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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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Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity
TL;DR: It is established that distal mutations that affect enzyme catalytic activity can be predicted computationally and thus provides the enzyme (re)design field with a rational strategy to determine promising sites for enhancing activity through mutation.
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Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation
TL;DR: Modern simulations offer a range of molecular-level insights into ion channel function and modulation as a learning platform for mechanistic discovery and drug development.
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Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose
TL;DR: In this article, a new approach to calculate conformational equilibria in complex molecules, multiple-copy locally enhanced sampling (LES), was proposed and applied to the well-known α → β anomeric equilibrium in glucose.
Journal ArticleDOI
Birch PR-10c interacts with several biologically important ligands
Kaisa M. Koistinen,Pasi Soininen,Tuomas A. Venäläinen,Jukka Häyrinen,Reino Laatikainen,Mikael Peräkylä,Arja Tervahauta,Sirpa Kärenlampi +7 more
TL;DR: The present results suggest that birch PR-10c is a multifunctional protein, which has diverse roles in plant stress responses, and clear ligand specificity could be observed in the binding of nucleotide derivatives.
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.