@article {18948282,
	title = {MODBASE, a database of annotated comparative protein structure models and associated resources},
	journal = {Nucleic Acids Res},
	volume = {37},
	number = {Database issue},
	year = {2009},
	note = {Pieper, Ursula Eswar, Narayanan Webb, Ben M Eramian, David Kelly, Libusha Barkan, David T Carter, Hannah Mankoo, Parminder Karchin, Rachel Marti-Renom, Marc A Davis, Fred P Sali, Andrej GM08284/GM/NIGMS NIH HHS/United States P01 GM71790/GM/NIGMS NIH HHS/United States R01 GM54762/GM/NIGMS NIH HHS/United States U01 GM61390/GM/NIGMS NIH HHS/United States U54 GM074929/GM/NIGMS NIH HHS/United States U54 GM074945/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, Non-P.H.S. England Nucleic acids research Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. Epub 2008 Oct 23.},
	pages = {D347-54},
	abstract = {MODBASE (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/).},
	keywords = {*Databases, Molecular Mutation Polymorphism, Protein Genomics Humans Ligands *Models, Protein User-Computer Interface, Single Nucleotide Protein Folding Protein Interaction Domains and Motifs *Protein Structure, Tertiary Proteins/genetics *Structural Homology},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18948282},
	author = {Pieper, U. and Eswar, N. and Webb, B. M. and Eramian, D. and Kelly, L. and Barkan, D. T. and Carter, H. and Mankoo, P. and Karchin, R. and M. A. Marti-Renom and Davis, F. P. and Sali, A.}
}
@article {17570147,
	title = {The AnnoLite and AnnoLyze programs for comparative annotation of protein structures},
	journal = {BMC Bioinformatics},
	volume = {8 Suppl 4},
	year = {2007},
	note = {Marti-Renom, Marc A Rossi, Andrea Al-Shahrour, Fatima Davis, Fred P Pieper, Ursula Dopazo, Joaquin Sali, Andrej Research Support, Non-U.S. Gov{\textquoteright}t England BMC bioinformatics BMC Bioinformatics. 2007 May 22;8 Suppl 4:S4.},
	pages = {S4},
	abstract = {BACKGROUND: Advances in structural biology, including structural genomics, have resulted in a rapid increase in the number of experimentally determined protein structures. However, about half of the structures deposited by the structural genomics consortia have little or no information about their biological function. Therefore, there is a need for tools for automatically and comprehensively annotating the function of protein structures. We aim to provide such tools by applying comparative protein structure annotation that relies on detectable relationships between protein structures to transfer functional annotations. Here we introduce two programs, AnnoLite and AnnoLyze, which use the structural alignments deposited in the DBAli database. DESCRIPTION: AnnoLite predicts the SCOP, CATH, EC, InterPro, PfamA, and GO terms with an average sensitivity of  90\% and average precision of  80\%. AnnoLyze predicts ligand binding site and domain interaction patches with an average sensitivity of  70\% and average precision of  30\%, correctly localizing binding sites for small molecules in  95\% of its predictions. CONCLUSION: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures can reliably and automatically annotate new protein structures. The programs are fully accessible via the Internet as part of the DBAli suite of tools at http://salilab.org/DBAli/.},
	keywords = {*Algorithms Amino Acid Sequence Confidence Intervals Data Interpretation, Amino Acid *Software Structure-Activity Relationship, Protein Information Storage and Retrieval/methods Molecular Sequence Data Proteins/*chemistry/classification/*metabolism Sensitivity and Specificity Sequence Alignment/*methods Sequence Analysis, Protein/*methods Sequence Homology, Statistical *Databases},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17570147},
	author = {M. A. Marti-Renom and Rossi, A. and Fatima Al-Shahrour and Davis, F. P. and Pieper, U. and Dopazo, J. and Sali, A.}
