Searching Proteins

Orengp C A, N P Brown and W R Taylor 1992. Fast Structure Alignment for Protein Datal Searching. Proteins Structure, Function and Genetics 14 139-167. 

WR Pearson. Comparison of methods for searching protein sequence databases. Protein Sci 4 1145-1160, 1995. 

J Moult, MNG James. An algorithm for determining the conformation of polypeptide segments m proteins by systematic search. Proteins 1 146-163, 1986. 

K Yue, KA Dill. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci 5 254-261, 1996. 

The data obtained in MS after the proteolytic digestion of gel-separated proteins into peptides and mass analysis of the peptides will enable the researcher to search protein and nucleotide sequences, which can then be checked against their theoretical fingerprints in databases. 

Relibase a Program for Searching Protein-Ligand Databases. Cambridge Crystallographic Data Centre, Cambridge, 2000. 

R. Lflthy, A. D. McLachlan, and D. Eisenbeig. Secondary structure breed profiles use protein sequence database for structural similarities. Proteins 70 229-239 (1991). 

Pearson, W. R. (1991). Searching protein sequence libraries comparison of the sensitivity and the selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11,635-50. 

Search protein sequence databases with peptide sequences... 

Bork, P. J., Gellerich, H., Groth, R., Hooft, A., and Martin, F., 1995, Divergent evolution of a beta/alpha barrel subclass detection of numerous phosphate-binding sites by motif search. Protein Sci 4 2689274. 

Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J., and Zhou, Y. (1997) Homology modeling with internal coordinate mechanics deformation zone mapping and improvements of models via conformational search. Proteins Suppl 1, 29-37. 

Hou, T., Wang, J., Chen, L. Xu, X. (1999). Automated docking of peptides and proteins by using a genetic algorithm combined with a tabu search. Protein Eng 12(8), 639-48. 

Public annotations Homology searching Protein structure homology Functional prediction Pattern matching Text mining... 

Marchler-Bauer A., and S. H. Bryant. 2004. CD-Search Protein domain annotations on the fly. Nucleic Acids Res 32, Web Server Issue W327-31. 

Templates can be selected using the target sequence as a query for searching protein structure databases [e.g. Brookhaven Protein Data Bank (PDB) http / /www.rcsb.org/pdb/index.html Structural Classification of Proteins (SCOP) scop.mrc-lmb.cam.ac.uk/scop/ DALI www2.ebi.ac.uk/dali/ Class, Architecture, Topology and Homologous superfamily classification at CATH www.biochem.ucl.a-c.uk/bsm/cath/). 

Hobohm, U., and Sander, C. (1995). A sequence property approach to searching protein databases. J. Mol. Biol. 251, 390—399. 

SA-Search http //bioserv.rpbs.jussieu.fr/cgi-bin/SA-search Protein structure mining ... 

Protein-ligand fingerprint similarity searches Contrarily to reverse docking and pharmacophore searches, protein-ligand fingerprints can be encoded in very simple bitstrings or real vectors, and do not necessitate true 3D information. 

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