The Protein Model Portal

The Protein Model Portal (PMP) is part of the Protein Structure Initiative Knowledgebase (PSI KB). The goal of the portal is to give unified access to the various models that can be leveraged from PSI targets and other experimental protein structures. Models are provided by the PSI centers (CSMP, JCSG, MCSG, NESG, NYSGRC, JCMM), and by independent modeling groups.

Table of contents

Querying the portal
Model Types
Target-Template Alignments
Model Quality
1) Model quality and applications of models
2) Determinants of model accuracy
a) Sequence identity between target and template of known structure
b) Actuality of template selection
c) Variability among available templates
3) Validation of protein models
a) By analysing the template situation
b) By analysing the model ensemble
c) By employing scoring functions to analyse the geometry of protein structures
Structure Comparison
Sequence Annotation
Model Preview Images & Visualization
PSI Partner Sites

PMP query types

The data leveraged by PMP is centered on md5 hashes of complete UniProt entries. This allows a unification of all provider data and rich queries to search it. The PMP main query page now allows queries of the following types:

  • Free text search, currently automatically activated, if the request contains non-amino acid characters (based on one-letter code) or is shorter than 30 amino acids
  • Sequences search, for either FASTA format or just raw sequences
  • Accession code searches, supporting Uniprot entries (AC and ID), entries from the NCBI Reference Sequence (RefSeq) and Protein Data Bank identifiers (PDB)
Additional queries available from the advanced query page:
  • Advanced text query: The indexed UniProt fields are Gene name/loci ("GN"), Organism Species ("OS"), Keywords ("KW"), Description ("DE"), Features ("FT") and several Database References ("DR"), including pathway annotation from Reactome, domain annotation from Pfam, SUPFAm, TIGRFAMs and Prosite as well as motif annotation from PRINTS. The ability to combine several search queries via logical operators AND/NOT/OR allows users to construct complex search queries. By delimiting the inputs with a semicolon, the given input phrases will be combined with a logical or.
  • Advanced accession code query: additionally accession codes for the NCBI Entrez and GI databases are supported.

PMP results

After a query from the PMP main page you are shown the "summary page" where a list of models and experimental structures are shown along with domain and UniProt information (ex: summary page).

PMP summary page image

From there you have a number of options to choose from:

  1. Additional individual structure information: Double clicking on any of the bars takes you either to the PDB (green bars) or to one of the PMP "model pages".PMP detail page image
    Here you can find more detailed information on a particular model, its predicted quality and its template (applicable only for single template modeling algorithms), especially a model coordinates download link in the section "Model information" and a link to a submission page
    PMP detail page quality and alignment image
    Here one submits to model quality estimation servers, both directly for PMP models and your own uploadable file (PDB format).
  2. Structure comparison of models/experimental structures (select the entries by either single clicking the bars or ticking the check box at the end of each row in the list of models and experimental structures
  3. Remodel the sequence: depending on the time of verification of a model we advise users to use this functionality to obtain an updated model via the "interactive modeling servers", a selection of registered modeling servers, which each individually send the model directly to your email address.

Model Types

Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Experimental structural biology and homology modeling thereby complement each other in the exploration of the protein structure space. For every structure determined, hundreds of models can be derived using a variety of established methods. Sequence-Centric Models (SC) are generated by searching the best available template structures to build a model for a given protein target sequence, while Template-Centric Models (TC) result from using a specific solved structure as a template to build a number of models for a series of target protein sequences.

Target-Template Alignments

The target-template alignment provided on the model info pages are generated dynamically by structural superposition of model and template structures using MAMMOTH (Lupyan D., Leo-Macias A., Ortiz AR. (2005) Bioinformatics, 21, 3255-3263). For colouring of the alignment mview (Brown, N.P., Leroy C., Sander C. (1998) Bioinformatics, 14(4):380-381) is used. The first two lines contain amino acids coloured by property (CLUSTAL colour map), while matching residues are displayed in a third line labelled consensus/100%

Model Quality

Protein structure models are theoretical models which may contain large errors and therefore need to be treated with caution. The quality of protein models therefore needs to be analysed carefully.

