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MODBASE, a database of annotated comparative protein structure models, and associated resources

U. Pieper
2004 Nucleic Acids Research  
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  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkh095 pmid:14681398 pmcid:PMC308829 fatcat:blq5hwxzh5gobc32e6c5y3gu6a

MODBASE: a database of annotated comparative protein structure models and associated resources

U. Pieper
2006 Nucleic Acids Research  
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.  ...  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  ...  For linking to MODBASE from their databases, we thank David Haussler, Jim Kent (UCSC Genome Browser), Amos Bairoch (SwissProt/TrEMBL), Rolf Apweiler (InterPro), Patsy Babbitt (SFLD), and Kathy Wu (PIR/  ... 
doi:10.1093/nar/gkj059 pmid:16381869 pmcid:PMC1347422 fatcat:quimgf3kibesrcsogatfoeizp4

ModBase, a database of annotated comparative protein structure models and associated resources

Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges (+1 others)
2013 Nucleic Acids Research  
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  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  ...  ACKNOWLEDGEMENTS We are grateful to Tom Ferrin, Daniel Greenblatt, Conrad Huang and Tom Goddard for CHIMERA and For linking to MODBASE from their databases, we thank Torsten Schwede (Protein Model Portal  ... 
doi:10.1093/nar/gkt1144 pmid:24271400 pmcid:PMC3965011 fatcat:qjyw5cf25ndxpmlts7drmoc5ku

ModBase, a database of annotated comparative protein structure models, and associated resources

U. Pieper, B. M. Webb, D. T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E. C. Meng, E. F. Pettersen, C. C. Huang, R. S. Datta, P. Sampathkumar (+5 others)
2010 Nucleic Acids Research  
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server  ...  Here, we describe the current state of the ModBase database of comparative protein structure models, the ModWeb comparative modeling web-server and several new associated resources: the SALIGN server for  ... 
doi:10.1093/nar/gkq1091 pmid:21097780 pmcid:PMC3013688 fatcat:kmqbpcx7sfek7jxgh4mmv2vley

MODBASE, a database of annotated comparative protein structure models and associated resources

U. Pieper, N. Eswar, B. M. Webb, D. Eramian, L. Kelly, D. T. Barkan, H. Carter, P. Mankoo, R. Karchin, M. A. Marti-Renom, F. P. Davis, A. Sali
2009 Nucleic Acids Research  
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  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn791 pmid:18948282 pmcid:PMC2686492 fatcat:uy2vgrqqljfuhozumatnojgolu

New developments in the InterPro database

N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, E. Courcelle, U. Das (+33 others)
2007 Nucleic Acids Research  
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF,  ...  The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for textand sequence-based searches via a webserver  ...  A large proportion of HMMERbased calculations are performed on the IBMP690 Supercomputer at HLRN.  ... 
doi:10.1093/nar/gkl841 pmid:17202162 pmcid:PMC1899100 fatcat:ditkwsqd5zctdb5wgxs36xhmum

High-Throughput Computational and Experimental Techniques in Structural Genomics

M. R. Chance
2004 Genome Research  
Comparative modeling of these structures has generated >40,000 structural models.  ...  The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining  ...  MODBASE (http://salilab.org/modbase) is a comprehensive database of annotated comparative protein structure models (Pieper et al.  ... 
doi:10.1101/gr.2537904 pmid:15489337 pmcid:PMC528931 fatcat:afjhww6uunhs5h6thcb6keefai

OnTheFly: a database ofDrosophila melanogastertranscription factors and their binding sites

Shula Shazman, Hunjoong Lee, Yakov Socol, Richard S. Mann, Barry Honig
2013 Nucleic Acids Research  
An important feature of the database is that all DNAbinding domains and their binding sites are fully annotated in a eukaryote using structural criteria and evolutionary homology.  ...  TFs predicted in the Drosophila melanogaster genome are annotated and classified and their structures, obtained via experiment or homology models, are provided.  ...  Overall annotations of a protein (GO term, EC class) and annotations associated with individual residues (UniProt sequence features, ligand interactions) can be displayed and used to filter structural  ... 
doi:10.1093/nar/gkt1165 pmid:24271386 pmcid:PMC3965123 fatcat:pk56picuxjdgflvrpvylyjkrha