}
@article {17478513,
	title = {DBAli tools: mining the protein structure space},
	journal = {Nucleic Acids Res},
	volume = {35},
	number = {Web Server issue},
	year = {2007},
	note = {Marti-Renom, Marc A Pieper, Ursula Madhusudhan, M S Rossi, Andrea Eswar, Narayanan Davis, Fred P Al-Shahrour, Fatima Dopazo, Joaquin Sali, Andrej GM 62529/GM/NIGMS NIH HHS/United States GM074929/GM/NIGMS NIH HHS/United States GM54762/GM/NIGMS NIH HHS/United States GM71790/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2007 Jul;35(Web Server issue):W393-7. Epub 2007 May 3.},
	pages = {W393-7},
	abstract = {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.},
	keywords = {*Algorithms Amino Acid Sequence Computational Biology/*methods Data Interpretation, Amino Acid *Software Structure-Activity Relationship, Protein Internet Molecular Sequence Data Protein Conformation Proteins/*chemistry/classification/*metabolism Pseudomonas aeruginosa/*metabolism Sequence Alignment/*methods Sequence Analysis, Protein/*methods Sequence Homology, Statistical *Databases},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17478513},
	author = {M. A. Marti-Renom and Pieper, U. and Madhusudhan, M. S. and Rossi, A. and Eswar, N. and Davis, F. P. and Fatima Al-Shahrour and Dopazo, J. and Sali, A.}
}
@article {16381869,
	title = {MODBASE: a database of annotated comparative protein structure models and associated resources},
	journal = {Nucleic Acids Res},
	volume = {34},
	number = {Database issue},
	year = {2006},
	note = {Pieper, Ursula Eswar, Narayanan Davis, Fred P Braberg, Hannes Madhusudhan, M S Rossi, Andrea Marti-Renom, Marc Karchin, Rachel Webb, Ben M Eramian, David Shen, Min-Yi Kelly, Libusha Melo, Francisco Sali, Andrej GM 08284/GM/NIGMS 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 U54 GM074945/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2006 Jan 1;34(Database issue):D291-5.},
	pages = {D291-5},
	abstract = {MODBASE (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).},
	keywords = {Binding Sites *Databases, Molecular Polymorphism, Protein Humans Internet Ligands *Models, Protein Systems Integration User-Computer Interface, Single Nucleotide Protein Structure, Tertiary Proteins/*chemistry/genetics/metabolism Software *Structural Homology},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=16381869},
	author = {Pieper, U. and Eswar, N. and Davis, F. P. and Braberg, H. and Madhusudhan, M. S. and Rossi, A. and M. A. Marti-Renom and Karchin, R. and Webb, B. M. and Eramian, D. and Shen, M. Y. and Kelly, L. and Melo, F. and Sali, A.}
}
@article {14681398,
	title = {MODBASE, a database of annotated comparative protein structure models, and associated resources},
	journal = {Nucleic Acids Res},
	volume = {32},
	number = {Database issue},
	year = {2004},
	note = {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{\textquoteright}t Research Support, U.S. Gov{\textquoteright}t, P.H.S. England Nucleic acids research Nucleic Acids Res. 2004 Jan 1;32(Database issue):D217-22.},
	pages = {D217-22},
	abstract = {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).},
	keywords = {Amino Acid Sequence Animals Binding Sites *Computational Biology *Databases, Molecular Molecular Sequence Data Polymorphism, Protein Genomics Humans Internet Ligands Models, Single Nucleotide Protein Binding Protein Conformation Proteins/*chemistry/genetics Sequence Alignment Software User-Computer Interface},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=14681398},
	author = {Pieper, U. and Eswar, N. and Braberg, H. and Madhusudhan, M. S. and Davis, F. P. and Stuart, A. C. and Mirkovic, N. and Rossi, A. and M. A. Marti-Renom and Fiser, A. and Webb, B. and Greenblatt, D. and Huang, C. C. and Ferrin, T. E. and Sali, A.}
}
