<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Madhusudhan, M. S.</style></author><author><style face="normal" font="default" size="100%">Webb, Benjamin M</style></author><author><style face="normal" font="default" size="100%">Marti-Renom, Marc A</style></author><author><style face="normal" font="default" size="100%">Eswar, Narayanan</style></author><author><style face="normal" font="default" size="100%">Sali, Andrej</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Alignment of multiple protein structures based on sequence and structure features.</style></title><secondary-title><style face="normal" font="default" size="100%">Protein engineering, design &amp; selection : PEDS</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">569-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Marti-Renom, Marc A</style></author><author><style face="normal" font="default" size="100%">Pieper, Ursula</style></author><author><style face="normal" font="default" size="100%">Madhusudhan, M S</style></author><author><style face="normal" font="default" size="100%">Rossi, Andrea</style></author><author><style face="normal" font="default" size="100%">Eswar, Narayanan</style></author><author><style face="normal" font="default" size="100%">Davis, Fred P</style></author><author><style face="normal" font="default" size="100%">Al-Shahrour, Fátima</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Sali, Andrej</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">DBAli tools: mining the protein structure space.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Data Interpretation, Statistical</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Conformation</style></keyword><keyword><style  face="normal" font="default" size="100%">Proteins</style></keyword><keyword><style  face="normal" font="default" size="100%">Pseudomonas aeruginosa</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Analysis, Protein</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Homology, Amino Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Structure-Activity Relationship</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">35</style></volume><pages><style face="normal" font="default" size="100%">W393-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB). These tools include (i) the DBAlit program that allows users to input the 3D coordinates of a protein structure for comparison by MAMMOTH against all chains in the PDB; (ii) the AnnoLite and AnnoLyze programs that annotate a target structure based on its stored relationships to other structures; (iii) the ModClus program that clusters structures by sequence and structure similarities; (iv) the ModDom program that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related protein structures. Thus, the DBAli tools, which are freely accessible via the World Wide Web at http://salilab.org/DBAli/, allow users to mine the protein structure space by establishing relationships between protein structures and their functions.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/17478513?dopt=Abstract</style></custom1></record></records></xml>