Alignment of multiple protein structures based on sequence and structure features. Export

@article{citeulike:5160186, abstract = {Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue type, residue position, residue accessible surface area, residue secondary structure state and the conformation of a short segment centered on the residue. The multiple alignment is built by following the 'guide' tree constructed from the matrix of all pairwise protein alignment scores. Importantly, the method does not depend on the exact values of various parameters, such as feature weights and gap penalties, because the optimal alignment across a range of parameter values is found. Using multiple structure alignments in the HOMSTRAD database, SALIGN was benchmarked against MUSTANG for multiple alignments as well as against TM-align and CE for pairwise alignments. On the average, SALIGN produces a 15\% improvement in structural overlap over HOMSTRAD and 14\% over MUSTANG, and yields more equivalent structural positions than TM-align and CE in 90\% and 95\% of cases, respectively. The utility of accurate multiple structure alignment is illustrated by its application to comparative protein structure modeling.}, author = {Madhusudhan, M. S. and Webb, Benjamin M. and Marti-Renom, Marc A. and Eswar, Narayanan and Sali, Andrej}, citeulike-article-id = {5160186}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/protein/gzp040}, citeulike-linkout-1 = {http://peds.oxfordjournals.org/cgi/content/abstract/22/9/569}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19587024}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19587024}, day = {1}, doi = {10.1093/protein/gzp040}, issn = {1741-0134}, journal = {Protein engineering, design \& selection : PEDS}, keywords = {alignment, multiple, protein, sep09, structure}, month = {September}, number = {9}, pages = {569--574}, posted-at = {2009-08-27 19:03:19}, priority = {0}, title = {Alignment of multiple protein structures based on sequence and structure features.}, url = {http://dx.doi.org/10.1093/protein/gzp040}, volume = {22}, year = {2009} }

TY - JOUR ID - citeulike:5160186 L3 - citeulike-article-id:5160186 N2 - Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue type, residue position, residue accessible surface area, residue secondary structure state and the conformation of a short segment centered on the residue. The multiple alignment is built by following the 'guide' tree constructed from the matrix of all pairwise protein alignment scores. Importantly, the method does not depend on the exact values of various parameters, such as feature weights and gap penalties, because the optimal alignment across a range of parameter values is found. Using multiple structure alignments in the HOMSTRAD database, SALIGN was benchmarked against MUSTANG for multiple alignments as well as against TM-align and CE for pairwise alignments. On the average, SALIGN produces a 15% improvement in structural overlap over HOMSTRAD and 14% over MUSTANG, and yields more equivalent structural positions than TM-align and CE in 90% and 95% of cases, respectively. The utility of accurate multiple structure alignment is illustrated by its application to comparative protein structure modeling. IS - 9 JF - Protein engineering, design & selection : PEDS SN - 1741-0134 EP - 574 TI - Alignment of multiple protein structures based on sequence and structure features. VL - 22 SP - 569 KW - alignment KW - multiple KW - protein KW - sep09 KW - structure AU - Madhusudhan, MS AU - Webb, Benjamin AU - Marti-Renom, Marc AU - Eswar, Narayanan AU - Sali, Andrej PY - 2009/09/01/ UR - http://dx.doi.org/10.1093/protein/gzp040 ER -