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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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A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen‐like peptides
TL;DR: The authors' molecular dynamics simulations of proline and hydroxyproline monomers as well as collagen‐like peptides, using the new parameters, support the theory that the role of hydroxylation in collagen is to stabilize the triple helix by adjusting to the right pucker conformation in the Y position.
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Assessing Ion–Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations
TL;DR: The DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.
Journal ArticleDOI
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB.
Donghyuk Shin,Donghyuk Shin,Rukmini Mukherjee,Yaobin Liu,Alexis Gonzalez,Florian Bonn,Yan Liu,Vladimir V. Rogov,Marcel Heinz,Marcel Heinz,Alexandra Stolz,Gerhard Hummer,Gerhard Hummer,Volker Dötsch,Zhao-Qing Luo,Sagar Bhogaraju,Ivan Dikic,Ivan Dikic +17 more
TL;DR: The deubiquitinases for PR ubiquitination (DUPs; DupA and DupB) were identified in Legionella pneumophila infection as mentioned in this paper, and they were used to identify host proteins involved in endoplasmic reticulum fragmentation and membrane recruitment to Legionella-containing vacuoles.
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A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP2
TL;DR: A force field is designed for the PIP(2) headgroup using quantum mechanical methods and its properties inside a lipid bilayer are characterized using molecular dynamics simulations, finding that area/headgroup, density profiles, and lipid order parameters calculated from these simulations agree well with the experimental values.
Journal ArticleDOI
Crystal structure of amine oxidase from bovine serum.
Michele Lunelli,Maria Luisa Di Paolo,Marianna Biadene,Vito Calderone,Roberto Battistutta,Marina Scarpa,Adelio Rigo,Giuseppe Zanotti +7 more
TL;DR: The comparison of the BSAO structure with those of other resolved AO structures shows strong dissimilarities in the architecture and charge distribution of the cavities leading to the active-site, possibly explaining the differences in substrate specificity.
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.