ArticleProteins2012
Minimal ensembles of side chain conformers for modeling protein-protein interactions.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- Virtual screenings of the bioactive constituents of tea, prickly chaff, catechu, lemon, black pepper, and synthetic compounds with the main protease (Mpro) and human angiotensin-converting enzyme 2 (ACE 2) of SARS-CoV-2.Future journal of pharmaceutical sciences · 2021Article
- New additions to the ClusPro server motivated by CAPRI.Proteins · 2017Article
- Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.PloS one · 2017Article
- Pushing the Backbone in Protein-Protein Docking.Structure (London, England : 1993) · 2016Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.Nature protocols · 2015Article
- The impact of side-chain packing on protein docking refinement.Journal of chemical information and modeling · 2015Article
- Protein-protein docking: from interaction to interactome.Biophysical journal · 2014Review
- FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots.Bioinformatics (Oxford, England) · 2013Article
- Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface.Journal of the American Chemical Society · 2013Article
- Low-resolution structural modeling of protein interactome.Current opinion in structural biology · 2013Review
- A New Distributed Algorithm for Side-Chain Positioning in the Process of Protein DockingProceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control · 2013Article
- Correlation analysis of the side-chains conformational distribution in bound and unbound proteins.BMC bioinformatics · 2012Article
- Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding.Proteins · 2012Article
- Side-chain Packing Using SE(3)-Transformer.Pacific Symposium on Biocomputing. Pacific Symposium on BiocomputingArticle
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Authors and funding
7 authors.
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Abstract
The goal of this article is to reduce the complexity of the side chain search within docking problems. We apply six methods of generating side chain conformers to unbound protein structures and determine their ability of obtaining the bound conformation in small ensembles of conformers. Methods are evaluated in terms of the positions of side chain end groups. Results for 68 protein complexes yield two important observations. First, the end-group positions change less than 1 Å on association for over 60% of interface side chains. Thus, the unbound protein structure carries substantial information about the side chains in the bound state, and the inclusion of the unbound conformation into the ensemble of conformers is very beneficial. Second, considering each surface side chain separately in its protein environment, small ensembles of low-energy states include the bound conformation for a large fraction of side chains. In particular, the ensemble consisting of the unbound conformation and the two highest probability predicted conformers includes the bound conformer with an accuracy of 1 Å for 78% of interface side chains. As more than 60% of the interface side chains have only one conformer and many others only a few, these ensembles of low-energy states substantially reduce the complexity of side chain search in docking problems. This approach was already used for finding pockets in protein-protein interfaces that can bind small molecules to potentially disrupt protein-protein interactions. Side-chain search with the reduced search space will also be incorporated into protein docking algorithms.
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