Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2001 May;15(5):411-28.
doi: 10.1023/a:1011115820450.

DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases

T J Ewing  1 , S Makino, A G Skillman, I D Kuntz
Affiliations

DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases

T J Ewing et al. J Comput Aided Mol Des. 2001 May.

Abstract

In this paper we describe the search strategies developed for docking flexible molecules to macomolecular sites that are incorporated into the widely distributed DOCK software, version 4.0. The search strategies include incremental construction and random conformation search and utilize the existing Coulombic and Lennard-Jones grid-based scoring function. The incremental construction strategy is tested with a panel of 15 crystallographic testcases, created from 12 unique complexes whose ligands vary in size and flexibility. For all testcases, at least one docked position is generated within 2 A of the crystallographic position. For 7 of 15 testcases, the top scoring position is also within 2 A of the crystallographic position. The algorithm is fast enough to successfully dock a few testcases within seconds and most within 100 s. The incremental construction and the random search strategy are evaluated as database docking techniques with a database of 51 molecules docked to two of the crystallographic testcases. Incremental construction outperforms random search and is fast enough to reliably rank the database of compounds within 15 s per molecule on an SGI R10000 cpu.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. J Comput Aided Mol Des. 1995 Apr;9(2):113-30 - PubMed
    1. Chem Biol. 1996 Jun;3(6):449-62 - PubMed
    1. J Comput Aided Mol Des. 1997 May;11(3):209-28 - PubMed
    1. Science. 1989 Jan 6;243(4887):85-8 - PubMed
    1. J Comput Aided Mol Des. 1996 Aug;10 (4):293-304 - PubMed

Publication types

Substances

LinkOut - more resources

-