Scripps VIVO scripps research logo

  • Index
  • Log in
  • Home
  • People
  • Organizations
  • Research
  • Events
Search form
As of April 1st VIVO Scientific Profiles will no longer updated for faculty, and the link to VIVO will be removed from the library website. Faculty profile pages will continue to be updated via Interfolio. VIVO will continue being used behind the scenes to update graduate student profiles. Please contact helplib@scripps.edu if you have questions.
How to download citations from VIVO | Alternative profile options

A semiempirical free energy force field with charge-based desolvation

Academic Article
uri icon
  • Overview
  • Research
  • Identity
  • Additional Document Info
  • View All
scroll to property group menus

Overview

authors

  • Huey, R.
  • Morris, G. M.
  • Olson, Arthur
  • Goodsell, David

publication date

  • April 2007

journal

  • Journal of Computational Chemistry  Journal

abstract

  • The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid-based docking methods. The force field is based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding. It also incorporates a charge-based method for evaluation of desolvation designed to use a typical set of atom types. The method has been calibrated on a set of 188 diverse protein-ligand complexes of known structure and binding energy, and tested on a set of 100 complexes of ligands with retroviral proteases. The force field shows improvement in redocking simulations over the previous AutoDock3 force field.

subject areas

  • Algorithms
  • Databases, Protein
  • Drug Design
  • HIV Protease
  • HIV Protease Inhibitors
  • Hydrogen Bonding
  • Ligands
  • Mathematical Computing
  • Models, Chemical
  • Models, Molecular
  • Molecular Conformation
  • Protein Binding
  • Proteins
  • Software
  • Static Electricity
  • Thermodynamics
  • Water
scroll to property group menus

Research

keywords

  • AutoDock4
  • computational docking
  • computer-aided drug design
  • desolvation models
  • force fields
  • prediction of free energy
scroll to property group menus

Identity

International Standard Serial Number (ISSN)

  • 0192-8651

Digital Object Identifier (DOI)

  • 10.1002/jcc.20634

PubMed ID

  • 17274016
scroll to property group menus

Additional Document Info

start page

  • 1145

end page

  • 1152

volume

  • 28

issue

  • 6

©2022 The Scripps Research Institute | Terms of Use | Powered by VIVO

  • About
  • Contact Us
  • Support