PROMALS3D web server for accurate multiple protein sequence and structure alignments

@article{citeulike:2843098, abstract = {Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. 10.1093/nar/gkn322}, author = {Pei, Jimin and Tang, Ming and Grishin, Nick V. }, citeulike-article-id = {2843098}, doi = {http://dx.doi.org/10.1093/nar/gkn322}, journal = {Nucl. Acids Res.}, keywords = {alignment, bioinformatics, protein, sequence, structure, webserver}, month = {May}, pages = {gkn322+}, posted-at = {2008-05-29 04:29:21}, priority = {2}, title = {PROMALS3D web server for accurate multiple protein sequence and structure alignments}, url = {http://dx.doi.org/10.1093/nar/gkn322}, year = {2008} }

TY - JOUR ID - citeulike:2843098 L3 - citeulike-article-id:2843098 TI - PROMALS3D web server for accurate multiple protein sequence and structure alignments JF - Nucl. Acids Res. SP - gkn322 N2 - Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. 10.1093/nar/gkn322 KW - alignment KW - bioinformatics KW - protein KW - sequence KW - structure KW - webserver AU - Pei, Jimin AU - Tang, Ming AU - Grishin, Nick PY - 2008/05/24/ UR - http://dx.doi.org/10.1093/nar/gkn322 ER -