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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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Computer Modeling of Halogen Bonds and Other $\sigma$-Hole Interactions
Michal Kolář,Pavel Hobza +1 more
TL;DR: In this article, the authors summarize advances from about the last 10 years in understanding those interactions related to the π-hole, and pay particular attention to theoretical and computational techniques, which play a crucial role in the field.
Journal ArticleDOI
Overcoming mutation-based resistance to antiandrogens with rational drug design
Minna D. Balbas,Michael J. Evans,David J. Hosfield,John Wongvipat,Vivek K. Arora,Philip A. Watson,Yu Chen,Geoffrey L. Greene,Yang Shen,Charles L. Sawyers +9 more
TL;DR: A reporter-based mutagenesis screen and molecular dynamics simulations suggested a mechanism by which the F876L substitution alleviates antagonism through repositioning of the coactivator recruiting helix 12, which provided the rationale for a focused chemical screen which identified three novel compounds that effectively antagonized AR F 876L to suppress the growth of prostate cancer cells resistant to enzalutamide.
Journal ArticleDOI
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
TL;DR: In this article, a methodology to derive RESP charges for molecular mechanical models that include "lone pairs" on lone-pair donor sites and atom-centered polarizabilities was developed.
Journal ArticleDOI
MCPB.py: A Python Based Metal Center Parameter Builder
Pengfei Li,Kenneth M. Merz +1 more
TL;DR: MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach with an optimized code structure, with far fewer required steps.
Journal ArticleDOI
Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF)
TL;DR: MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model into the AMBER Force Field (FF), was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs.
References
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Journal ArticleDOI
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.