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CASP3

1998 Structure prediction experiment

CASP2

1996 Structure prediction experiment

Threading

Protein Fold Recognition


MMDB

NCBI's structure database

PDBeast

Taxonomy in MMDB

Cn3D v4.1

3D-structure viewer

VAST

Structure comparisons

VAST Search

Submit structure database searches

CDD

Conserved Domain Database


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
email bryant@ncbi.nlm.nih.gov

Comparative macromolecular 3D-structure analysis

Cn3D: Visualization of 3D structures and alignments

MMDB: "Computer-friendly" structure database

Threading: Algorithms for protein fold recognition

VAST: Protein structure-structure comparisons

CDD: A Conserved Domain Database

Entrez3D: WWW-retrieval tools for all of the above

Selected Online Publications:

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.


see also:

1995: Successful Leptin structure prediction

Personnel (Click on link to send E-mail):

Tom Madej
Aron Marchler-Bauer
Yanli Wang
Anna Panchenko
Lewis Geer
Jie Chen
Paul Thiessen
David Hurwitz
Ben Shoemaker
Siqian He
Natasha Sefcovic
John Anderson
Roxanne Yamashita
Cynthia Liebert
James Song
Gabriele Marchler
Maricel Kann
Hsin-Yi Tsang
Carol DeWeese-Scott
Christopher Lanczycki
John Jackson
Chunlei Liu
Jodie Yin
Vahan Simonyan Kenneth Evan Thompson
Ming Xu
Praveen Cherukuri
Evan Bolton
Wolf-Dietrich Ihlenfeldt
Jeff Zhang
Jane He
Shennan Lu
Jewen Xiao
Dachuan Zhang
Marc Gwadz
Mikhail Mullokandov
Fu Lu
Saikat Chakrabarti
Zhaoxi Ke
Luning Hao
Myra Derbyshire
Abby Ngau NEW!
Noreen Gonzales NEW!

Structure Group Alumni (addresses):

Francois Major
Jean-Francois Gibrat
Hitomi Ohkawa
Christopher Hogue
Qiuwei Xu
Yo Matsuo
Wei Ding
Ken Addess
Naomi Ariel
Diane Zimmerman
Anastasia Nikolskaya
Raja Mazumder
Natalie Fedorova
Aviva Jacobs
Sona Vasudevan
B. Sridhar Rao

Publications in Entrez



Updated 10/18/04

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