02308nas a2200325   4500008004100000245009900041210006900140300001200209490000700221520117300228653001501401653003601416653004401452653003601496653009601532653005201628100001501680700001401695700001701709700001601726700001401742700001901756700001501775700001501790700001601805700002401821700001801845700001301863856010601876       2009                        eng d00aMODBASE, a database of annotated comparative protein structure models and associated resources0 aMODBASE a database of annotated comparative protein structure mo  aD347-540 v373 aMODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by MODPIPE, an automated modeling pipeline that relies primarily on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE currently contains 5,152,695 reliable models for domains in 1,593,209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct fold are included. MODBASE also allows users to calculate comparative models on demand, through an interface to the MODWEB modeling server (http://salilab.org/modweb). Other resources integrated with MODBASE include databases of multiple protein structure alignments (DBAli), structurally defined ligand binding sites (LIGBASE), predicted ligand binding sites (AnnoLyze), structurally defined binary domain interfaces (PIBASE) and annotated single nucleotide polymorphisms and somatic mutations found in human proteins (LS-SNP, LS-Mut). MODBASE models are also available through the Protein Model Portal (http://www.proteinmodelportal.org/).10a*Databases10aMolecular Mutation Polymorphism10aProtein Genomics Humans Ligands *Models10aProtein User-Computer Interface10aSingle Nucleotide Protein Folding Protein Interaction Domains and Motifs *Protein Structure10aTertiary Proteins/genetics *Structural Homology1 aPieper, U.1 aEswar, N.1 aWebb, B., M.1 aEramian, D.1 aKelly, L.1 aBarkan, D., T.1 aCarter, H.1 aMankoo, P.1 aKarchin, R.1 aMarti-Renom, M., A.1 aDavis, F., P.1 aSali, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1894828202671nas a2200349   4500008004100000245009900041210006900140300001100209490000700220520147800227653002901705653002701734653004401761653005601805653004001861653008301901100001501984700001401999700001802013700001602031700002402047700001402071700002402085700001602109700001702125700001602142700001702158700001402175700001302189700001302202856010602215       2006                        eng d00aMODBASE: a database of annotated comparative protein structure models and associated resources0 aMODBASE a database of annotated comparative protein structure mo  aD291-50 v343 aMODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, http://salilab.org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP).10aBinding Sites *Databases10aMolecular Polymorphism10aProtein Humans Internet Ligands *Models10aProtein Systems Integration User-Computer Interface10aSingle Nucleotide Protein Structure10aTertiary Proteins/*chemistry/genetics/metabolism Software *Structural Homology1 aPieper, U.1 aEswar, N.1 aDavis, F., P.1 aBraberg, H.1 aMadhusudhan, M., S.1 aRossi, A.1 aMarti-Renom, M., A.1 aKarchin, R.1 aWebb, B., M.1 aEramian, D.1 aShen, M., Y.1 aKelly, L.1 aMelo, F.1 aSali, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1638186903269nas a2200337   4500008004100000245010000041210006900141300001200210490000700222520201600229653008002245653005102325653005202376653014002428100001502568700001402583700001602597700002402613700001802637700001902655700001702674700001402691700002402705700001402729700001302743700001902756700001802775700001902793700001302812856010602825       2004                        eng d00aMODBASE, a database of annotated comparative protein structure models, and associated resources0 aMODBASE a database of annotated comparative protein structure mo  aD217-220 v323 aMODBASE (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).10aAmino Acid Sequence Animals Binding Sites *Computational Biology *Databases10aMolecular Molecular Sequence Data Polymorphism10aProtein Genomics Humans Internet Ligands Models10aSingle Nucleotide Protein Binding Protein Conformation Proteins/*chemistry/genetics Sequence Alignment Software User-Computer Interface1 aPieper, U.1 aEswar, N.1 aBraberg, H.1 aMadhusudhan, M., S.1 aDavis, F., P.1 aStuart, A., C.1 aMirkovic, N.1 aRossi, A.1 aMarti-Renom, M., A.1 aFiser, A.1 aWebb, B.1 aGreenblatt, D.1 aHuang, C., C.1 aFerrin, T., E.1 aSali, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14681398