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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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TLDR
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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What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations
TL;DR: By examining seven ligands interacting with five proteins, a linear correlation between the value of β and the weighted non‐polar desolvation ratio (WNDR) is discovered, and the ability of this correlation to predict optimal values of β for different ligands binding to a single protein is examined.
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On the Mechanism of ATP Hydrolysis in F1-ATPase
TL;DR: The simulations suggest that the reaction path with the lowest potential energy barrier proceeds via nucleophilic attack on the gamma-phosphate involving two water molecules, and the ATP hydrolysis reaction in beta(TP) is found to be endothermic, demonstrating that the catalytic site is able to support the synthesis of ATP and does not promote ATP Hydrolysis in the particular conformation studied.
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Protective hinge in insulin opens to enable its receptor engagement.
John G. Menting,Yanwu Yang,Shu Jin Chan,Nelson B. Phillips,Brian J. Smith,Jonathan Whittaker,Nalinda P. Wickramasinghe,Linda Whittaker,Vijay Pandyarajan,Zhu Li Wan,Satya P. Yadav,Julie M. Carroll,Natalie Strokes,Charles T. Roberts,Charles T. Roberts,Faramarz Ismail-Beigi,Wieslawa Milewski,Donald F. Steiner,Virander S. Chauhan,Colin W. Ward,Michael A. Weiss,Michael C. Lawrence,Michael C. Lawrence +22 more
TL;DR: A conformational switch that enables otherwise hidden nonpolar surfaces in the hormone to engage its receptor is described, envisaging that a switch between free and receptor-bound conformations of insulin evolved as a solution to conflicting structural determinants of biosynthesis and function.
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Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations.
Luca Mollica,Sergio Decherchi,Syeda Rehana Zia,Roberto Gaspari,Andrea Cavalli,Walter Rocchia +5 more
TL;DR: A simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time, and was validated against experimental information available on biological systems of pharmacological relevance.
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Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry
TL;DR: A multiscale quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation model for photoactive molecules that are strongly coupled to confined light in optical cavities or surface plasmons is presented and it is anticipated that this method will lead to a better understanding of the effects of strong coupling on chemical reactivity.
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.