1) Model quality and applications of models
Generally, protein structure models can support the design of experiments and may help explaining experimental observations but have only limited predictive value. The quality of a model determines its suitability for a particular application ( see schematic representation below).

Applications of protein models have been extensively discussed in a recent workshop on "Applications of Protein Models in Biomedical Research" at the UCSF in July 2008. Examples of applications of computational models with a significant impact on various areas of life science research are described in the workshop White Paper (Schwede et al. 2009).

sources of error

Schematic representation of possible sources of errors in modeling and important areas of applications of theoretical protein structure models.

Knowledge of the expected accuracy of a protein structure model is of crucial importance for a biologist intending to use the model. The importance of quality estimation in modeling has been underlined in the literature (Hooft et al. 1996, Martí-Renom et al. 2000, Fischer 2006, Kryshtafovych&Fidelis 2008, Cozzetto et al. 2007+2009, Bordoli et al. 2009, Schwede et al.2009). There are basically two sources of information supporting the estimation of the accuracy of homology models.

The first source is the availability of structural knowledge which is primarily determined by the evolutionary distance between the query protein and template proteins of known structure. This is based on the observation that there is a direct correlation between sequence identity of a pair of proteins and the structural similarity of their common core (Chothia&Lesk 1986, Rost 1999). Section 2 describes in detail several 'determinants of model accuracy' given the structural information of known templates.

The second source of information comes from the analysis of the geometry of the model. Especially when the sequence identity is low, individual models may vary considerably from the expect average quality due to various sources of errors in modeling (see scheme above) and inaccuracies introduced by the modeling programs. It is therefore necessary to independently check the geometric plausibility and the 'energy' of the model. For this purpose scoring (or energy) functions have been developed which are discribed in the last section including a short description of the quality estimation server integrated in PMP.

2) Determinants of model accuracy
a) Sequence identity between target and template of known structure

The sequence identity between the target protein and template of known structure is commonly seen as a first indicator for the expected accuracy of a model, as confirmed by various studies (Chothia&Lesk 1986, Rost 1999, Baker&Sali 2001, Koh et al. 2003).

Based on the sequence identity to the template we assign a model to one of three categories of modeling complexity (see traffic light symbol). The classification roughly agrees with the one introduced by Rost (Rost 1999) who defines three zones of sequence similarity: midnight zone (zone A, red), twilight zone (zone B, yellow), safe zone (zone C, green). A rough description of the three zones is given below followed by a more detailed explanation of possible next steps.

The coloring roughly also corresponds to the one chosen in the schematic representation above which allows to relate modeling difficulty to different area of applications in life science research.

seq id vs rmsd

Schematic representation of the 3 zones of sequence/structure similarity. Within PMP, the location of the query model is represented by a red vertical line assigning it to a of the three categories described below.

A: In models based on a target-template sequence alignment lower than 30% sequence identity frequently substantial alignment errors and suboptimal template selection are observed (Rost 1999, Martí-Renom et al. 2000). Careful validation of these models quality is strongly advised.

B: In models based on a target-template sequence alignment between 30% and 50% sequence identity alignment errors in non-conserved segments of the target protein, structural variation in templates, and incorrect reconstruction of loops (insertions and deletions) are frequent sources of model inaccuracies (Martí-Renom et al. 2000, Fiser et al. 2000). Careful validation of the model quality and variability among template structures is advised.

C: Models based on a target-template sequence alignment higher than 50% sequence identity typically have the correct fold and the alignments tends to be mainly correct. Structural variation in templates, and incorrect reconstruction of loops (insertions and deletions) are the main sources of model inaccuracies (Fiser et al. 2000, Zhang 2009). Validation of the model quality and analysis of the variability among template structures is advised.

b) Actuality of template selection
The Protein Model Portal provides access to several modeling repositories. These repositories contain models based on the best available template at the time of model building. It should be therefore always checked whether a newer template with a considerably higher sequence identity with respect to the query protein has become available in the PDB. The model creation date as well as the date of the latest verification of the template selection actuality ('Template verification') are provided in the model detail section. Outdated models older than 3 months are clearly highlighted allowing for straightforward identification of models potentially based on lower quality templates. The sequence of the query protein can be sent to several modeling servers by selecting under 'modeling services' in the PMP navigation menu.