Structural Annotation of Mycobacterium tuberculosis Proteome

Praveen Anand, Sandhya Sankaran, Sumanta Mukherjee, Kalidas Yeturu, Roman Laskowski, Anshu Bhardwaj, Raghu Bhagavat, Samir K. Brahmachari, Nagasuma Chandra, Denis Dupuy
2011 PLoS ONE  
Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association.  ...  Structural models were obtained and validated for ,2877 ORFs, covering ,70% of the genome.  ...  Acknowledgments This work forms a part of the Connect2Decode project (http://c2d.osdd. net/) for 'Re-annotation of Mycobacterium tuberculosis', an initiative of the Open Source Drug Discovery project.  ... 
doi:10.1371/journal.pone.0027044 pmid:22073123 pmcid:PMC3205055 fatcat:exqhqpoj2vdk3ge3th7qbqsj7m

Structural Annotation of the Mycobacterium tuberculosis Proteome

Nagasuma Chandra, Sankaran Sandhya, Praveen Anand
2014 Microbiology spectrum  
Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association.  ...  Structural models were obtained and validated for ,2877 ORFs, covering ,70% of the genome.  ...  Acknowledgments This work forms a part of the Connect2Decode project (http://c2d.osdd. net/) for 'Re-annotation of Mycobacterium tuberculosis', an initiative of the Open Source Drug Discovery project.  ... 
doi:10.1128/microbiolspec.mgm2-0027-2013 pmid:26105824 fatcat:dcup7tpzmjc6xgomusgbietpvy

Bioinformatic Tools for Identifying Disease Gene and SNP Candidates [chapter]

Sean D. Mooney, Vidhya G. Krishnan, Uday S. Evani
2010 Msphere  
As databases of genome data continue to grow, our understanding of the functional elements of the genome grows as well.  ...  In this protocol manuscript, methods for understanding the molecular functions of single nucleotide polymorphisms (SNPs) and mutations are reviewed and described.  ...  LS-SNP stands out as a useful and unique resource because it provides annotations of nsSNPs that have been mapped to homology models from the MODBASE (http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi  ... 
doi:10.1007/978-1-60327-367-1_17 pmid:20238089 pmcid:PMC3957484 fatcat:z3svbfpslbajrbioo2qrjwwkei

Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria

Phelelani T Mpangase, Michal J Szolkiewicz, Misha le Grange, Jeanré H Smit, Pieter B Burger, Fourie Joubert
2013 Malaria Journal  
advanced filtering and selection of proteins based on a relevant range of molecular characteristics.  ...  Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be  ...  Acknowledgements We thank John Overington and the ChEMBL group for hosting PM and MS for a research visit. We are grateful to ChemAxon for the FreeWeb license.  ... 
doi:10.1186/1475-2875-12-116 pmid:23537208 pmcid:PMC3637051 fatcat:tjpfomfagfc2ndzadfi2wlgcse

Discovery: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria

Fourie Joubert, Claudia M Harrison, Riaan J Koegelenberg, Christiaan J Odendaal, Tjaart AP de Beer
2009 Malaria Journal  
advanced filtering and selection of proteins based on a relevant range of molecular characteristics.  ...  Discovery-2 is an update of the original Discovery in silico resource for the rational selection of putative drug target proteins, enabling researchers to obtain information for a protein which may be  ...  Acknowledgements We thank John Overington and the ChEMBL group for hosting PM and MS for a research visit. We are grateful to ChemAxon for the FreeWeb license.  ... 
doi:10.1186/1475-2875-8-178 pmid:19642978 pmcid:PMC2724543 fatcat:yjm6x3ilengkjkufwjngxe3sbq

InterPro: the integrative protein signature database

S. Hunter, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, U. Das, L. Daugherty, L. Duquenne, R. D. Finn, J. Gough (+26 others)
2009 Nucleic Acids Research  
Additionally, if a protein has a solved 3D structure in PDB or a structure modelled in either the MODBASE (22) or SWISS-MODEL (23) databases, this information is shown together with the member databases  ...  Each unique protein sequence is stored only once in A new file (feature.xml) has been created which contains non-signature match data from the structural databases (PDB, MODBASE and SWISS-MODEL) for UniProtKB  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn785 pmid:18940856 pmcid:PMC2686546 fatcat:6ehhtr3amzazll5wha5itvjzba

The SWISS-MODEL Repository and associated resources

F. Kiefer, K. Arnold, M. Kunzli, L. Bordoli, T. Schwede
2009 Nucleic Acids Research  
SWISS-MODEL Repository (http://swissmodel. expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline.  ...  facilitates the navigation between protein sequence and structure resources.  ...  ACKNOWLEDGEMENTS We are grateful to Rainer Po¨hlmann, [BC] 2 & Biozentrum University of Basel, for professional systems support, Pascal Benkert for fruitful discussions on model quality assessment and  ... 
doi:10.1093/nar/gkn750 pmid:18931379 pmcid:PMC2686475 fatcat:tzaquxsk3vffzdprb7h5efkasq
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