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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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Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.
Marola M. H. Van Lipzig,Antonius Ter Laak,Aldo Jongejan,Nico P. E. Vermeulen,Mirjam M.C. Wamelink,Daan P. Geerke,John H. N. Meerman +6 more
TL;DR: A computational model was developed for prediction of binding affinities of ligands to the ERalpha isoform, using MD simulations in combination with the linear interaction energy (LIE) approach, and it provides a very good method for Prediction of absolute ligand binding Affinities.
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Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances
Christine Cézard,Xavier Trivelli,Xavier Trivelli,Frédéric Aubry,Florence Djedaïni-Pilard,François-Yves Dupradeau +5 more
TL;DR: A homogeneous force field, namely "q4md-CD", has been built from the development of a new force field topology database and from a combination of the GLYCAM04 and Amber99SB force fields to correctly describe the geometrical, structural, dynamical and hydrogen bonding aspects of heterogeneous cyclodextrin based systems.
Journal ArticleDOI
Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations.
TL;DR: The results suggest a possible molecular mechanism for the early steps of intramolecular signal transduction in a prototypical G-protein-coupled receptor.
Journal ArticleDOI
Electrostatic complementarity in an aldose reductase complex from ultra-high-resolution crystallography and first-principles calculations
TL;DR: The charge density refinement of the protein was performed with the program mopro by using the transferability principle and the database of charge density parameters built from crystallographic analyses of peptides and amino acids, and the potentials obtained directly from the database are in excellent agreement with the experimental ones.
Journal ArticleDOI
The human DNA repair factor XPC‐HR23B distinguishes stereoisomeric benzo[ a ]pyrenyl‐DNA lesions
Vincent Mocquet,Konstantin Kropachev,Marina Kolbanovskiy,Alexander Kolbanovskiy,Angels Tapias,Yuqin Cai,Suse Broyde,Nicholas E. Geacintov,Jean-Marc Egly +8 more
TL;DR: The different extents of helix distortions, as well as differences in the overall binding of XPC/HR23B to double‐stranded DNA containing either of the three stereoisomeric B[a]P‐N2‐dG lesions, are correlated with dual incisions catalyzed by a reconstituted incision system of six purified NER factors, and by the full NER apparatus in cell‐free nuclear extracts.
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.