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MMDB: 3D structure data in Entrez

Y. Wang
2000 Nucleic Acids Research  
Entrez's MMDB (Molecular Modeling DataBase) may be accessed at: http:// www.ncbi.nlm.nih.gov/Entrez/structure.html  ...  To this end, Entrez's search engine provides three powerful features: (i) Links between databases; one may search by term matching in Medline ® , for example, and link to 3D structures reported in these  ...  ACKNOWLEDGEMENTS We thank Colombe Chappey, Jonathan Kans, Tatiana Tatusova and the other members of the NCBI software team for their help in adding structure visualization to Entrez.  ... 
doi:10.1093/nar/28.1.243 pmid:10592236 pmcid:PMC102448 fatcat:o4lfdvympne35bpwmixhx6wfri

MMDB: 3D structures and macromolecular interactions

T. Madej, K. J. Addess, J. H. Fong, L. Y. Geer, R. C. Geer, C. J. Lanczycki, C. Liu, S. Lu, A. Marchler-Bauer, A. R. Panchenko, J. Chen, P. A. Thiessen (+3 others)
2011 Nucleic Acids Research  
MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank.  ...  to 3D structure data not only for structural biologists, but also for molecular biologists and chemists.  ...  known 3D structures tracked in MMDB.  ... 
doi:10.1093/nar/gkr1162 pmid:22135289 pmcid:PMC3245041 fatcat:63sbhrttvngx7axcs36yxdccly

MMDB: Entrez's 3D structure database

A. Marchler-Bauer, K. J. Addess, C. Chappey, L. Geer, T. Madej, Y. Matsuo, Y. Wang, S. H. Bryant
1999 Nucleic Acids Research  
The goal of Entrez's 3D-structure database is to make this information accessible and usable by molecular biologists (http://www.ncbi.nlm.nih.gov/Entrez ).  ...  The three dimensional structures for representatives of nearly half of all protein families are now available in public databases.  ...  For researchers wishing to perform their own computations both structure and structure-structure alignment data in the ASN.1 format used by Entrez are available for bulk download.  ... 
doi:10.1093/nar/27.1.240 pmid:9847190 pmcid:PMC148145 fatcat:2wf5i7o7erdg5aodabeqomo7qa

MMDB: Entrez's 3D-structure database

J. Chen
2003 Nucleic Acids Research  
MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/ structure.html. CONTENTS Access  ...  Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative  ...  At the time of writing, MMDB serves about 50 000 queries per day. Data sources Experimental 3D structure data are retrieved from the Protein Data Bank (2) .  ... 
doi:10.1093/nar/gkg086 pmid:12520055 pmcid:PMC165533 fatcat:6olyiaitk5bi3cgjqufknjd234

MMDB: Entrez's 3D-structure database

Y. Wang
2002 Nucleic Acids Research  
MMDB is available at: http://www.ncbi.nlm.nih.gov/Entrez/ structure.html. CONTENTS Access  ...  Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative  ...  At the time of writing, MMDB serves about 50 000 queries per day. Data sources Experimental 3D structure data are retrieved from the Protein Data Bank (2) .  ... 
doi:10.1093/nar/30.1.249 pmid:11752307 pmcid:PMC99072 fatcat:7h543blngjf6dcned5wqb6uou4

MMDB: annotating protein sequences with Entrez's 3D-structure database

Y. Wang, K. J. Addess, J. Chen, L. Y. Geer, J. He, S. He, S. Lu, T. Madej, A. Marchler-Bauer, P. A. Thiessen, N. Zhang, S. H. Bryant
2007 Nucleic Acids Research  
The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?  ...  Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation.  ...  Data sources Experimental three-dimensional (3D) structure data are obtained from the Protein Data Bank (PDB) (2) . Authorannotated features provided by PDB are recorded in MMDB.  ... 
doi:10.1093/nar/gkl952 pmid:17135201 pmcid:PMC1751549 fatcat:ogsj353nmrhddfzlql2fpwrpay

MMDB and VAST+: tracking structural similarities between macromolecular complexes

