Journal ArticleDOI
Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.
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TLDR
This work uses explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules and shows that predictions can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.Abstract:
The accurate prediction of protein−ligand binding free energies is a primary objective in computer-aided drug design. The solvation free energy of a small molecule provides a surrogate to the desolvation of the ligand in the thermodynamic process of protein−ligand binding. Here, we use explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules. We also compare the performance of absolute solvation free energies obtained using the OPLS_2005 force field with two other commonly used small molecule force fields—general AMBER force field (GAFF) with AM1-BCC charges and CHARMm-MSI with CHelpG charges. Using the OPLS_2005 force field, we obtain high correlation with experimental solvation free energies (R2 = 0.94) and low average unsigned errors for a majority of the functional groups compared to AM1-BCC/GAFF or CHelpG/CHARMm-MSI. However, ...read more
Citations
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Journal ArticleDOI
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
TL;DR: It is shown that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets.
Journal ArticleDOI
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
Edward Harder,Wolfgang Damm,Jon R. Maple,Chuanjie Wu,Mark Reboul,Jin Yu Xiang,Lingle Wang,Dmitry Lupyan,Markus K. Dahlgren,Jennifer L. Knight,Joseph W. Kaus,David S. Cerutti,Goran Krilov,William L. Jorgensen,Robert Abel,Richard A. Friesner +15 more
TL;DR: Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
Journal ArticleDOI
Improved Docking of Polypeptides with Glide
TL;DR: The optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.
Journal ArticleDOI
KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks
TL;DR: This work proposes here a fast machine-learning approach for predicting binding affinities using state-of-the-art 3D-convolutional neural networks and compares this approach to other machine- learning and scoring methods using several diverse data sets.
Journal ArticleDOI
Virtual screening strategies in drug discovery: a critical review.
Antonio Lavecchia,C. Di Giovanni +1 more
TL;DR: This review provides a comprehensive appraisal of several VS approaches currently available and special emphasis will be given to in silico chemogenomics approaches which utilize annotated ligand-target as well as protein-ligand interaction databases and which could predict or reveal promiscuous binding and polypharmacology.
References
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Journal ArticleDOI
Comparison of simple potential functions for simulating liquid water
TL;DR: In this article, the authors compared the Bernal Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P potential functions for liquid water in the NPT ensemble at 25°C and 1 atm.
Journal ArticleDOI
A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Journal ArticleDOI
Development and testing of a general amber force field.
TL;DR: A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
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GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
TL;DR: In this article, the parametrization and testing of the OPLS all-atom force field for organic molecules and peptides are described, and the parameters for both torsional and non-bonded energy properties have been derived, while the bond stretching and angle bending parameters have been adopted mostly from the AMBER force field.