<?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%">Pieper, U.</style></author><author><style face="normal" font="default" size="100%">Eswar, N.</style></author><author><style face="normal" font="default" size="100%">Braberg, H.</style></author><author><style face="normal" font="default" size="100%">Madhusudhan, M. S.</style></author><author><style face="normal" font="default" size="100%">Davis, F. P.</style></author><author><style face="normal" font="default" size="100%">Stuart, A. C.</style></author><author><style face="normal" font="default" size="100%">Mirkovic, N.</style></author><author><style face="normal" font="default" size="100%">Rossi, A.</style></author><author><style face="normal" font="default" size="100%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">Fiser, A.</style></author><author><style face="normal" font="default" size="100%">Webb, B.</style></author><author><style face="normal" font="default" size="100%">Greenblatt, D.</style></author><author><style face="normal" font="default" size="100%">Huang, C. C.</style></author><author><style face="normal" font="default" size="100%">Ferrin, T. E.</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%">MODBASE, a database of annotated comparative protein structure models, and associated resources</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 Sequence Animals Binding Sites *Computational Biology *Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Molecular Sequence Data Polymorphism</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Genomics Humans Internet Ligands Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Single Nucleotide Protein Binding Protein Conformation Proteins/*chemistry/genetics Sequence Alignment Software User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2004</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=14681398</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">Database issue</style></number><volume><style face="normal" font="default" size="100%">32</style></volume><pages><style face="normal" font="default" size="100%">D217-22</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).</style></abstract><notes><style face="normal" font="default" size="100%">Pieper, Ursula Eswar, Narayanan Braberg, Hannes Madhusudhan, M S Davis, Fred P Stuart, Ashley C Mirkovic, Nebojsa Rossi, Andrea Marti-Renom, Marc A Fiser, Andras Webb, Ben Greenblatt, Daniel Huang, Conrad C Ferrin, Thomas E Sali, Andrej P41 RR01081/RR/NCRR NIH HHS/United States 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. 2004 Jan 1;32(Database issue):D217-22.</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%">Madhusudhan, M. S.</style></author><author><style face="normal" font="default" size="100%">Fiser, A.</style></author><author><style face="normal" font="default" size="100%">Rost, 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%">Reliability of assessment of protein structure prediction methods</style></title><secondary-title><style face="normal" font="default" size="100%">Structure</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">*Computer Simulation Humans *Models</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular *Protein Conformation Proteins/*chemistry Reproducibility of Results</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2002</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=12005441</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">435-40</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 reliability of ranking of protein structure modeling methods is assessed. The assessment is based on the parametric Student’s t test and the nonparametric Wilcox signed rank test of statistical significance of the difference between paired samples. The approach is applied to the ranking of the comparative modeling methods tested at the fourth meeting on Critical Assessment of Techniques for Protein Structure Prediction (CASP). It is shown that the 14 CASP4 test sequences may not be sufficient to reliably distinguish between the top eight methods, given the model quality differences and their standard deviations. We suggest that CASP needs to be supplemented by an assessment of protein structure prediction methods that is automated, continuous in time, based on several criteria applied to a large number of models, and with quantitative statistical reliability assigned to each characterization.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;Marti-Renom, Marc A Madhusudhan, M S Fiser, Andras Rost, Burkhard Sali, Andrej GM 54762/GM/NIGMS NIH HHS/United States GM62413/GM/NIGMS NIH HHS/United States Comparative Study Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. United States Structure (London, England : 1993) Structure. 2002 Mar;10(3):435-40.&lt;/p&gt;</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%">Eyrich, V. A.</style></author><author><style face="normal" font="default" size="100%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">Przybylski, D.</style></author><author><style face="normal" font="default" size="100%">Madhusudhan, M. S.</style></author><author><style face="normal" font="default" size="100%">Fiser, A.</style></author><author><style face="normal" font="default" size="100%">Pazos, F.</style></author><author><style face="normal" font="default" size="100%">Valencia, A.</style></author><author><style face="normal" font="default" size="100%">Sali, A.</style></author><author><style face="normal" font="default" size="100%">Rost, B.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">EVA: continuous automatic evaluation of protein structure prediction servers</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%">Automation Internet *Protein Conformation Proteins/*analysis *Software</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=11751240</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">12</style></number><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">1242-3</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY: http://cubic.bioc.columbia.edu/eva. CONTACT: eva@cubic.bioc.columbia.edu</style></abstract><notes><style face="normal" font="default" size="100%">Eyrich, V A Marti-Renom, M A Przybylski, D Madhusudhan, M S Fiser, A Pazos, F Valencia, A Sali, A Rost, B England Bioinformatics (Oxford, England) Bioinformatics. 2001 Dec;17(12):1242-3.</style></notes></record></records></xml>