Jokent Gaza, Emiliano Brini, Justin L MacCallum, Ken A Dill, Alberto Perez
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引用次数: 0
Abstract
We review MELD, an accelerator of Molecular Dynamics simulations of biomolecules. MELD (Modeling Employing Limited Data) integrates molecular dynamics (MD) with a variety of types of structural information through Bayesian inference, generating ensembles of protein and DNA structures having proper Boltzmann populations. MELD minimizes the computational sampling of irrelevant regions of phase space by applying energetic penalties to areas that conflict with the available data. MELD is effective in refining protein structures using NMR or cryo-EM data or predicting protein-ligand binding poses. As a plugin for OpenMM, MELD is interoperable with other enhanced sampling methods, offering a versatile tool for structural determination in computational chemistry and biophysics.
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The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field.
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