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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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A toolkit to assist ONIOM calculations
Peng Tao,H. Bernhard Schlegel +1 more
TL;DR: This toolkit is designed to assist in the different stages of an ONIOM QM/MM study of biomolecules, including input file preparation and checking, job monitoring, production calculations, and results analysis.
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Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome.
Xiaoxia Ge,Benoît Roux +1 more
TL;DR: The interactions of the 50S subunit of bacterial ribosome with antibiotic sparsomycin andFive analogs and five analogs are investigated through the calculation of the standard (absolute) binding free energy and the characterization of conformational dynamics.
Journal ArticleDOI
Charge parameterization of the metal centers in cytochrome c oxidase.
TL;DR: A systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand, is presented, with a notable difference to previous procedures to include an outer region around the actual system of interest.
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The folding energy landscape and phosphorylation: modeling the conformational switch of the NFAT regulatory domain
TL;DR: The tertiary effects of phosphorylation caused by the extensive charge modification are more pronounced and collectively change the conformation of the regulatory domain of NFAT from a flexible globular ensemble to a rather rigid helical bundle, blocking access to the nuclear localization sequence.
Journal ArticleDOI
Molecular modeling and crystal structure of ERK2–hypothemycin complexes
TL;DR: The structure of ERK2-hypothemycin reversible and covalent complexes is modeled and the results were used to discuss structure-activity relationships, and provide a structural template for the development of irreversible inhibitors that complement the ATP binding site of kinases.
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.