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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.  ...  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

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: 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.  ...  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

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.  ...  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

Ayisha Amanullah, Suad Naheed
2018 RADS Journal of Biological Research & Applied Science  
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

A. Marchler-Bauer
2004 Nucleic Acids Research  
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

D. L. Wheeler
2001 Nucleic Acids Research  
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

M. K. Derbyshire, C. J. Lanczycki, S. H. Bryant, A. Marchler-Bauer
2012 Database: The Journal of Biological Databases and Curation  
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

Changhoon Kim, Byungkook Lee
2007 BMC Bioinformatics  
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

Nataly P. Podolnikova, Andriy V. Podolnikov, Thomas A. Haas, Valeryi K. Lishko, Tatiana P. Ugarova
2015 Biochemistry  
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

Nadim El-Awar, Paul I. Terasaki, Anh Nguyen, Nori Sasaki, Luis E. Morales-Buenrostro, Hiroh Saji, Etsuko Maruya, Francesca Poli
2009 Human Immunology  
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)

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.  ...  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]

Lauren Maxwell, Priya Shreedhar, Delphine Dauga, Peter McQuilton, Robert F Terry, Alisa Denisiuk, Fruzsina Molnar-Gabor, Abha Saxena, Susanna-Assunta Sansone
2021 Zenodo  
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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