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A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.Abstract:
We present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactionsread more
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Comparison of three ionic liquid-tolerant cellulases by molecular dynamics.
TL;DR: Molecular dynamics allows us to predict specific atomic-level structural and dynamical changes in an enzyme's behavior induced by ionic liquids and other mixed solvents, and proposes specific experimentally testable hypotheses regarding the origin of activity loss.
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Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
TL;DR: The rigorous methodology formulated by Lifson, and later Allinger to derive molecular FFs, not only obtain optimal parameters but also uncover deficiencies in the representation of the physics and improve the functional form to account for this physics.
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Withanone binds to mortalin and abrogates mortalin-p53 complex: computational and experimental evidence.
Abhinav Grover,Didik Priyandoko,Ran Gao,Ashutosh Shandilya,Nashi Widodo,Virendra S. Bisaria,Sunil C. Kaul,Renu Wadhwa,Durai Sundar +8 more
TL;DR: A molecular interaction basis that could be used for screening and development of anticancer drugs with low toxicity to normal cells is established and accurate knowledge of the 3D structure of mortalin would further enhance the potential of such analyses to understand the molecular basis ofmortalin biology and mortalin based cancer therapy.
Journal ArticleDOI
Target flexibility in molecular recognition
TL;DR: Some recent progress in methods for including target flexibility in computational studies of molecular recognition are outlined, including the "relaxed complex method," in which ligands are docked to an ensemble of conformations of the target, and the best complexes are re-scored to provide predictions of optimal binding geometries.
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate.
TL;DR: Results suggest that dissociation of gelsolin from actin by PIP2 lipids may involve entering of the PIP1 molecules to the gelsol–actin interface, thereby weakening the interactions between these proteins.
References
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The MIDAS display system
TL;DR: At the core of MIDAS is a hierarchical database system, designed specifically for macromolecules, that is both compact in its storage requirements and fast in its data access.