ArticleJournal of computer-aided molecular design2009
What induces pocket openings on protein surface patches involved in protein-protein interactions?
Article in Journal of computer-aided molecular design, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.Nucleic acids research · 2025Article
- Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology.International journal of molecular sciences · 2023Review
- Computational approaches for the design of modulators targeting protein-protein interactions.Expert opinion on drug discovery · 2023Review
- Article
- Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV.Journal of molecular structure · 2022Article
- An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors.Scientific reports · 2020Article
- Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach.Journal of computer-aided molecular design · 2020Article
- Docking-based identification of small-molecule binding sites at protein-protein interfaces.Computational and structural biotechnology journal · 2020Article
- Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis.ACS central science · 2017Article
- Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.The journal of physical chemistry letters · 2016Article
- Article
- Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles.Journal of chemical theory and computation · 2013Article
- Contributions of the RAD51 N-terminal domain to BRCA2-RAD51 interaction.Nucleic acids research · 2013Article
- New pockets in dengue virus 2 surface identified by molecular dynamics simulation.Journal of molecular modeling · 2013Article
- Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface.PLoS computational biology · 2013Article
- Article
- Pocket-based drug design: exploring pocket space.The AAPS journal · 2013Review
- Transient pockets on XIAP-BIR2: toward the characterization of putative binding sites of small-molecule XIAP inhibitors.Journal of molecular modeling · 2012Article
- Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.BMC bioinformatics · 2012Article
- Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.Journal of the Royal Society, Interface · 2012Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We previously showed for the proteins BCL-X(L), IL-2, and MDM2 that transient pockets at their protein-protein binding interfaces can be identified by applying the PASS algorithm to molecular dynamics (MD) snapshots. We now investigated which aspects of the natural conformational dynamics of proteins induce the formation of such pockets. The pocket detection protocol was applied to three different conformational ensembles for the same proteins that were extracted from MD simulations of the inhibitor bound crystal conformation in water and the free crystal/NMR structure in water and in methanol. Additional MD simulations studied the impact of backbone mobility. The more efficient CONCOORD or normal mode analysis (NMA) techniques gave significantly smaller pockets than MD simulations, whereas tCONCOORD generated pockets comparable to those observed in MD simulations for two of the three systems. Our findings emphasize the influence of solvent polarity and backbone rearrangements on the formation of pockets on protein surfaces and should be helpful in future generation of transient pockets as putative ligand binding sites at protein-protein interfaces.
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Registered trials
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