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Literature DB >> 15870211

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

William L Jorgensen¹, Julian Tirado-Rives.

Abstract

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

Entities: Chemical

Mesh：

Substances：

Year: 2005 PMID： 15870211 PMCID： PMC1100738 DOI： 10.1073/pnas.0408037102

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

32 in total

1. Interplay between time-temperature transformation and the liquid-liquid phase transition in water.

Authors: Masako Yamada; Stefano Mossa; H Eugene Stanley; Francesco Sciortino
Journal: Phys Rev Lett Date: 2002-04-26 Impact factor: 9.161

2. Ion solvation thermodynamics from simulation with a polarizable force field.

Authors: Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal: J Am Chem Soc Date: 2003-12-17 Impact factor: 15.419

3. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors: Araz Jakalian; David B Jack; Christopher I Bayly
Journal: J Comput Chem Date: 2002-12 Impact factor: 3.376

Review 4. Force fields for protein simulations.

Authors: Jay W Ponder; David A Case
Journal: Adv Protein Chem Date: 2003

5. Improved treatment of the protein backbone in empirical force fields.

Authors: Alexander D MacKerell; Michael Feig; Charles L Brooks
Journal: J Am Chem Soc Date: 2004-01-28 Impact factor: 15.419

6. Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP.

Authors: Jason D Thompson; Christopher J Cramer; Donald G Truhlar
Journal: J Comput Chem Date: 2003-08 Impact factor: 3.376

7. Development and testing of a general amber force field.

Authors: Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal: J Comput Chem Date: 2004-07-15 Impact factor: 3.376

8. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

Authors: Sandeep Patel; Alexander D Mackerell; Charles L Brooks
Journal: J Comput Chem Date: 2004-09 Impact factor: 3.376

9. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Authors: Chris Oostenbrink; Alessandra Villa; Alan E Mark; Wilfred F van Gunsteren
Journal: J Comput Chem Date: 2004-10 Impact factor: 3.376

10. Excess free energy of liquids from molecular dynamics simulations. Application to water models.

Authors: J Hermans; A Pathiaseril; A Anderson
Journal: J Am Chem Soc Date: 1988-08-01 Impact factor: 15.419

178 in total

1. Identification of a second substrate-binding site in solute-sodium symporters.

Authors: Zheng Li; Ashley S E Lee; Susanne Bracher; Heinrich Jung; Aviv Paz; Jay P Kumar; Jeff Abramson; Matthias Quick; Lei Shi
Journal: J Biol Chem Date: 2014-11-14 Impact factor: 5.157

Review 2. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors: Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal: Chem Rev Date: 2020-06-29 Impact factor: 60.622

3. Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors.

Authors: James Luccarelli; Julien Michel; Julian Tirado-Rives; William L Jorgensen
Journal: J Chem Theory Comput Date: 2010-01-01 Impact factor: 6.006

4. Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.

Authors: Oliver Beckstein; Bogdan I Iorga
Journal: J Comput Aided Mol Des Date: 2011-12-21 Impact factor: 3.686

5. Natural polarizability and flexibility via explicit valency: the case of water.

Authors: Seyit Kale; Judith Herzfeld
Journal: J Chem Phys Date: 2012-02-28 Impact factor: 3.488

Review 6. Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.

Authors: Pierre Tuffery; Philippe Derreumaux
Journal: J R Soc Interface Date: 2011-10-12 Impact factor: 4.118

10. Simulation of homology models for the extracellular domains (ECD) of ErbB3, ErbB4 and the ErbB2-ErbB3 complex in their active conformations.

Authors: Juan Felipe Franco-Gonzalez; Javier Ramos; Victor L Cruz; Javier Martínez-Salazar
Journal: J Mol Model Date: 2012-10-23 Impact factor: 1.810