The Protein Model Portal

By Konstantin Arnold, Florian Kiefer, Jürgen Kopp, J. Battey, Michael Podvinec, John D. Westbrook, Helen M. Berman, Lorenza Bordoli, Torsten Schwede. 2008

136 citations recorded by the source corpus.

Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Critical assessment of methods of protein structure prediction (CASP) — round x (2013, methodology): “…has been the emergence of robust on-line6 and off-line7–9 user-friendly modeling software packages, and the provision of databases of models.10 –12 The accuracy of homology models, as monitored by CASP, has improved dramatically, through a combination of improved methods, larger databases…”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, unknown): “Finally to estimate the quality of the obtained models, PMP provides an interface to submit models in parallel to several model quality estimation tools, e.g. ModEval (43), ModFold (58), and QMEAN (41, 51).”
The Protein Structure Initiative: achievements and visions for the future (2012, methodology): “The PSI-SBKB also provides access to 3D protein models generated using various comparative modeling methods [14], together with coordinates of structures solved by the PSI program.”
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences (2015, methodology): “The server recently become a partner site of the protein model portal (30) for interactive 3D modelling and is continuously benchmarked by CAMEO (http://www.”
Comparative Protein Structure Modeling Using Modeller (2006, methodology): “It is also accessible from the Protein Model Portal ( http://proteinmodelportal.org ; Arnold et al., 2009; Haas et al., 2013) and is crosslinked to many other databases, such as UniProt.”
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, unknown): “The structural model of α-globin gene domain was determined based on Chromosome Conformation Capture Carbon Copy (5C) experiments (Bau et al., 2011).”
Protein Modelling: What Happened to the “Protein Structure Gap”? (2013, unknown): “…1 Commonly used tools and services for protein structure modeling and prediction Protein Model Portal http://www.proteinmodelportal.org (Arnold et al., 2009; Haas et al., 2013) Model Archive http://modelarchive.org HHpred http://toolkit.tuebingen.mpg.de/hhpred (Hildebrand et al.,…”
Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “It is also accessible from the Protein Model Portal (http://proteinmodelportal.org; Arnold et al., 2009; Haas et al., 2013) and is cross-linked to many other databases, such as UniProt.”
The ModFOLD4 server for the quality assessment of 3D protein models (2013, background): “The server is also a partner site of the protein model portal (26) (http://www.”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, methodology): “ModBase models are also available through the Protein Model Portal (http://www.prote inmodelportal.org/).”
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive (2017, methodology): “The Protein Modeling Portal was established in 2007 [26].”
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era (2013, methodology): “We constructed a dataset of 329 protein targets selected from the Continuous, Automated Model Evaluation (CAMEO) server (7) (Dataset S1, details in Materials).”