Journal ArticleDOI
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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Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient
Junmei Wang,Tingjun Hou +1 more
TL;DR: It is concluded that the sampling strategy that averaging the mean square displacement collected in multiple short‐MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.
Journal ArticleDOI
QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.
Louis Vanduyfhuys,Steven Vandenbrande,Toon Verstraelen,Rochus Schmid,Michel Waroquier,Veronique Van Speybroeck +5 more
TL;DR: QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner and is used to determine force field parameters for MIL‐53(Al) and MOF‐5.
Journal ArticleDOI
Theoretical perspectives on the reaction mechanism of serine proteases: the reaction free energy profiles of the acylation process.
Toyokazu Ishida,Shigeki Kato +1 more
TL;DR: In this article, the authors studied the reaction mechanism of serine proteases (trypsin), which catalyzes peptide hydrolysis, by ab initio QM/MM electronic structure calculations combined with Molecular Dynamics−Free Energy Perturbation calculations.
Journal ArticleDOI
Binding affinity prediction with different force fields: examination of the linear interaction energy method.
TL;DR: Free energy calculations clearly indicate that the coefficients of the LIE method are independent of the force field used, and the only free parameter of the best model is γ, which is found to depend on the hydrophobicity of the binding site.
Journal ArticleDOI
Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody
K.S. Midelfort,Hector H. Hernandez,Shaun M. Lippow,Bruce Tidor,Catherine L. Drennan,K.D. Wittrup +5 more
TL;DR: These data provide an example where very high binding affinity is achieved through the cumulative effect of many small structural alterations, and several mechanistic explanations for a portion of the improvement are revealed.
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.