Critical assessment of the automated AutoDock as a new docking tool for virtual screening

被引：166

作者：

Park, Hwangseo ^{[1
]}

Lee, Jinuk

Lee, Sangyoub

机构：

[1] Sejong Univ, Dept Biosci & Biotechnol, Seoul 143747, South Korea

[2] Seoul Natl Univ, Dept Chem, Seoul 151747, South Korea

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2006年 / 65卷 / 03期

关键词：

virtual screening; drug discovery; docking; AutoDock; chemical database; automation;

D O I：

10.1002/prot.21183

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

A major problem in virtual screening concerns the accuracy of the binding free energy between a target protein and a putative ligand. Here we report an example supporting the outperformance of the AutoDock scoring firnction in virtual screening in comparison to the other popular docking programs. The original AutoDock program is in itself inefficient to be used in virtual screening because the grids of interaction energy have to be calculated for each putative ligand in chemical database. However, the automation of the AutoDock program with the potential grids defined in common for all putative ligands leads to more than twofold increase in the speed of virtual database screening. The utility of the automated AutoDock in virtual screening is further demonstrated by identifying the actual inhibitors of various target enzymes in chemical databases with accuracy higher than the other docking tools including DOCK and F'IexY- These results exemplify the usefulness of the automated AutoDock as a new promising tool in structure-based virtual screening.

引用

页码：549 / 554

页数：6

共 38 条

[1] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[2] Small molecule peptidomimetics containing a novel phosphotyrosine bioisostere inhibit protein tyrosine phosphatase 1B and augment insulin actions [J].

Bleasdale, JE ;

Ogg, D ;

Palazuk, BJ ;

Jacob, CS ;

Swanson, ML ;

Wang, XY ;

Thompson, DP ;

Conradi, RA ;

Mathews, WR ;

Laborde, AL ;

Stuchly, CW ;

Heijbel, A ;

Bergdahl, K ;

Bannow, CA ;

Smith, CW ;

Svensson, C ;

Liljebris, C ;

Schostarez, HJ ;

May, PD ;

Stevens, FC ;

Larsen, SD .

BIOCHEMISTRY, 2001, 40 (19) :5642-5654

[3] THE DEVELOPMENT OF A SIMPLE EMPIRICAL SCORING FUNCTION TO ESTIMATE THE BINDING CONSTANT FOR A PROTEIN LIGAND COMPLEX OF KNOWN 3-DIMENSIONAL STRUCTURE [J].

BOHM, HJ .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 1994, 8 (03) :243-256

[4] Comparative study of several algorithms for flexible ligand docking [J].

Bursulaya, BD ;

Totrov, M ;

Abagyan, R ;

Brooks, CL .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2003, 17 (11) :755-763

[5] Structural basis for the activity of drugs that inhibit phosphodiesterases [J].

Card, GL ;

England, BP ;

Suzuki, Y ;

Fong, D ;

Powell, B ;

Lee, B ;

Luu, C ;

Tabrizizad, M ;

Gillette, S ;

Ibrahim, PN ;

Artis, DR ;

Bollag, G ;

Milburn, MV ;

Kim, SH ;

Schlessinger, J ;

Zhang, KYJ .

STRUCTURE, 2004, 12 (12) :2233-2247

[6] Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins [J].

Charifson, PS ;

Corkery, JJ ;

Murcko, MA ;

Walters, WP .

JOURNAL OF MEDICINAL CHEMISTRY, 1999, 42 (25) :5100-5109

[7] THE MOLECULAR-SURFACE PACKAGE [J].

CONNOLLY, ML .

JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 1993, 11 (02) :139-143

[8] Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor [J].

Davies, TG ;

Bentley, J ;

Arris, CE ;

Boyle, FT ;

Curtin, NJ ;

Endicott, JA ;

Gibson, AE ;

Golding, BT ;

Griffin, RJ ;

Hardcastle, IR ;

Jewsbury, P ;

Johnson, LN ;

Mesguiche, V ;

Newell, DR ;

Noble, MEM ;

Tucker, JA ;

Wang, L ;

Whitfield, HJ .

NATURE STRUCTURAL BIOLOGY, 2002, 9 (10) :745-749

[9] DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases [J].

Ewing, TJA ;

Makino, S ;

Skillman, AG ;

Kuntz, ID .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2001, 15 (05) :411-428

[10] Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy [J].

Friesner, RA ;

Banks, JL ;

Murphy, RB ;

Halgren, TA ;

Klicic, JJ ;

Mainz, DT ;

Repasky, MP ;

Knoll, EH ;

Shelley, M ;

Perry, JK ;

Shaw, DE ;

Francis, P ;

Shenkin, PS .

JOURNAL OF MEDICINAL CHEMISTRY, 2004, 47 (07) :1739-1749

← 1 2 3 4 →