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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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The application of three approximate free energy calculations methods to structure based ligand design: trypsin and its complex with inhibitors.
TL;DR: Three approximate free energy calculation methods are examined and applied to an example ligand design problem, indicating that they might be useful for suggesting how ligands could be modified to improve binding and, consequently, useful in structure-based drug design.
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Molecular dynamics simulation of a model oligomer for poly(N-isopropylamide) in water
TL;DR: In this article, the authors used molecular dynamics to simulate a dilute aqueous solution of a 50-units oligomer model for the thermoresponsive polymer poly(N-isopropylacrylamide) at 300 and 310 K, i.e., below and above its lower critical solution temperature (LCST) in water.
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Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.
TL;DR: Estimating affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum Lie, and Glide score methods, finds that the success of the methods is system-dependent.
Journal ArticleDOI
Molecular dynamics at the root of expansion of function in the M69L inhibitor-resistant tem β-lactamase from Escherichia coli
Samy O. Meroueh,Pierre Roblin,Dasantila Golemi,Laurent Maveyraud,Sergei B. Vakulenko,Yun Zhang,Jean-Pierre Samama,Shahriar Mobashery +7 more
TL;DR: It would appear that nature has selected for incorporation of the most benign alteration in the structure of the wild-type TEM-1 beta-lactamase that is sufficient to give the inhibitor-resistant trait.
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Origins of Water Molecules in the Photosystem II Crystal Structure
TL;DR: The accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics simulations, providing key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.
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.