<?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%">Mirkovic, N.</style></author><author><style face="normal" font="default" size="100%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">Weber, B. L.</style></author><author><style face="normal" font="default" size="100%">Sali, A.</style></author><author><style face="normal" font="default" size="100%">Monteiro, A. N.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition</style></title><secondary-title><style face="normal" font="default" size="100%">Cancer Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">BRCA1 Genetic Predisposition to Disease Humans *Mutation</style></keyword><keyword><style  face="normal" font="default" size="100%">BRCA1 Protein/*chemistry/genetics Breast Neoplasms/*genetics Female *Genes</style></keyword><keyword><style  face="normal" font="default" size="100%">Missense Ovarian Neoplasms/*genetics Pedigree Protein Conformation Structure-Activity Relationship Transcriptional Activation</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=15172985</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">11</style></number><volume><style face="normal" font="default" size="100%">64</style></volume><pages><style face="normal" font="default" size="100%">3790-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The BRCA1 gene from individuals at risk of breast and ovarian cancers can be screened for the presence of mutations. However, the cancer association of most alleles carrying missense mutations is unknown, thus creating significant problems for genetic counseling. To increase our ability to identify cancer-associated mutations in BRCA1, we set out to use the principles of protein three-dimensional structure as well as the correlation between the cancer-associated mutations and those that abolish transcriptional activation. Thirty-one of 37 missense mutations of known impact on the transcriptional activation function of BRCA1 are readily rationalized in structural terms. Loss-of-function mutations involve nonconservative changes in the core of the BRCA1 C-terminus (BRCT) fold or are localized in a groove that presumably forms a binding site involved in the transcriptional activation by BRCA1; mutations that do not abolish transcriptional activation are either conservative changes in the core or are on the surface outside of the putative binding site. Next, structure-based rules for predicting functional consequences of a given missense mutation were applied to 57 germ-line BRCA1 variants of unknown cancer association. Such a structure-based approach may be helpful in an integrated effort to identify mutations that predispose individuals to cancer.</style></abstract><notes><style face="normal" font="default" size="100%">Mirkovic, Nebojsa Marti-Renom, Marc A Weber, Barbara L Sali, Andrej Monteiro, Alvaro N A CA92309/CA/NCI NIH HHS/United States GM54762/GM/NIGMS NIH HHS/United States GM61390/GM/NIGMS NIH HHS/United States Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. Research Support, U.S. Gov’t, P.H.S. United States Cancer research Cancer Res. 2004 Jun 1;64(11):3790-7.</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></records></xml>