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MMDB: Entrez's 3D structure database
1999
Nucleic Acids Research
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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. ...
To illustrate the analysis tools of Entrez's (2,3) 3D-structure database we describe how it may be used to answer the following question: is the 3D structure known for the PTEN gene product, or a homologous ...
doi:10.1093/nar/27.1.240
pmid:9847190
pmcid:PMC148145
fatcat:2wf5i7o7erdg5aodabeqomo7qa
MMDB: Entrez's 3D-structure database
2003
Nucleic Acids Research
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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
2002
Nucleic Acids Research
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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: annotating protein sequences with Entrez's 3D-structure database
2007
Nucleic Acids Research
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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. ...
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? ...
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: 3D structure data in Entrez
2000
Nucleic Acids Research
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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
2003
Nucleic Acids Research
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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. ...
CD-Search results, and pre-computed links from Entrez's protein database, are calculated using the RPS-BLAST algorithm and Position Specific Score Matrices (PSSMs) derived from CDD alignments. ...
Conserved Domains are linked to the NCBI Taxonomy Database, PubMed 1 , and Entrez's protein database, which provides additional search mechanisms. ...
doi:10.1093/nar/gkg087
pmid:12520028
pmcid:PMC165534
fatcat:qexucece6reudeilu2swyzjg3i
Structural Bioinformatics: Computational Software and Databases for the Evaluation of Protein Structure
2018
RADS Journal of Biological Research & Applied Science
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Most familiar biological databases that store 3D protein and other macromolecules structures include, PDB, 3D Genomics, CATH, & SCOP. ...
The wide variety of different levels and types of information content related to 3D protein structures are available on web-based databases. ...
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
2004
Nucleic Acids Research
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The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. ...
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. ...
, PubMed 1 and Entrez's protein database. ...
doi:10.1093/nar/gki069
pmid:15608175
pmcid:PMC540023
fatcat:yk7toda26vee7jutivsxy5mete
Database resources of the National Center for Biotechnology Information
2001
Nucleic Acids Research
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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 ...
The structures in the MMDB are linked to sequences in Entrez and to the Conserved Domain Database (6) . The conserved domain database and conserved domain architecture retrieval tool. ...
doi:10.1093/nar/29.1.11
pmid:11125038
pmcid:PMC29800
fatcat:mstubvho65h2noojeknidcplwi
Annotation of functional sites with the Conserved Domain Database
2012
Database: The Journal of Biological Databases and Curation
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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
Accuracy of structure-based sequence alignment of automatic methods
2007
BMC Bioinformatics
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Abbreviations Program names CE, Combinatorial Extension; DaliLite, standalone version of DALI (Distance mAtrix ALIgnment); DSSP, Definition of Secondary Structure of Proteins given a set of 3D coordinates ...
study, we evaluate CE, DaliLite, FAST, LOCK2, MATRAS, SHEBA and VAST in terms of the accuracy of the sequence alignments they produce, using sequence alignments from NCBI's human-curated Conserved Domain Database ...
We also thank the authors of CHIMERA and of the structure alignment programs for making their programs available. ...
doi:10.1186/1471-2105-8-355
pmid:17883866
pmcid:PMC2039753
fatcat:bt5mfakv4jdhjjtis6c263n7mi
Ligand Recognition Specificity of Leukocyte Integrin αMβ2 (Mac-1, CD11b/CD18) and Its Functional Consequences
2015
Biochemistry
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MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31, 474-477). Application of the developed algorithm (IRMA) to predict the α M I-domain binding sites in HMGN1. ...
The figure was constructed using the Entrez's 3D-structure database (Chen, J., Anderson, J.B., DeWeese-Scott, C., Fedorova, N.D., Geer, L.Y., He S., Hurwitz, D.I., Jackson, J.D., Jacobs, A.R., Lanczycki ...
doi:10.1021/bi5013782
pmid:25613106
pmcid:PMC4532391
fatcat:mi6ntjyms5b3fiicx2rb4hxd5i
Epitopes of human leukocyte antigen class I antibodies found in sera of normal healthy males and cord blood
2009
Human Immunology
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structure of an HLA-A0201 molecule 1QEW (Orth et al., MMDB: Entrez's 3D-structure database on the National Center for Biotechnology Information Web site) [10] . ...
positions within the antibodybinding span, estimated at 494 Å 2 (19 ϫ 26 Å) [7] or 750 Å 2 [8] , approximate distances in Ångstroms between two aa calculated with Cn3D Viewer software [9] and the 3D ...
doi:10.1016/j.humimm.2009.06.020
pmid:19580837
fatcat:t7xrpqkc65ahtfzgwbdei5ieqq
Binding MOAD (Mother Of All Databases)
2005
Proteins: Structure, Function, and Bioinformatics
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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. ...
Binding MOAD uses a Java 2 Enterprise Edition (J2EE) framework and 3-tier model (client, application, and database). ...
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]
2021
Zenodo
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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 ...
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 Does not collect, harmonize ...
We singled out titles in the CORD-19 database with desired relatability to the publication using the keywords: registry, registries, database, databases, platform, platforms, repository, repositories, ...
doi:10.5281/zenodo.5642634
fatcat:6iafdybbw5dd7ojjxzmlieckxq
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