Example: Before the release of the experimental structures of the β1 and the β2 adrenergic receptors as well as the A2A adenosine receptor (2007-2008), GPCR models were built based on the Rhodopsin structure (and earlier on Bacteriorhodopsin) which differs significantly. Old templates based on Rhodopsin should therefore not be used anymore. The use of the best available template structure has a direct effect on the outcome of subsequent experiments based on the model such as for example structure-based drug design (i.e. ligand docking and virtual screening).

c) Variability among available templates
In homology modeling, often several evolutionarily related proteins with known experimental structure are detected for a given query protein of interest. Depending on the protein family these templates may be structurally quite similar or vary considerably. Usually, some regions in the core of the templates agree more (the 'structural core') and some parts, mainly protein surface loops, are less similar (the 'structurally variable regions'). The structural core, which also tends to be also more conserved in sequence, serves a template for structural extrapolation. These parts of the model which are directly inherited from the template(s) are generally more accurate compared to the remaining regions which need to be predicted from scratch.

Structural variations among templates can have several regions such as differences in experimental conditions, presence or absence of ligands/co-factors but also evolutionary reasons. The variations may be characteristic for the family and a sign for flexibility or disorder. There are many examples of proteins which largely disordered and whose function can only be explained by taking into account the non-existence of a well-defined three-dimensional structure (see e.g. Dunker et al. 2002, Pentony et al. 2010).


Example: Adenylate kinases catalyze the interconversion of adenine nucleotides. They undergo large conformational changes from the open form (PDB id 4ake, depicted in grey) to the enzymatically-active closed conformation in presence of the ligand (1ake, structure colored according to the local deviation to the open form). In homology modeling, template selection in this case would have a strong effect on the explanatory value of the resulting model and its applicability for subsequent experiment.

3) Validation of protein models
In this section, a guide to a stepwise analysis of a protein model is provided, in order to have a first guess about its quality and as a consequence its suitability for specific experiments.
How can we predict the quality of a model without knowing the correct answer?
a) By analysing the template situation:
Is the model based on the best available template?

  • check up-to-dateness of template selection -> 'verification date'
  • sequence identity correlates with modeling difficulty
  • check the resolution of the experimental structure
  • check the experimental conditions and the environment (e.g. solved with or w/o ligand)?

The analysis of variability among templates:

  • regions not differing between various templates (i.e. the structural core) can be inherited directly and are therefore modelled potentially more accurately than structurally variable regions (e.g. surface loops)
  • Where is the structural variability located?
  • Are flexible loops part of the active site?
  • Are there shift/distortions in the core of the protein (e.g. among secondary structure elements)? This would indicate a difficult modeling case with lower expected model accuracy
  • Variation may be sign of flexibility in the protein family or there may be even disordered regions (i.e. regions not resolved in many templates) This flexibility may be needed for protein function (use of disorder prediction tools may help in this situation, see Pentony et al. 2010)

b) By analysing the model ensemble:
The variability among the models of a given protein predicted by different programs/servers may be to a large extend explained by the variation in the templates but the model ensemble also contains additional information:

  • A strong consensus among models of various servers is a good sign for the correctness of a model since the probability that many modeling resources predict the same feature all wrong is much lower than doing it all right.
  • On the query result page of PMP, the structure comparison tool can be used to compare any subset of models and analyse the variability among them. See also section [ Structure Comparison ] described below.

Structure comparison
c) By employing scoring functions to analyse the geometry of protein structures

Scientific background:
Errors in models tend to increase with decreasing sequence identity to available templates (see see schematic representation above), at the same time inaccuracies introduced by the modeling programs increase as well, which make it necessary to independently check the geometry (or 'energy') of the models. Several methods and scoring functions have been described in the literature analysing different aspects of proteins and investigating both the global quality of the entire model as well as local aspects.

In the early 1990's tools analysing the stereo-chemical plausibility of a protein structures came up (Laskowski et al. 1993, Hooft et al. 1996). Deviations from ideal stereo-chemical values are reported by programs such as ProCheck and WhatCheck which are still widely used especially in the field of experimental structure determination. But they can also help identifying 'suspicious geometries' in models.

