Molecular Modeling Database (MMDB) Publications

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Citing the Molecular Modeling Database (MMDB)

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan 1;42(1):D297-303. Epub 2013 Dec 6. doi: 10.1093/nar/gkt1208. [PubMed PMID: 24319143] [Full Text at Oxford Academic] Click here to read

Additional Journal Articles

Pan Y, Cheng T, Wang Y, Bryant SH. Pathway Analysis for Drug Repositioning Based on Public Database Mining. J Chem Inf Model. 2014 Jan 26 (Epub ahead of print) doi: 10.1021/ci4005354 [PubMed PMID: 24460210] [Full Text at ACS Publications] Click here to read

Madej T, Addess KJ, Fong JH, Geer LY, Geer RC, Lanczycki CJ, Liu C, Lu S, Marchler-Bauer A, Panchenko AR, Chen J, Thiessen PA, Wang Y, Zhang D, Bryant SH. MMDB: 3D structures and macromolecular interactions. Nucleic Acids Res. 2012 Jan; 40(Database issue):D461-4. doi: 10.1093/nar/gkr1162. Epub 2011 Dec 1. doi: 10.1093/nar/gkr1162. [PubMed PMID: 22135289] [Full Text at Oxford Academic] Click here to read

Wang Y, Addess KJ, Chen J, Geer LY, He J, He S, Lu S, Madej T, Marchler-Bauer A, Thiessen PA, Zhang N, Bryant SH. MMDB: annotating protein sequences with Entrez's 3D-structure database. Nucleic Acids Res. 2007 Jan; 35(Database issue): D298-300. doi: 10.1093/nar/gkl952 [PubMed PMID: 17135201] [Full Text at Oxford Academic] Click here to read

Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 2003 Jan; 31(1): 474-7. [PubMed PMID: 12520055] [Full Text at Oxford Academic] Click here to read

Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH, Marchler-Bauer A, Panchenko AR, Shoemaker BA, Song JS, Thiessen PA, Yamashita RA, Bryant SH. MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 2002 Jan 1;30(1):249-52. [PubMed PMID: 11752307] [Full Text at Oxford Academic] Click here to read

Wang Y, Addess KJ, Geer L, Madej T, Marchler-Bauer A, Zimmerman D, Bryant SH. MMDB: 3D structure data in Entrez. Nucleic Acids Res. 2000 Jan 1;28(1):243-5. [PubMed PMID: 10592236] [Full Text at Oxford Academic] Click here to read

Marchler-Bauer A, Addess KJ, Chappey C, Geer L, Madej T, Matsuo Y, Wang Y, Bryant SH. MMDB: Entrez's 3D structure database. Nucleic Acids Res. 1999 Jan 1;27(1):240-3. [PubMed PMID: 9847190] [Full Text at Oxford Academic] Click here to read

Bryant SH and Hogue CW. Structural neighbors and structural alignments: The science behind Entrez/3D. Presented at the IUCr Macromolecular Crystallography Computing School, August 1996.

Hogue CW, Ohkawa H, Bryant SH. A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci. 1996 Jun;21(6):226-9. [PubMed PMID: 8744358] [Full Text at Elsevier]

Ohkawa H, Ostell J, Bryant S. MMDB: an ASN.1 specification for macromolecular structure. Proc Int Conf Intell Syst Mol Biol. 1995;3:259-67. [PubMed PMID: 7584445]

(See all publications about NCBI's 3D Macromolecular Structures Resources, including those listed here plus articles by the NCBI Structure group describing the results of computational biology research on the Molecular Modeling Database, such as 3D structure comparisons, biomolecular interactions, and more.)

Book Chapters

Sayers E. NCBI Protein Resources. IN The NCBI Handbook, 2nd edition [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2013 Nov. 12, 2013 [revised 2013 Nov. 21]. [cited 2017 Feb 02]. Available from /books/NBK169830/ in Entrez Books (/books).

Sayers E, Bryant SH. Macromolecular Structure Databases. Chapter 3 IN The NCBI Handbook [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, 2002 Oct. 9 [revised 2003 Aug. 13]. [cited 2009 Feb 04]. Available from /books/NBK21095/ in Entrez Books (/books).

Revised 21 February 2017