ZINCPharmer: pharmacophore search of the ZINC database

被引：309

作者：

Koes, David Ryan ^{[1
]}

Camacho, Carlos J. ^{[1
]}

机构：

[1] Univ Pittsburgh, Dept Computat & Syst Biol, Pittsburgh, PA 15260 USA

来源：

NUCLEIC ACIDS RESEARCH | 2012年 / 40卷 / W1期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gks378

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

ZINCPharmer (http://zincpharmer.csb.pitt.edu) is an online interface for searching the purchasable compounds of the ZINC database using the Pharmer pharmacophore search technology. A pharmacophore describes the spatial arrangement of the essential features of an interaction. Compounds that match a well-defined pharmacophore serve as potential lead compounds for drug discovery. ZINCPharmer provides tools for constructing and refining pharmacophore hypotheses directly from molecular structure. A search of 176 million conformers of 18.3 million compounds typically takes less than a minute. The results can be immediately viewed, or the aligned structures may be downloaded for off-line analysis. ZINCPharmer enables the rapid and interactive search of purchasable chemical space.

引用

页码：W409 / W414

页数：6

共 22 条

[1]

A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): Theory and application [J].

Baroni, Massimo ;

Cruciani, Gabriele ;

Sciabola, Simone ;

Perruccio, Francesca ;

Mason, Jonathan S. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2007, 47 (02) :279-294

[2]

A web-based 3D-database pharmacophore searching tool for drug discovery [J].

Fang, XL ;

Wang, SM .

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 2002, 42 (02) :192-198

[3]

Swimming into peptidomimetic chemical space using pepMMsMIMIC [J].

Floris, Matteo ;

Masciocchi, Joel ;

Fanton, Marco ;

Moro, Stefano .

NUCLEIC ACIDS RESEARCH, 2011, 39 :W261-W269

[4]

EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities [J].

Hsin, Kun-Yi ;

Morgan, Hugh P. ;

Shave, Steven R. ;

Hinton, Andrew C. ;

Taylor, Paul ;

Walkinshaw, Malcolm D. .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D1042-D1048

[5]

ZINC - A free database of commercially available compounds for virtual screening [J].

Irwin, JJ ;

Shoichet, BK .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2005, 45 (01) :177-182

[6]

Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations [J].

Kirchmair, Johannes ;

Wolber, Gerhard ;

Laggner, Christian ;

Langer, Thierry .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2006, 46 (04) :1848-1861

[7]

Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure [J].

Koes, David Ryan ;

Camacho, Carlos J. .

BIOINFORMATICS, 2012, 28 (06) :784-791

[8]

Pharmer: Efficient and Exact Pharmacophore Search [J].

Koes, David Ryan ;

Camacho, Carlos J. .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 51 (06) :1307-1314

[9]

Langer T, 2003, CURR OPIN DRUG DISC, V6, P370

[10]

Three-Dimensional Pharmacophore Methods in Drug Discovery [J].

Leach, Andrew R. ;

Gillet, Valerie J. ;

Lewis, Richard A. ;

Taylor, Robin .

JOURNAL OF MEDICINAL CHEMISTRY, 2010, 53 (02) :539-558

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