November 2007
Volume 2, Issue 11
Chemoinformatics
     
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Jürgen Bajorath
The View from Here
Jürgen Bajorath

What is chemoinformatics? Johnny Gasteiger, one of the pioneers in this field, simply defined it as “the application of informatics methods to solve chemical problems”. Today we indeed require a definition as broad and general as this one...
Read more...

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A review of 2006


  Top Reviews
Data reduction and representation in drug discovery

Howe TJ, Mahieu G, Marichal P, Tabruyn T, Vugts P
Drug Discovery Today

Pre-clinical drug discovery relies increasingly on huge volumes of inter-related multivariate data. To
make sense of these data and enable quality decision-making based on this plethora of information they must be presented in an interpretable form...


Similarity-based virtual screening using 2D fingerpints

Willett P
Drug Discovery Today

This paper summarizes recent work at the University of Sheffield on virtual screening methods that use 2D fingerprint measures of structural similarity. A detailed comparison of a large number of similarity coefficients demonstrates that the well-known Tanimoto coefficient remains...

Knowledge-based chemoinformatic approaches to drug discovery

Ghose AK, Herbertz T, Salvino JM, Mallamo JP
Drug Discovery Today

The modern drug discovery process is steadily becoming more information driven. Structural, physicochemical and ADME–Tox property profiles of reference (successful) ligands, along with structural information of their target proteins, have been extremely useful for early-stage drug discovery...


  Abstracts of Key Research Articles

Advanced biological and chemical discovery (ABCD): centralizing discovery knowledge in an inherently decentralized world
Agrafiotis DK, Alex S, Dai H, Derkinderen A, Farnum M, Gates P, Izrailev S, Jaeger EP, Konstant P, Leung A, Lobanov VS, Marichal P, Martin D, Rassokhin DN, Shemanarev M, Skalkin A, Stong J, Tabruyn T, Vermeiren M, Wan J, Xu XY, Yao X
J Chem Inf Model. 2007; in press (doi: 10.1021/ci700267w)

ChemBank: a small molecule screening and cheminformatics resource database
Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA.
Nucl Acid Res. 2007; in press (doi: 10.1093/nar/gkm843)

A cheminformatic toolkit for mining biomedical knowledge
Rosania GR, Crippen G, Woolf P, States D,
Shedden K
Pharm Res. 2007; 24: 1791-1802

Large compound databases for structure-activity relationships studies in drug discovery
Scior T, Bernard P, Medina-Franco JL, Maggiora GM
Mini Rev Med Chem. 2007; 7: 851-860

Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches
Eckert H, Bajorath J
Drug Discov Today 2007; 12: 225-233

Molecular conceptor for training in medicinal chemistry, drug design, and chemoinformatics
Cohen C, Fischel O, Cohen E
Chem Biol Drug Des. 2007; 69: 75-82

Chemoinformatics: past, present, and future
Chen WL
J Chem Inf Model. 2006; 46: 2230-2255

Virtual screening: are we there yet?
Jalaie M, Shanmugasundaram V
Mini Rev Med Chem. 2006; 6: 1159-1167

Challenges for chemoinformatics education in drug discovery
Wild DJ, Wiggins GD
Drug Discov Today 2006; 11: 436-439

DrugBank: a comprehensive resource for in silico drug discovery and exploration
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J
Nucl Acid Res. 2006; 34: D668-D672


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