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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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An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes.
Tarun Jain,Bhyravabhotla Jayaram +1 more
TL;DR: A computationally fast protocol for predicting binding affinities of non‐metallo protein–ligand complexes using an all atom energy based empirical scoring function comprising electrostatics, van der Waals, hydrophobicity and loss of conformational entropy of protein side chains upon ligand binding.
Journal ArticleDOI
The nature of intermolecular interactions between aromatic amino acid residues.
TL;DR: The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field.
Journal ArticleDOI
Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding.
Maria Luisa Verteramo,Olof Stenström,Majda Misini Ignjatović,Octav Caldararu,Martin A. Olsson,Francesco Manzoni,Hakon Leffler,Esko Oksanen,Derek T. Logan,Ulf J. Nilsson,Ulf Ryde,Mikael Akke +11 more
TL;DR: The molecular determinants underlying differences in ligand affinity to the carbohydrate recognition domain of galectin-3 are pinpointed, highlighting an interplay between conformational entropy and solvation entropy, pointing to both opportunities and challenges in drug design.
Journal ArticleDOI
Modulation of aldose reductase inhibition by halogen bond tuning.
Jindřich Fanfrlík,Michal Kolář,Martin Kamlar,David Hurný,F.X. Ruiz,Alexandra Cousido-Siah,Andre Mitschler,Jan Řezáč,Elango Munusamy,Martin Lepšík,Pavel Matějíček,Jan Veselý,Alberto Podjarny,Pavel Hobza +13 more
TL;DR: The study shows that it is possible to modulate the strength of a halogen bond in a protein-ligand complex as was designed based on the previous studies of low-molecular-weight complexes.
Journal ArticleDOI
How accurate are continuum solvation models for drug-like molecules?
TL;DR: The hydration free energy is estimated for 20 neutral drug-like molecules as well as for three series of 6–11 inhibitors to avidin, factor Xa, and galectin-3 with four different continuum solvent approaches, and the generalised Born methods typically give better results than the Poison–Boltzmann methods.
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.