ArticleNucleic acids research2013
MoMA-LigPath: a web server to simulate protein-ligand unbinding.
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 17 papers.
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Who cites it
17 citing papers in PubMed.
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.Journal of cheminformatics · 2024Article
- pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support.Bioinformatics (Oxford, England) · 2023Article
- Variability in the Responses of Hepatitis B Virus D-Subgenotypes to Antiviral Therapy: Designing Pan-D-Subgenotypic Reverse Transcriptase Inhibitors.Journal of virology · 2022Article
- Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web.Computational and structural biotechnology journal · 2022Article
- Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace.Briefings in bioinformatics · 2021Review
- A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction.Journal of chemical information and modeling · 2020Article
- The Relevance of Glutathione Reductase Inhibition by Fluoxetine to Human Health and Disease: Insights Derived from a Combined Kinetic and Docking Study.The protein journal · 2019Article
- ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.Journal of computer-aided molecular design · 2019Article
- GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm.International journal of molecular sciences · 2019Article
- Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock.Frontiers in chemistry · 2019Article
- Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.International journal of computational biology and drug design · 2018Article
- Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis.Scientific reports · 2017Article
- Interactive exploration of ligand transportation through protein tunnels.BMC bioinformatics · 2017Article
- Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.Frontiers in molecular biosciences · 2017Article
- Article
- Computational insights into the inhibitory mechanism of human AKT1 by an orally active inhibitor, MK-2206.PloS one · 2014Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Protein-ligand interactions taking place far away from the active site, during ligand binding or release, may determine molecular specificity and activity. However, obtaining information about these interactions with experimental or computational methods remains difficult. The computational tool presented in this article, MoMA-LigPath, is based on a mechanistic representation of the molecular system, considering partial flexibility, and on the application of a robotics-inspired algorithm to explore the conformational space. Such a purely geometric approach, together with the efficiency of the exploration algorithm, enables the simulation of ligand unbinding within short computing time. Ligand unbinding pathways generated by MoMA-LigPath are a first approximation that can provide useful information about protein-ligand interactions. When needed, this approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. MoMA-LigPath is available at http://moma.laas.fr. The web server is free and open to all users, with no login requirement.
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