Literature DB >> 28444340

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands.

Leela S Dodda1, Israel Cabeza de Vaca1, Julian Tirado-Rives1, William L Jorgensen1.   

Abstract

The accurate calculation of protein/nucleic acid-ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements.
© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2017        PMID： 28444340      PMCID： PMC5793816          DOI： 10.1093/nar/gkx312

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  32 in total

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Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-07-21

3.  Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges.

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Review 4.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors:  William L Jorgensen; Julian Tirado-Rives
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

5.  Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors:  Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
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6.  CHARMM-GUI: a web-based graphical user interface for CHARMM.

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Journal:  J Comput Chem       Date:  2008-08       Impact factor: 3.376

7.  Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

Authors:  K Vanommeslaeghe; E Prabhu Raman; A D MacKerell
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Authors:  Robert B Best; Xiao Zhu; Jihyun Shim; Pedro E M Lopes; Jeetain Mittal; Michael Feig; Alexander D Mackerell
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Review 10.  Molecular dynamics simulations: advances and applications.

Authors:  Adam Hospital; Josep Ramon Goñi; Modesto Orozco; Josep L Gelpí
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  84 in total

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Journal:  J Chem Theory Comput       Date:  2019-03-12       Impact factor: 6.006

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Authors:  Leela S Dodda; Julian Tirado-Rives; William L Jorgensen
Journal:  J Phys Chem B       Date:  2019-01-03       Impact factor: 2.991

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Authors:  Yue Qian; Israel Cabeza de Vaca; Jonah Z Vilseck; Daniel J Cole; Julian Tirado-Rives; William L Jorgensen
Journal:  J Phys Chem B       Date:  2019-10-07       Impact factor: 2.991

Review 4.  Free Energy Calculations for Protein-Ligand Binding Prediction.

Authors:  Willem Jespers; Johan Åqvist; Hugo Gutiérrez-de-Terán
Journal:  Methods Mol Biol       Date:  2021

5.  Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge.

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Journal:  J Comput Aided Mol Des       Date:  2020-02-27       Impact factor: 3.686

6.  Robust Free Energy Perturbation Protocols for Creating Molecules in Solution.

Authors:  Israel Cabeza de Vaca; Ricardo Zarzuela; Julian Tirado-Rives; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2019-06-24       Impact factor: 6.006

7.  SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches.

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Journal:  J Comput Aided Mol Des       Date:  2019-10-17       Impact factor: 3.686

8.  Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet.

Authors:  Lukas Eberlein; Frank R Beierlein; Nico J R van Eikema Hommes; Ashish Radadiya; Jochen Heil; Steven A Benner; Timothy Clark; Stefan M Kast; Nigel G J Richards
Journal:  J Chem Theory Comput       Date:  2020-03-20       Impact factor: 6.006

9.  A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.

Authors:  Reza Salari; Thomas Joseph; Ruchi Lohia; Jérôme Hénin; Grace Brannigan
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Review 10.  Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.

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