro substrate for
human hepsin, a membrane-anchored serine protease implicated in prostate and
ovarian cancers. Biochem. J., 390, 125–136.
Hillisch,A. et al. (2004) Utility of homology models in the drug discovery process.
Drug Discov. Today, 9, 659–669.
Hooft,R.W. et al. (1996) Errors in protein structures. Nature, 381, 272.
Hughey,R. and Krogh,A. (1996) Hidden Markov models for sequence analysis: exten-
sion and analysis of the basic method. Comput. Appl. Biosci., 12, 95–107.
Hutchinson,E.G. and Thornton,J.M. (1996) PROMOTIF—a program to identify and
analyze structural motifs in proteins. Protein Sci., 5, 212–220.
Iakoucheva,L.M. et al. (2002) Intrinsic disorder in cell-signaling and cancer-associated
proteins. J. Mol. Biol., 323, 573–584.
Jeffrey,P.D. et al. (1995) Mechanism of CDK activation revealed by the structure of a
cyclinA-CDK2 complex. Nature, 376, 313–320.
Jones,D.T. (1999) Protein secondary structure prediction based on position-specific
scoring matrices. J. Mol. Biol., 292, 195–202.
Jones,D.T. and Ward,J.J. (2003) Prediction of disordered regions in proteins from
position specific score matrices. Proteins, 53 (Suppl. 6), 573–578.
Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern
recognition of hydrogen-bonded and geometrical features. Biopolymers, 22,
Karplus,K. et al. (1998) Hidden Markov models for detecting remote protein homo-
logies. Bioinformatics, 14, 846–856.
Koh,I.Y. et al. (2003) EVA: evaluation of protein structure prediction servers. Nucleic
Acids Res., 31, 3311–3315.
Kopp,J. and Schwede,T. (2004a) Automated protein structure homology modeling: a
progress report. Pharmacogenomics, 5, 405–416.
Kopp,J. and Schwede,T. (2004b) The SWISS-MODEL Repository of annotated three-
dimensional protein structure homology models. Nucleic Acids Res., 32,
Lambert,C. et al. (2002) ESyPred3D: prediction of proteins 3D structures. Bioinform-
atics, 18, 1250–1256.
Laskowski,R.A. et al. (1993) PROCHECK: a program to check the stereochemical
quality of protein structures. J. Appl. Cryst., 26, 283–291.
Laskowski,R.A. et al. (2005) PDBsum more: new summaries and analyses of the
known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33,
Lee,Y.J. et al. (2003) Pathogenic mutations but not polymorphisms in congenital and
childhood onset autosomal recessive deafness disrupt the proteolytic activity of
TMPRSS3. J. Med. Genet., 40, 629–631.
Li,W. et al. (2001) Clustering of highly homologous sequences to reduce the size of
large protein databases. Bioinformatics, 17, 282–283.
K.Arnold et al.
by guest on May 30, 2013
Li,W. et al. (2002) Sequence clustering strategies improve remote homology recog-
nitions while reducing search times. Protein Eng., 15, 643–649.
Liu,D. et al. (1998) Cyclin A1 is required for meiosis in the male mouse. Nat. Genet.,
Lund,O. et al. (1997) Protein distance constraints predicted by neural networks and
probability density functions. Protein Eng., 10, 1241–1248.
Marti-Renom,M.A. et al. (2000) Comparative protein structure modeling of genes and
genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291–325.
Masmoudi,S. et al. (2001) Novel missense mutations of TMPRSS3 in two consan-
guineous Tunisian families with non-syndromic autosomal recessive deafness.
Hum. Mutat., 18, 101–108.
Melo,F. and Feytmans,E. (1998) Assessing protein structures with a non-local atomic
interaction energy. J. Mol. Biol., 277, 1141–1152.
Moult,J. (2005) A decade of CASP: progress, bottlenecks and prognosis in protein
structure prediction. Curr. Opin. Struct. Biol., 15, 285–289.
Mulder,N.J. et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33
(Database issue), D201–D205.
Pearl,F. et al. (2005) The CATH Domain Structure Database and related resources
Gene3D and DHS provide comprehensive domain family information for genome
analysis. Nucleic Acids Res., 33 (Database issue), D247–D251.
Peitsch,M.C. (1995) Protein modelling by E-Mail. BioTechnology, 13, 658–660.
Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12,
Rychlewski,L. and Fischer,D. (2005) LiveBench-8: the large-scale, continuous assess-
ment of automated protein structure prediction. Protein Sci., 14, 240–245.
Schwede,T. et al. (2003) SWISS-MODEL: an automated protein homology-modeling
server. Nucleic Acids Res., 31, 3381–3385.
Scott,H.S. et al. (2001) Insertion of beta-satellite repeats identifies a transmembrane
protease causing both congenital and childhood onset autosomal recessive deaf-
ness. Nat. Genet., 27, 59–63.
Shindyalov,I.N. and Bourne,P.E. (2000) Improving alignments in HM protocol with
intermediate sequences. In Proceedings of the Fourth Meeting on the Critical
Assessment of Techniques for Protein Structure Prediction, December 3, A,
Asilomar, CA, 92.
Somoza,J.R. et al. (2003) The structure of the extracellular region of human hepsin
reveals a serine protease domain and a novel scavenger receptor cysteine-rich
(SRCR) domain. Structure (Camb) 11, 1123–1131.
Tramontano,A. and Morea,V. (2003) Assessment of homology-based predictions in
CASP5. Proteins, 53 (Suppl. 6), 352–368.
Tress,M. et al. (2005) Assessment of predictions submitted for the CASP6 comparative
modelling category. Proteins, Doi:10.1002/prot.20739.
Mark,A.E., Scott,W.R.P. and Tironi,I.G. (1996) Biomolecular Simulations:
The GROMOS96 Manual and User Guide. VdF Hochschulverlag ETHZ,
Velankar,S. et al. (2005) E-MSD: an integrated data resource for bioinformatics.
Nucleic Acids Res., 33 (Database issue), D262–D265.
Wattenhofer,M. et al. (2002) Mutations in the TMPRSS3 gene are a rare cause of
childhood nonsyndromic deafness in Caucasian patients. J. Mol. Med., 80,
Westbrook,J. et al. (2003) The Protein Data Bank and structural genomics. Nucleic
Acids Res., 31, 489–491.
Wheeler,D.L. et al. (2005) Database resources of the National Center for
Wolgemuth,D.J. et al. (2004) The A-type cyclins and the meiotic cell cycle in mam-
malian male germ cells. Int. J. Androl., 27, 192–199.
Zdobnov,E.M. and Apweiler,R. (2001) InterProScan—an integration platform for
Hu ¨nenberger,P.H.,Kru ¨ger,P.,
by guest on May 30, 2013