Binding MOAD, a high-quality protein-ligand database

被引：128

作者：

Benson, Mark L. ^{[1
]}

Smith, Richard D. ^{[2
]}

Khazanov, Nickolay A. ^{[1
]}

Dimcheff, Brandon ^{[3
]}

Beaver, John ^{[3
]}

Dresslar, Peter ^{[3
,4
]}

Nerothin, Jason ^{[4
]}

Carlson, Heather A. ^{[1
,2
,4
]}

机构：

[1] Univ Michigan, Bioinformat Grad Program, Ann Arbor, MI 48109 USA

[2] Univ Michigan, Div Biophys Res, Ann Arbor, MI 48109 USA

[3] Torrey Path LLC, Ann Arbor, MI 48104 USA

[4] Univ Michigan, Dept Med Chem, Ann Arbor, MI 48109 USA

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm911

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：

Binding MOAD (Mother of All Databases) is a database of 9836 proteinligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the proteinligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Lastly, logins are no longer necessary, and Binding MOAD is freely available to all at http://www.BindingMOAD.org.

引用

页码：D674 / D678

页数：5

共 19 条

[1] The Protein Data Bank
Berman, HM
Westbrook, J
Feng, Z
Gilliland, G
Bhat, TN
Weissig, H
Shindyalov, IN
Bourne, PE
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
[2] AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB
Block, Peter
Sotriffer, Christoph A.
Dramburg, Ingo
Klebe, Gerhard
[J]. NUCLEIC ACIDS RESEARCH, 2006, 34 : D522 - D526
[3] PDBLIG: Classification of small molecular protein binding in the protein data bank
Chalk, AJ
Worth, CL
Overington, JP
Chan, AWE
[J]. JOURNAL OF MEDICINAL CHEMISTRY, 2004, 47 (15) : 3807 - 3816
[4] Ligand Depot: a data warehouse for ligands bound to macromolecules
Feng, ZK
Chen, L
Maddula, H
Akcan, O
Oughtred, R
Berman, HM
Westbrook, J
[J]. BIOINFORMATICS, 2004, 20 (13) : 2153 - 2155
[5] MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites
Golovin, A
Dimitropoulos, D
Oldfield, T
Rachedi, A
Henrick, K
[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 58 (01) : 190 - 199
[6] Relibase:: Design and development of a database for comprehensive analysis of protein-ligand interactions
Hendlich, M
Bergner, A
Günther, J
Klebe, G
[J]. JOURNAL OF MOLECULAR BIOLOGY, 2003, 326 (02) : 607 - 620
[7] Binding MOAD (Mother of All Databases)
Hu, LG
Benson, ML
Smith, RD
Lerner, MG
Carlson, HA
[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 60 (03) : 333 - 340
[8] PDBSite: a database of the 3D structure of protein functional sites
Ivanisenko, VA
Pintus, SS
Grigorovich, DA
Kolchanov, NA
[J]. NUCLEIC ACIDS RESEARCH, 2005, 33 : D183 - D187
[9] sc-PDB: an annotated database of druggable binding sites from the protein data bank
Kellenberger, E
Muller, P
Schalon, C
Bret, G
Foata, N
Rognan, D
[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2006, 46 (02) : 717 - 727
[10] Kinoshita Kengo, 2002, Journal of Structural and Functional Genomics, V2, P9, DOI 10.1023/A:1011318527094

← 1 2 →