ArticleNucleic acids research2013
MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- AlloBench: A Data Set Pipeline for the Development and Benchmarking of Allosteric Site Prediction Tools.ACS omega · 2025Article
- MD Multi-Sector Selector: Recursive Extraction and Refinement of Molecular Dynamics Based Sectors Yields Two Sectors in p53 Tumor Suppressor Protein.The journal of physical chemistry. B · 2025Article
- Allosteric Modulators of Dopamine DMolecules (Basel, Switzerland) · 2022Review
- ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules.Nucleic acids research · 2021Article
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures.International journal of molecular sciences · 2020Article
- PI3K inhibitors: review and new strategies.Chemical science · 2020Review
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Unraveling allosteric landscapes of allosterome with ASD.Nucleic acids research · 2020Article
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- Recent Insights from Molecular Dynamics Simulations for G Protein-Coupled Receptor Drug Discovery.International journal of molecular sciences · 2019Review
- AlloDriver: a method for the identification and analysis of cancer driver targets.Nucleic acids research · 2019Article
- Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.PLoS computational biology · 2019Review
- Seeking allosteric networks in PDZ domains.Protein engineering, design & selection : PEDS · 2018Review
- AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses.Nucleic acids research · 2018Article
- A novel allosteric site in casein kinase 2α discovered using combining bioinformatics and biochemistry methods.Acta pharmacologica Sinica · 2017Article
- Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.PLoS computational biology · 2017Article
- Prediction of allosteric sites and mediating interactions through bond-to-bond propensities.Nature communications · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.PLoS computational biology · 2016Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allosteric mechanism of proteins is essential in biomolecular signaling. An important aspect underlying this mechanism is the communication pathways connecting functional residues. Here, a Monte Carlo (MC) path generation approach is proposed and implemented to define likely allosteric pathways through generating an ensemble of maximum probability paths. The protein structure is considered as a network of amino acid residues, and inter-residue interactions are described by an atomistic potential function. PDZ domain structures are presented as case studies. The analysis for bovine rhodopsin and three myosin structures are also provided as supplementary case studies. The suggested pathways and the residues constituting the pathways are maximally probable and mostly agree with the previous studies. Overall, it is demonstrated that the communication pathways could be multiple and intrinsically disposed, and the MC path generation approach provides an effective tool for the prediction of key residues that mediate the allosteric communication in an ensemble of pathways and functionally plausible residues. The MCPath server is available at http://safir.prc.boun.edu.tr/clbet_server.
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