article Closed Access EN 2016-10-12

Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP‐11 structural models

Marwa El Houasli, Bernard Maigret, Marie‐Dominique Devignes, Anisah W. Ghoorah, Sergei Grudinin, David W. Ritchie

Proteins Structure Function and Bioinformatics, Vol. 85, Issue 3, pp. 463–469 (2016)

Institut national de recherche en sciences et technologies du numérique, CAPSID: Computational Algorithms for Protein Structures and Interactions, University of Mauritius, Institut polytechnique de Grenoble, Centre National de la Recherche Scientifique, Centre Inria de l'Université Grenoble Alpes, Laboratoire Jean Kuntzmann

DOI: 10.1002/prot.25182 PMID: 27701764

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Abstract

Many of the modeling targets in the blind CASP-11/CAPRI-30 experiment were protein homo-dimers and homo-tetramers. Here, we perform a retrospective docking-based analysis of the perfectly symmetrical CAPRI Round 30 targets whose crystal structures have been published. Starting from the CASP "stage-2" fold prediction models, we show that using our recently developed "SAM" polar Fourier symmetry docking algorithm combined with NAMD energy minimization often gives acceptable or better 3D models of the target complexes. We also use SAM to analyze the overall quality of all CASP structural models for the selected targets from a docking-based perspective. We demonstrate that docking only CASP "center" structures for the selected targets provides a fruitful and economical docking strategy. Furthermore, our results show that many of the CASP models are dockable in the sense that they can lead to acceptable or better models of symmetrical complexes. Even though SAM is very fast, using docking and NAMD energy minimization to pull out acceptable docking models from a large ensemble of docked CASP models is computationally expensive. Nonetheless, thanks to our SAM docking algorithm, we expect that applying our docking protocol on a modern computer cluster will give us the ability to routinely model 3D structures of symmetrical protein complexes from CASP-quality models. Proteins 2017; 85:463-469. © 2016 Wiley Periodicals, Inc.

Topics

Protein Structure and Dynamics 1.00 Enzyme Structure and Function 1.00 Computational Drug Discovery Methods 1.00

Field: Biochemistry, Genetics and Molecular Biology · Subfield: Molecular Biology

Keywords

CASP,Docking (animal),Protein–ligand docking,Protein structure prediction,Searching the conformational space for docking,Computer science,Energy minimization,Macromolecular docking,Computational biology,Protein structure

MeSH Terms

AlgorithmsAlgorithmsAlgorithmsBinding SitesBinding SitesBinding SitesProtein BindingProtein Binding

UN Sustainable Development Goals

Affordable and clean energy (0.88)

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