NCBI Structure Group Research

Senior Investigator: Stephen H. Bryant

Affiliation:

Computational Biology Branch,
National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM).
Contact: Dr. S. H. Bryant, Bldg. 38A, Room 5S504, NLM, NIH, 8600 Rockville Pike, Bethesda, MD 20894.
Tel: (301) 435-7792
Fax: (301) 480-9241 or (301) 435-7793
email bryant@ncbi.nlm.nih.gov

Selected Online Publications:

Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH. Refining multiple sequence alignments with conserved core regions. Nucleic Acids Res 2006; 34:2598-2606.

Panchenko AR, Madej T. Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol. Biol. 2005; 5:10.

Kann MG, Thiessen PA, Panchenko AR, Schaffer AA, Altschul SF, Bryant SH. A structure-based method for protein sequence alignment. Bioinformatics 2005; 21:1451-1456.

Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a Conserved Domain Databse for protein classification. Nucleic Acids Res. 2005; 33:192-196.

Panchenko AR, Wolf YI, Panchenko LA, Madej T. Evolutionary plasticity of protein families: coupling between sequence and structure variation. Proteins 2005; Nov 15;61(3):535-44.

Panchenko AR, Madej T. Analysis of protein homology by assessing the (dis)similarity in protein loop regions. Proteins 2004; 57(3) 539-547.

Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004; 32:327-331.

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; 31:474-477.

Marchler-Bauer A, 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 GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 2003; 31:383-387.

Geer LY, Domrachev M, Lipman DJ, Bryant SH. CDART: protein homology by domain architecture. Genome Res. 2002; 12:1619-1623.

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; 30:249-252.

Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 2002; 30:281-283.

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; 28:243-245.

Panchenko A, Marchler-Bauer A, Bryant SH. Threading with Explicit Models for Evolutionary Conservation of Structure and Sequence. Proteins Suppl 1999; 3:133-140.

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; 27:240-243.

Hogue CWV. Cn3D: a new generation of three-dimensional molecular structure viewer. Trends Biochem Sci 1997; 22:314-316.

Marchler-Bauer A, Bryant SH. A measure of success in fold recognition. Trends Biochem Sci 1997; 22:236-240.

Hogue CWV, Ohkawa H, Bryant SH. A dynamic look at structures: WWW-Entrez and the molecular modeling database. Trends Biochem. Sci 1996; 21:226-229.