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• W3186109768 endingPage "3751" @default.
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• W3186109768 abstract "A protein performs its task by binding a variety of ligands in its local region that is also known as the ligand-binding-site (LBS). Therefore, accurate prediction, characterization, and refinement of LBS can facilitate protein functional annotations and structure-based drug design. In this work, we present CHARMM-GUI LBS Finder& Refiner (https://www.charmm-gui.org/input/lbsfinder) that predicts potential LBS, offers interactive features for local LBS structure analysis, and prepares various molecular dynamics (MD) systems and inputs by setting up distance restraint potentials for LBS structure refinement. LBS Finder& Refiner supports 5 different commonly used simulation programs, such as NAMD, AMBER, GROMACS, GENESIS, and OpenMM, for LBS structure refinement together with hydrogen mass repartitioning. The capability of LBS Finder& Refiner is illustrated through LBS structure predictions and refinements of 48 modeled and 20 apo benchmark target proteins. Overall, successful LBS structure predictions and refinements are seen in our benchmark tests. We hope that LBS Finder& Refiner is useful to predict, characterize, and refine potential LBS on any given protein of interest." @default.
• W3186109768 created "2021-08-02" @default.
• W3186109768 creator A5030884127 @default.
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• W3186109768 creator A5091902232 @default.
• W3186109768 date "2021-07-23" @default.
• W3186109768 modified "2023-09-29" @default.
• W3186109768 title "CHARMM-GUI <i>LBS Finder & Refiner</i> for Ligand Binding Site Prediction and Refinement" @default.
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• W3186109768 doi "https://doi.org/10.1021/acs.jcim.1c00561" @default.
• W3186109768 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8384712" @default.
• W3186109768 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34296608" @default.
• W3186109768 hasPublicationYear "2021" @default.
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