What Can We Learn from Bioactivity Data? Chemoinformatics Tools and Applications in Chemical Biology Research

被引:16
作者
Humbeck, Lina [1 ]
Koch, Oliver [1 ]
机构
[1] TU Dortmund Univ, Fac Chem & Chem Biol, Otto Hahn Str 6, D-44227 Dortmund, Germany
关键词
DRUG DISCOVERY; MACROMOLECULAR TARGETS; MEDICINAL CHEMISTRY; PDBBIND DATABASE; ENTITIES; UNIVERSE; PUBCHEM; SPACE; ZINC; WEB;
D O I
10.1021/acschembio.6b00706
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
The ever increasing bioactivity data that are produced nowadays allow exhaustive data mining and knowledge discovery approaches that change chemical biology research. A wealth of chemoinformatics tools, web services, and applications therefore exists that supports a careful evaluation and analysis of experimental data to draw conclusions that can influence the further development of chemical probes and potential lead structures. This review focuses on open-source approaches that can be handled by scientists who are not familiar with computational methods having no expert knowledge in chemoinformatics and modeling. Our aim is to present an easily manageable toolbox for support of every day laboratory work. This includes, among other things, the available bioactivity and related molecule databases as well as tools to handle and analyze in-house data.
引用
收藏
页码:23 / 35
页数:13
相关论文
共 67 条
[1]   The Cambridge Structural Database: a quarter of a million crystal structures and rising [J].
Allen, FH .
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 2002, 58 (3 PART 1) :380-388
[2]  
[Anonymous], 1990, Journal of Computational, DOI DOI 10.1002/JCC.540130415
[3]   Chemical con artists foil drug discovery [J].
Baell, Jonathan ;
Walters, Michael A. .
NATURE, 2014, 513 (7519) :481-483
[4]   PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening [J].
Baell, Jonathan B. ;
Ferrins, Lori ;
Falk, Hendrik ;
Nikolakopoulos, George .
AUSTRALIAN JOURNAL OF CHEMISTRY, 2013, 66 (12) :1483-1494
[5]   Analyzing Promiscuity at the Level of Active Compounds and Targets [J].
Bajorath, Juergen .
MOLECULAR INFORMATICS, 2016, 35 (11-12) :583-587
[6]   The ChEMBL bioactivity database: an update [J].
Bento, A. Patricia ;
Gaulton, Anna ;
Hersey, Anne ;
Bellis, Louisa J. ;
Chambers, Jon ;
Davies, Mark ;
Krueger, Felix A. ;
Light, Yvonne ;
Mak, Lora ;
McGlinchey, Shaun ;
Nowotka, Michal ;
Papadatos, George ;
Santos, Rita ;
Overington, John P. .
NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D1083-D1090
[7]  
Berthold M. R, 2008, STUDIES CLASSIFICATI, V31
[8]  
Berthold MR., 2009, ACM SIGKDD Explor. Newsl., V11, P26, DOI [DOI 10.1145/1656274.1656280, DOI 10.1145/1656274]
[9]  
Breinbauer R, 2002, ANGEW CHEM INT EDIT, V41, P2879
[10]   Rules for Identifying Potentially Reactive or Promiscuous Compounds [J].
Bruns, Robert F. ;
Watson, Ian A. .
JOURNAL OF MEDICINAL CHEMISTRY, 2012, 55 (22) :9763-9772