The Protein Model Portal—a comprehensive resource for protein structure and model information

Juergen Haas,Steven Roth,Konstantin Arnold,Florian Kiefer,Lorenza Bordoli,Torsten Schwede,Tobias Schmidt

doi:10.1093/database/bat031

Abstract

The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology.Database URL: http://www.proteinmodelportal.org

Highlights

Three-dimensional protein structures are crucial for developing a detailed understanding of the many functions of proteins occurring in nature
From the main Protein Model Portal (PMP) entry site, it is possible to search for experimental structures or theoretical models for a target protein, using amino acid sequence, free text (e.g. ‘oxygen sensor protein’) or biological database accession codes (e.g. UniProt, RefSeq, PDB, . . .) in the same query box without the need for the user to specify the input format
The PMP displays the structural coverage available for a given protein in a summary page (Figure 2)

Summary

Introduction

Three-dimensional protein structures are crucial for developing a detailed understanding of the many functions of proteins occurring in nature. Structural genomics efforts [1,2,3] have contributed to the field by establishing high-throughput structure determination approaches and determining the structures of many unique proteins Despite these achievements, the number of protein sequences in current databases remains orders of magnitude larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods are currently the most accurate approaches (especially for larger proteins and protein complexes) for obtaining all-atom models of proteins [4,5,6] and bridging this knowledge gap These methods make use of experimental protein structures (‘templates’) to build models for evolutionarily related proteins (‘targets’). Experimental structural biology and homology modeling thereby complement each other in the exploration of the protein structure space and as a result structural coverage to a large extent is available for the proteomes of many model organisms such as Escherichia coli [7] or Thermotoga maritima [8]

Methods

Results

Conclusion