ArticleStructure (London, England : 1993)2017
Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints.
Article in Structure (London, England : 1993), 2017. 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.
- Structural stability of Calmodulin-target peptide complex at different temperatures based on molecular dynamics simulation.BMC chemistry · 2025Article
- Targeting TUBG1 in RB1-negative tumors.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Protein Multiple Conformation Prediction Using Multi-Objective Evolution Algorithm.Interdisciplinary sciences, computational life sciences · 2024Article
- Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators.Communications chemistry · 2023Article
- Julia for biologists.Nature methods · 2023Review
- Machine learning and protein allostery.Trends in biochemical sciences · 2023Review
- DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.Bioinformatics (Oxford, England) · 2022Article
- The Impact of the Secondary Binding Pocket on the Pharmacology of Class A GPCRs.Frontiers in pharmacology · 2022Review
- Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors.International journal of molecular sciences · 2020Article
- Unraveling allosteric landscapes of allosterome with ASD.Nucleic acids research · 2020Article
- Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.Journal of medicinal chemistry · 2019Review
- Analysis of tractable allosteric sites in G protein-coupled receptors.Scientific reports · 2019Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- On identifying collective displacements in apo-proteins that reveal eventual binding pathways.PLoS computational biology · 2019Article
- Efficient flexible backbone protein-protein docking for challenging targets.Bioinformatics (Oxford, England) · 2018Article
- AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses.Nucleic acids research · 2018Article
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3 authors.
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Abstract
The related concepts of protein dynamics, conformational ensembles and allostery are often difficult to study with molecular dynamics (MD) due to the timescales involved. We present ExProSE (Exploration of Protein Structural Ensembles), a distance geometry-based method that generates an ensemble of protein structures from two input structures. ExProSE provides a unified framework for the exploration of protein structure and dynamics in a fast and accessible way. Using a dataset of apo/holo pairs it is shown that existing coarse-grained methods often cannot span large conformational changes. For T4-lysozyme, ExProSE is able to generate ensembles that are more native-like than tCONCOORD and NMSim, and comparable with targeted MD. By adding additional constraints representing potential modulators, ExProSE can predict allosteric sites. ExProSE ranks an allosteric pocket first or second for 27 out of 58 allosteric proteins, which is similar and complementary to existing methods. The ExProSE source code is freely available.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.