links to publication data etc

QUICK LINKS
 
Here you'll find links to data, software and other stuff that may be useful...
 
The ReactionExtractor : A Java program implementing the algorithm described in the paper by Czarnecki et al. for extracting metabolic reactions from plain text files. Available from the publisher's site.
Reference: Czarnecki et al.: A text-mining system for extracting metabolic reactions from full-text articles. BMC Bioinformatics 2012 13, 172.
 
The Provar software for probabilistic analysis and visualisation of pocket variability across protein ensembles, is now available to download from Dr Mark Williams' website.
Reference: Ashford, P., Moss, D.S., Alex, A., Yeap, S.K., Povia, A., Nobeli, I., Williams, M.A. (2012). Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. BMC Bioinformatics 13, 39.
 
SERAPhiC , a high quality protein-fragment complex data set is now available in a ready to dock format through IIT.
Reference: Favia, A.D., Bottegoni, G., Nobeli, I., Bisignano, P., Cavalli, A. (2011). SERAPhiC: a Benchmark for in Silico Fragment-Based Drug Design. J. Chem. Inf. Model. 51, 2882-2896.
 
PROCOGNATE , a database of cognate ligands for the domains of enzymes in the SCOP and CATH protein classifications, is available at the EBI.
References: Bashton, M., Nobeli, I., and Thornton, J.M. (2008). PROCOGNATE: A cognate ligand domain mapping for enzymes. Nucleic Acids Res., 36, D618-D622.
Bashton, M., Nobeli, I., and Thornton, J.M. (2006). Cognate ligand domain mapping for enzymes. J. Mol. Biol., 364, 836-852.