Thomas Madej, Christopher J. Lanczycki, Dachuan Zhang, Paul A. Thiessen, Renata C. Geer, Aron Marchler-Bauer, Stephen H. Bryant
2013 Nucleic Acids Research  
VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system.  ...  VAST+simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity.  ...  It facilitates searching for macromolecular structure data in NCBI's Entrez query and retrieval system (3); links and associates macromolecular structure data with a variety of other resources such as  ... 
doi:10.1093/nar/gkt1208 pmid:24319143 pmcid:PMC3965051 fatcat:ahptxplnojbqtglstonppvu33i

SeqHound: biological sequence and structure database as a platform for bioinformatics research

Katerina Michalickova, Gary D Bader, Michel Dumontier, Hao Lieu, Doron Betel, Ruth Isserlin, Christopher W V Hogue
2002 BMC Bioinformatics  
It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional  ...  Structures are available in ASN.1, XML and PDB formats.  ...  Modules are groups of tables and API calls that are filled using a common data resource, for example the 3D structures.  ... 
pmid:12401134 pmcid:PMC138791 fatcat:xf23nq5rendr7lhd5ycavsda24

Database resources of the National Center for Biotechnology Information: update

D. L. Wheeler
2004 Nucleic Acids Research  
The structures in MMDB are linked to one another by VAST structure±structure neighboring, and to entries in the Conserved Domain Database (CDD) (25) by RPS-BLAST neighboring.  ...  sites in UniSTS, genetic variations in dbSNP, protein structures from the Molecular Modeling Database (MMDB) (7) , 3D and alignment-based protein domains, and the biomedical literature via PubMed, PubmedCentral  ... 
doi:10.1093/nar/gkh073 pmid:14681353 pmcid:PMC308807 fatcat:s3wdhcgegfexrokvqtbtpvotf4

CDD: conserved domains and protein three-dimensional structure

Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu (+6 others)
2012 Nucleic Acids Research  
To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts  ...  CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml.  ...  in protein 3D structure.  ... 
doi:10.1093/nar/gks1243 pmid:23197659 pmcid:PMC3531192 fatcat:kyfhbmseffcrjpuj7ie33t7trq

Database resources of the National Center for Biotechnology Information

2019 Nucleic Acids Research  
The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system.  ...  database of citations and abstracts published in life science journals.  ...  The structures in the MMDB are linked to sequences in Entrez and to the Conserved Domain Database (CDD).  ... 
doi:10.1093/nar/gkz899 pmid:31602479 pmcid:PMC6943063 fatcat:coscu5vbd5gtnhii2uj7czx7au

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2000 Nucleic Acids Research  
its entirety but only in part or as a derivative work this must be clearly indicated.  ...  attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in  ...  The structures in the MMDB are linked to sequences in Entrez and to the Conserved Domain Database (CDD).  ... 
doi:10.1093/nar/28.1.10 pmid:10592169 pmcid:PMC102437 fatcat:xhsgpitasrd3na5mmjgz274zcq

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2006 Nucleic Acids Research  
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and  ...  other biological data made available through  ...  The structures in the MMDB are linked to sequences in Entrez and to the Conserved Domain Database (CDD).  ... 
doi:10.1093/nar/gkj158 pmid:16381840 pmcid:PMC1347520 fatcat:ajgh422s6nbi3o4beemsncsyzi

CDD: NCBI's conserved domain database

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu (+8 others)
2014 Nucleic Acids Research  
CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved  ...  We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk.  ...  We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI's Protein Clusters database for providing access to their resources and data, and the users of CDD for their acknowledgements and  ... 
doi:10.1093/nar/gku1221 pmid:25414356 pmcid:PMC4383992 fatcat:fmwggydorjhetcwv6griivaci4

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2001 Nucleic Acids Research  
, its 3D-structure.  ...  SNP reports link to 3D structures from the MMDB via NCBI's interactive macromolecular structure viewer, Cn3D (24) , to highlight implied amino acid changes in coding regions. dbSNP provides additional  ... 
doi:10.1093/nar/29.1.11 pmid:11125038 pmcid:PMC29800 fatcat:mstubvho65h2noojeknidcplwi
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