<?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%">Ilyin, V. A.</style></author><author><style face="normal" font="default" size="100%">Pieper, U.</style></author><author><style face="normal" font="default" size="100%">Stuart, A. C.</style></author><author><style face="normal" font="default" size="100%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">McMahan, L.</style></author><author><style face="normal" font="default" size="100%">Sali, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">ModView, visualization of multiple protein sequences and structures</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*Database Management Systems Documentation/methods Imaging</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein/*methods *User-Computer Interface</style></keyword><keyword><style  face="normal" font="default" size="100%">Three-Dimensional/methods Protein Conformation Proteins/*chemistry/genetics Sequence Alignment/*methods Sequence Analysis</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=12499313</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">1</style></number><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">165-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">SUMMARY: We describe ModView, a web application for visualization of multiple protein sequences and structures. ModView integrates a multiple structure viewer, a multiple sequence alignment editor, and a database querying engine. It is possible to interactively manipulate hundreds of proteins, to visualize conservative and variable residues, active and binding sites, fragments, and domains in protein families, as well as to display large macromolecular complexes such as ribosomes or viruses. As a Netscape plug-in, ModView can be included in HTML pages along with text and figures, which makes it useful for teaching and presentations. ModView is also suitable as a graphical interface to various databases because it can be controlled through JavaScript commands and called from CGI scripts. AVAILABILITY: ModView is available at http://guitar.rockefeller.edu/modview.</style></abstract><notes><style face="normal" font="default" size="100%">Ilyin, Valentin A Pieper, Ursula Stuart, Ashley C Marti-Renom, Marc A McMahan, Linda Sali, Andrej P50-GM62529/GM/NIGMS NIH HHS/United States Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. England Bioinformatics (Oxford, England) Bioinformatics. 2003 Jan;19(1):165-6.</style></notes></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%">Eswar, N.</style></author><author><style face="normal" font="default" size="100%">John, B.</style></author><author><style face="normal" font="default" size="100%">Mirkovic, N.</style></author><author><style face="normal" font="default" size="100%">Fiser, A.</style></author><author><style face="normal" font="default" size="100%">Ilyin, V. A.</style></author><author><style face="normal" font="default" size="100%">Pieper, U.</style></author><author><style face="normal" font="default" size="100%">Stuart, A. C.</style></author><author><style face="normal" font="default" size="100%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">Madhusudhan, M. S.</style></author><author><style face="normal" font="default" size="100%">Yerkovich, B.</style></author><author><style face="normal" font="default" size="100%">Sali, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Tools for comparative protein structure modeling and analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid *Software *Structural Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Protein Folding Proteins/chemistry Reproducibility of Results Sequence Alignment Sequence Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Systems Integration</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2003</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=12824331</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">13</style></number><volume><style face="normal" font="default" size="100%">31</style></volume><pages><style face="normal" font="default" size="100%">3375-80</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.</style></abstract><notes><style face="normal" font="default" size="100%">Eswar, Narayanan John, Bino Mirkovic, Nebojsa Fiser, Andras Ilyin, Valentin A Pieper, Ursula Stuart, Ashley C Marti-Renom, Marc A Madhusudhan, M S Yerkovich, Bozidar Sali, Andrej P50 GM62529/GM/NIGMS NIH HHS/United States R01 GM 54762/GM/NIGMS NIH HHS/United States R33 CA84699/CA/NCI NIH HHS/United States Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. England Nucleic acids research Nucleic Acids Res. 2003 Jul 1;31(13):3375-80.</style></notes></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%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">Ilyin, V. A.</style></author><author><style face="normal" font="default" size="100%">Sali, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">DBAli: a database of protein structure alignments</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computational Biology *Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Proteins/*chemistry/*genetics Sequence Alignment/*statistics &amp; numerical data Software Software Design</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2001</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=11524379</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">8</style></number><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">746-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">SUMMARY: The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al., Nucleic Acids Res., 28, 257-259, 2000) and CE (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence-sequence and sequence-structure alignment methods under a variety of conditions. AVAILABILITY: http://guitar.rockefeller.edu/DBAli/</style></abstract><notes><style face="normal" font="default" size="100%">Marti-Renom, M A Ilyin, V A Sali, A Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. England Bioinformatics (Oxford, England) Bioinformatics. 2001 Aug;17(8):746-7.</style></notes></record></records></xml>