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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  
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.  ...  Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence.  ...  Sequences derived from MMDB are entered into Entrez's protein or nucleic acid sequence database, preserving links to the corresponding 3D structures.  ... 
doi:10.1093/nar/gkl952 pmid:17135201 pmcid:PMC1751549 fatcat:ogsj353nmrhddfzlql2fpwrpay

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 ).  ...  From a protein's sequence 'neighbors' one may rapidly identify other members of a protein family, including those where 3D structure is known.  ...  Entrez's 3D structure database is currently updated once per month. It contains all structures in the PDB (5), with the exception of theoretical models.  ... 
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  
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  ...  The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists.  ...  Molecular Modeling Database (MMDB) is Entrez's 'Structure' database (1) . Querying by terms, for example, one may identify structures of interest based on a protein name.  ... 
doi:10.1093/nar/gkg086 pmid:12520055 pmcid:PMC165533 fatcat:6olyiaitk5bi3cgjqufknjd234

MMDB: Entrez's 3D-structure database

Y. Wang
2002 Nucleic Acids Research  
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  ...  The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists.  ...  Molecular Modeling Database (MMDB) is Entrez's 'Structure' database (1) . Querying by terms, for example, one may identify structures of interest based on a protein name.  ... 
doi:10.1093/nar/30.1.249 pmid:11752307 pmcid:PMC99072 fatcat:7h543blngjf6dcned5wqb6uou4

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  ...  The goal of Entrez's 3D structure database is to make this information accessible and useful to molecular biologists.  ...  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

CDD: a curated Entrez database of conserved domain alignments

A. Marchler-Bauer
2003 Nucleic Acids Research  
This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database.  ...  Structure information is used to identify the core substructure likely to be present in all family members, and to produce sequence alignments consistent with structure conservation.  ...  We thank the authors of Pfam, SMART and LOAD, for creating invaluable resources and for helping with access to data.  ... 
doi:10.1093/nar/gkg087 pmid:12520028 pmcid:PMC165534 fatcat:qexucece6reudeilu2swyzjg3i

Structural Bioinformatics: Computational Software and Databases for the Evaluation of Protein Structure

Ayisha Amanullah, Suad Naheed
2018 RADS Journal of Biological Research & Applied Science  
These databases contain valuable information of overall protein structures, domains and motif structures, protein-protein complex systems and complex of protein with other biomolecules.  ...  index among biological sequences and structures.  ...  MMDB can be accessed through NCBI Entrez's search engine 21 .  ... 
doi:10.37962/jbas.v9i2.124 fatcat:ufrbn64tcje6jpvlmdvtweg4ha

CDD: a Conserved Domain Database for protein classification

A. Marchler-Bauer
2004 Nucleic Acids Research  
CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request.  ...  CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/ cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences.  ...  ACKNOWLEDGEMENTS We thank the authors of Pfam, SMART and COG, for creating invaluable resources and for helping with access to data. We also thank the NIH Intramural Research Program for support.  ... 
doi:10.1093/nar/gki069 pmid:15608175 pmcid:PMC540023 fatcat:yk7toda26vee7jutivsxy5mete

Annotation of functional sites with the Conserved Domain Database

M. K. Derbyshire, C. J. Lanczycki, S. H. Bryant, A. Marchler-Bauer
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We thank the Conserved Domain Curators for compiling the site annotations analyzed in this work, Farideh Chitsaz, Noreen Gonzales, Marc Gwadz, Fu Lu, Gabriele Marchler, James Song, Narmada  ...  CDD curators make extensive use of protein 3D structure, when available, as in-house curation tools are tightly coupled to the Entrez 3D structure database Molecular Modeling Database (MMDB) (10) and structure  ...  such clusters can be used to infer interactions for proteins sequence similar to those with known 3D structure.  ... 
doi:10.1093/database/bar058 pmid:22434827 pmcid:PMC3308149 fatcat:xwt5xq6kwrgedmsbf7ujgsp32e

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2001 Nucleic Acids Research  
, its 3D-structure.  ...  Wherever possible CDD hits are linked to structures which, coupled with a multiple sequence alignment of representatives of the domain hit, can be viewed with NCBI's 3D molecular structure viewer, Cn3D  ... 
doi:10.1093/nar/29.1.11 pmid:11125038 pmcid:PMC29800 fatcat:mstubvho65h2noojeknidcplwi

Binding MOAD (Mother Of All Databases)

Liegi Hu, Mark L. Benson, Richard D. Smith, Michael G. Lerner, Heather A. Carlson
2005 Proteins: Structure, Function, and Bioinformatics  
The viewers display secondary structure, ligand interactions, and cavities. MMDB is Entrez's 3D-structure database.  ...  NCBI developed the Molecular Modeling DataBase (MMDB) and EBI developed PDBsum and E-MSD.  ...  The database tier is where data is stored and retrieved. A.2 Client Tier The client tier is how the user interacts with the application.  ... 
doi:10.1002/prot.20512 pmid:15971202 fatcat:qya7yxhipzes7ng3dgnc6da4au

FAIR, ethical, and coordinated data sharing for COVID-19 response: a review of COVID-19 data sharing platforms and registries [article]

Lauren Maxwell, Priya Shreedhar, Delphine Dauga, Peter McQuilton, Robert F Terry, Alisa Denisiuk, Fruzsina Molnar-Gabor, Abha Saxena, Susanna-Assunta Sansone
2021 Zenodo  
We review gaps and redundancies in COVID-19 data sharing efforts and outline recommendations to build on existing synergies and align with frameworks for effective and equitable data reuse.  ...  Pharm/Tox Database Does not collect, harmonize, share COVID-19 participant-level data 23 MMDB: annotating protein sequences with Entrez's 3D-structure database Does not collect, harmonize, share COVID  ...  : a database and analysis of 63951 Does not collect, harmonize, share COVID-19 participant-level data Greek scientists 65 PFDB: a generic protein family database integrating the CATH domain structure database  ... 
doi:10.5281/zenodo.5642634 fatcat:6iafdybbw5dd7ojjxzmlieckxq

Further studies on AGA production by Pantoea agglomerans strain Eh1087 [article]

Matthew Dominic Galbraith, University Of Canterbury
2012
Comparison of EhpM with known structures, and preliminary analysis of the subcellular location of EhpMNO suggest that these proteins may be localised to the cytoplasmic side of the inner membrane, rather  ...  Comparison of EhpA to related proteins of known structure suggested a catalytic function, and EhpA was found to influence the relative amounts of phenazine-1-carboxylic acid and phenazine-1,6- dicarboxylic  ...  MMDB: Entrez's 3D-structure database. Nucl. Acids Res. 30: 249-252. Wilson, C. A, Kreychman, J. and Gerstein, M. 2000.  ... 
doi:10.26021/7564 fatcat:u6hoadu5lnhppft4imnbpxiiim