Another category of methods investigates the compatibility of individual amino acids or the entire sequence (i.e. threading) with the structural environment described by the model (Luthy et al. 1992, Jones et al. 1992).

The most extensively used methods for assessing protein models are scoring functions based on statistical potentials or potentials of mean force (PMF's) (Sippl 1990). Statistical potentials are usually formalised as distance-dependent non-bonded interaction potentials (Melo&Feytmans 1998, Samudrala&Moult 1998, Zhou&Zhou 2002, Shen&Sali 2006) but also other structural features are are used such as torsion angles, contacts, residue burialness, hydrogen bonds, etc. Combining different geometrical features in a composite scoring function has been shown to further improve the performance of these methods in identifying good models (Wallner&Elofsson 2003, Pettitt et al. 2005, Tosatto 2005, Benkert et al. 2008, McGuffin 2008, Randall&Baldi 2008).

Stepwise analysis:

  • The analyse of the geometric plausibility of a model helps identifying unusual geometries as a result of modeling errors or inaccuracies of the modeling program.
  • If the target-template sequence identity is very low, models may have even have the wrong fold:
    • There are a few methods available which allow to estimate whether a structure has the correct fold by delivering a Z-score or expectation value relating the model energy to a random (or other) background distribution
  • If multiple models with alternative conformations are available a ranking of the model ensemble using a scoring function analysing different geometrical aspects of protein structures may help identifying more reliable candidates.
    • In PMP, each single model can be sent to several model quality estimation servers covering several scoring functions (see below)
    • The possibility to send multiple models from the PMP overview page will be provided soon
  • For the analysis of the quality of a single model local scoring functions can be used in order to try to locate regions potentially deviating stronger. The local estimation of model quality is still an active field of research.

Scoring functions available in PMP:
From the model detail page in PMP, a model can be sent to several scoring function for model quality estimation. Currently, the following four state-of-the-art model quality estimation servers are accessible. The model coordinates are sent to the server and the user receives the answer by e-mail.

model quality application
ModFOLD (McGuffin & Roche 2010) ( is a Model Quality Assessment Program (MQAP) used for the global and local assessment of models. The original ModFOLD method is a combination of the ModSSEA method (McGuffin, 2007), MODCHECK (Pettitt et al., 2005) and two scores provided by ProQ (Wallner and Elofsson, 2003). The scores are combined using a neural network.

QMEAN server
QMEAN (Benkert et al. 2008) is a composite scoring function for the quality estimation of protein structure models. QMEAN consists of six structural descriptors. Four of them are statistical potentials analyzing torsion angles, solvation and non-bonded interactions. The other two terms reflect the agreement between predicted and calculated secondary structure and solvent accessibility.

ModEval evaluates various aspects of model quality and reports quality scores such as predicted RMSD and native overlap, along with the atomic distance-dependent statistical potential DOPE (Discrete Optimized Protein Energy). DOPE is based on an improved reference state, accounting for the finite and spherical shape of the native structures. Further it reports a score based on statistical potentials (GA341) assessing the reliability of a model.

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Structure Comparison

The variability among the models (the term 'model' here applies to both homology models and experimental structures) of a given protein predicted by different programs/servers may be to a large extend explained by the variation in the templates but the model ensemble also contains additional information. A strong consensus among models of various servers, e.g., is a good sign for the correctness of a model since the probability that many modeling resources predict the same feature all wrong is much lower than doing it all right. In the model overview page of PMP, the structure comparison tool can be used to compare any subset of models and analyse the variability among the them

