@article {16522224, title = {Discovery and hypothesis generation through bioinformatics}, journal = {Genome Biol}, volume = {7}, number = {2}, year = {2006}, note = {Dopazo, Joaquin Aloy, Patrick Congresses England Genome biology Genome Biol. 2006;7(2):307. Epub 2006 Feb 27.}, pages = {307}, abstract = {A report on the 4th European Conference on Computational Biology and the 6th Spanish Annual Meeting on Bioinformatics, Madrid, Spain, 28 September-1 October 2005.}, keywords = {*Computational Biology Genome, Genetic Phylogeny, Human *Genomics Humans *Models}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=16522224}, author = {Dopazo, J. and Aloy, P.} } @article {11394740, title = {Classification of protein disulphide-bridge topologies}, journal = {J Comput Aided Mol Des}, volume = {15}, number = {5}, year = {2001}, note = {Mas, J M Aloy, P Marti-Renom, M A Oliva, B de Llorens, R Aviles, F X Querol, E Comparative Study Research Support, Non-U.S. Gov{\textquoteright}t Netherlands Journal of computer-aided molecular design J Comput Aided Mol Des. 2001 May;15(5):477-87.}, pages = {477-87}, abstract = {The preferential occurrence of certain disulphide-bridge topologies in proteins has prompted us to design a method and a program, KNOT-MATCH, for their classification. The program has been applied to a database of proteins with less than 65\% homology and more than two disulphide bridges. We have investigated whether there are topological preferences that can be used to group proteins and if these can be applied to gain insight into the structural or functional relationships among them. The classification has been performed by Density Search and Hierarchical Clustering Techniques, yielding thirteen main protein classes from the superimposition and clustering process. It is noteworthy that besides the disulphide bridges, regular secondary structures and loops frequently become correctly aligned. Although the lack of significant sequence similarity among some clustered proteins precludes the easy establishment of evolutionary relationships, the program permits us to find out important structural or functional residues upon the superimposition of two protein structures apparently unrelated. The derived classification can be very useful for finding relationships among proteins which would escape detection by current sequence or topology-based analytical algorithms.}, keywords = {Algorithms Computer Simulation Databases as Topic Disulfides/*chemistry Models, Molecular Protein Structure, Secondary Protein Structure, Tertiary Proteins/*chemistry/*classification Software}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=11394740}, author = {Mas, J. M. and Aloy, P. and M. A. Marti-Renom and Oliva, B. and de Llorens, R. and Aviles, F. X. and Querol, E.} }