3-Dimensional Structures

NCBI Home NCBI Site Map      brief/complete Course Description Schedule Introduction Genetics Review Types of Databases Format of Sequence Record Entrez BLAST 3-D Structures Genomes and Maps Librarian Roles WWW Sites Glossaries and Dictionaries

Databases MMDB: Molecular Modeling Database drawn from PDB sequence and structure integration extensive validation explicit chemical graph showing the bonding between atoms atomic substructure classification direct 3-D structure comparisons using the VAST (Vector Alignment Search Tool) algorithm to identify structural neighbors. PDB: Protein Data Bank accepts direct submissions of structure data includes structures solved by X-ray crystallography and nuclear magnetic resonance (NMR) refer to PDB web site for more information Sample Record view the record for 1AMC, Alzheimer's Disease Amyloid Beta-Peptide (Residues 1 - 28), in PDB format p53 Tumor Suppressor retrieve the 1TUP structure record from MMDB Tumor Suppressor P53 Complexed With DNA view structure summary launch Cn3D viewer to see the default Cn3D subset experiment with the various controls Structure Viewers Cn3D: "See in 3-D" http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html Stand-alone software or component of Network Entrez. Kinemage http://www.ncbi.nlm.nih.gov/Structure/CN3D/mage.html Rasmol http://www.ncbi.nlm.nih.gov/Structure/CN3D/rasmol.html VAST Structure Similarity Searching Vector Alignment Search Tool pre-computed VAST neighbors for each structure in Entrez/MMDB on-the-fly VAST search tool for neighboring new structures to those in MMDB Exercises tour the Cn3D tutorial References Articles: Gibrat J.F., Madej T., Bryant S.H. 1996. Surprising similarities in structure comparison. Curr Opin Struct Biol. 6(3):377-385 [PubMed] Hogue, C.W., H. Ohkawa, and S.H. Bryant. 1996. A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends in Biochemical Sciences 21:226-229. [PubMed] Hogue C.W.V. 1997. Cn3D: a new generation of three-dimensional molecular structure viewer. Trends in Biochemical Sciences 22:314-316. [PubMed] Marchler-Bauer, A., Addess, K.J., Chappey, C., Geer, L., Madej, T., Matsuo, Y., Wang, Y., Bryant, S.H. 1999. MMDB: Entrez's 3D structure database. Nucleic Acids Research. 27(1):240-243. [PubMed] Additional Resources: Bryant, S.H. and Hogue, C.W.V. 1996. Structural Neighbors and Structural Alignments: The Science Behind Entrez/3D. Presented at the IUCr Macromolecular Crystallography Computing School, August, 1996. http://www.ncbi.nlm.nih.gov/Structure/RESEARCH/iucrabs.html MMDB: A Molecular Modeling Database. NCBI News, March 1995 http://www.ncbi.nlm.nih.gov/Web/Newsltr/mar95.html#mmdb Structure Neighbors. NCBI News, August 1997 http://www.ncbi.nlm.nih.gov/Web/Newsltr/aug97.html#Neighbors

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Revised March 30, 2001 Comments/questions about course to Renata Geer renata@ncbi.nlm.nih.gov Questions about NCBI resources to info@ncbi.nlm.nih.gov