Analysis of structural variability

Experimental structures for a given protein may show substantial structural variability due to domain motions, mobile loops, different functional states, or induced fit upon ligand binding. The analysis of the ensemble of models is an effective way of distinguishing structurally conserved regions in a protein family from more variable regions. Besides these native effects additional variability is added in the case of theoretical models by differences in algorithmic approaches, the choice of template(s) and modeling errors. Regions with large variability within an ensemble of theoretical models often reflect segments which cannot be predicted with high confidence, e.g. due to the variation in alternative template structures, flexible loop regions, or unaligned regions (indels) in the target-template alignment (3). For these reasons, PMP provides an interface to analyze the variability within an ensemble of experimental structures and models for a protein which is built based on the computational structural biology framework OpenStructure(4). (Please note, that the range information about experimental structures is based on SEQRES, which may differ from the actual sequence obtained from the crystal structure). In the results overview page of PMP, the structure comparison tool (panel I), can be used to compare an overlapping subset of structures and models. Local deviation plots indicate for each amino acid residue the divergence from the ensemble (panel II) for each model or structure. Alternative visualizations of the structural variability information include distance variance maps (panel III) or the visualization of structural superpositions using an interactive Jmol applet (2) (panel IV).

structure comparison

The structural variability analysis

Structural variability among a set of experimental structures and/or models is determined with a superposition-free -distance based approach.

First for each model m, where m=1,..,n, an all-against-all distance matrix Am is generated from the atoms. A column i in one of these matrices contains distances dm,ij of the atom i to all other atoms j where j=1,..,L for a protein of length L. Second, the standard deviation sij of the distances is calculated following formula (1) for each pair of atoms. In order to focus the analysis on local accuracy, the influence of long-range distances is weighted down. To achieve this, the Euclidean distance from the mean formula is weighted with an exponential term analogous to the Holm/Sander approach (1). The element sij is then stored in the matrix S, representing the variability within the selected set of models. A graph of S is shown on the "Structure Comparison Results" page of PMP (panel III). Regions in blue correspond to low, while regions in red represent high variability. The exponential weighting term has been parameterized in a set of single domain proteins such that 1.4 Å deviation in a structure based superposition is visually detectable in the graph.

formula (1)

To identify regions of high variability between individual models, the per-residue deviation is shown in a second plot. Here, the meanformula is calculated from each of the cells containing formula in column i and row j of each of the n matrices of type A. Subsequently for each model m the absolute difference formulabetween formula and the mean  formula are computed and averaged over the number of residues L of the model (formula (2), panel II).



1.         Holm, L., Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol, 233, 123-38.

2.         Jmol: an open-source Java viewer for chemical structures in 3D.

3.         Chivian, D., Baker, D. (2006) Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res, 34, e112.

4.         Biasini, M., Mariani, V., Haas, J., et al. (2010) OpenStructure: a flexible software framework for computational structural biology. Bioinformatics, 26, 2626-8.

Sequence Annotation

Annotation of the target model sequences is retrieved from UniProt using the REST interface (Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O Donovan C., Redaschi N., Yeh L.S. Nucleic Acids Res.(2005) 33, D154-159). PFAM Domain structure for the model target sequence is annotated using the InterPro Distributed Annotation System ( R.D. Finn, J. Mistry, B. Schuster-Böckler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, R. Durbin, S.R. Eddy, E.L.L. Sonnhammer and A. Bateman Nucleic Acids Research (2006) 34:D247-D251).

Model Preview Images & Visualization

The model preview images on the model info pages are generated dynamically using Molscript (Per J. Kraulis, Journal of Applied Crystallography (1991) 24,946-950.) and Raster3d (E.A. Merritt & M.E.P. Murphy, Acta. Cryst. (1994) D50,869-873.).

Interactive in-line visualization using Jmol (Jmol: an open-source Java viewer for chemical structures in 3D.)

PSI Partner Sites

Models and interactive tools made accessible by the Protein Model Portal are provided by the following partners:

  • CSMP - Center for Structures of Membrane Proteins
  • JCSG - Joint Center for Structural Genomics
  • MCSG - Midwest Center for Structural Genomics
  • NESG - Northeast Structural Genomics Consortium
  • NMHRCM - New Methods for High-Resolution Comparative Modeling
  • NYSGRC - New York Structural Genomics Research Consortium
  • JCMM - Joint Center for Molecular Modeling
  • ModBase and ModPipe - UCSF University of California, San Francisco
  • SWISS-MODEL - SIB Swiss Institute of Bioinformatics & Biozentrum University of Basel
  • GPCRDB - Information system for G protein-coupled receptors


PMP is developed by the Computational Structural Biology Group at the Swiss Institute of Bioinformatics (SIB) and the Biozentrum of the University of Basel.