Protein folds and families: sequence and structure alignments. Export

@article{citeulike:814642, abstract = {Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36\% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/}, address = {European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge CB10 1SD, UK. holm@embl-ebi.ac.uk}, author = {Holm, L. and Sander, C.}, citeulike-article-id = {814642}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/9847191}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=9847191}, day = {1}, issn = {0305-1048}, journal = {Nucleic Acids Res}, keywords = {comps, evolution, fold-space, major-proposal, protein}, month = {January}, number = {1}, pages = {244--247}, posted-at = {2006-08-23 22:46:55}, priority = {4}, title = {Protein folds and families: sequence and structure alignments.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/9847191}, volume = {27}, year = {1999} }

TY - JOUR ID - citeulike:814642 L3 - citeulike-article-id:814642 N2 - Dali and HSSP are derived databases organizing protein space in the structurally known regions. We use an automatic structure alignment program (Dali) for the classification of all known 3D structures based on all-against-all comparison of 3D structures in the Protein Data Bank. The HSSP database associates 1D sequences with known 3D structures using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). As a result, the HSSP database not only provides aligned sequence families, but also implies secondary and tertiary structures covering 36% of all sequences in Swiss-Prot. The structure classification by Dali and the sequence families in HSSP can be browsed jointly from a web interface providing a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences. In particular, this results in a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The organization of protein structures and families provides a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The databases are available from http://www.embl-ebi.ac.uk/dali/ IS - 1 JF - Nucleic Acids Res SN - 0305-1048 AD - European Bioinformatics Institute, EMBL-EBI, Genome Campus, Cambridge CB10 1SD, UK. holm@embl-ebi.ac.uk EP - 247 TI - Protein folds and families: sequence and structure alignments. VL - 27 SP - 244 KW - comps KW - evolution KW - fold-space KW - major-proposal KW - protein AU - Holm, L AU - Sander, C PY - 1999/01/01/ UR - http://view.ncbi.nlm.nih.gov/pubmed/9847191 ER -