Nucleic Acids Research, 2002, Vol. 30, No. 1 260-263
© 2002 Oxford University Press
ASTRAL compendium enhancements
1Berkeley Structural Genomics Center, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA, 3MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK and 4Department of Structural Biology, D-109 Fairchild, Stanford University, Stanford, CA, USA
The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these sequences and domain structures. Several major improvements have been made to the ASTRAL compendium since its initial release 2 years ago. The number of protein domain sequences included has doubled from 15 190 to 30 867, and additional databases have been added. The Rapid Access Format (RAF) database contains manually curated mappings linking the biological amino acid sequences described in the SEQRES records of PDB entries to the amino acid sequences structurally observed (provided in the ATOM records) in a format designed for rapid access by automated tools. This information is used to derive sequences for protein domains in the SCOP database. In cases where a SCOP domain spans several protein chains, all of which can be traced back to a single genetic source, a ‘genetic domain’ sequence is created by concatenating the sequences of each chain in the order found in the original gene sequence. Both the original-style library of SCOP sequences and a new library including genetic domain sequences are available. Selected representative subsets of each of these libraries, based on multiple criteria and degrees of similarity, are also included. ASTRAL may be accessed at http://astral.stanford.edu/.
* To whom correspondence should be addressed at: Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA. Tel: +1 510 643 9131; Fax: +1 208 279 8978; Email: brenner{at}compbio.berkeley.edu
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. A. C. Beck, D. O. V. Alonso, D. Inoyama, and V. Daggett The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins PNAS, August 26, 2008; 105(34): 12259 - 12264. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A.C. Beck, A. L. Jonsson, R. D. Schaeffer, K. A. Scott, R. Day, R. D. Toofanny, D. O.V. Alonso, and V. Daggett Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations Protein Eng. Des. Sel., June 1, 2008; 21(6): 353 - 368. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J.-M. Chandonia StrBioLib: a Java library for development of custom computational structural biology applications Bioinformatics, August 1, 2007; 23(15): 2018 - 2020. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Pandini, G. Mauri, A. Bordogna, and L. Bonati Detecting similarities among distant homologous proteins by comparison of domain flexibilities Protein Eng. Des. Sel., June 30, 2007; (2007) gzm021v2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Portugaly, N. Linial, and M. Linial EVEREST: a collection of evolutionary conserved protein domains Nucleic Acids Res., January 12, 2007; 35(suppl_1): D241 - D246. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-K. Yu, E. M. Gertz, R. Agarwala, A. A. Schaffer, and S. F. Altschul Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches Nucleic Acids Res., November 6, 2006; 34(20): 5966 - 5973. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. A. Fodor and R. W. Aldrich Statistical Limits to the Identification of Ion Channel Domains by Sequence Similarity J. Gen. Physiol., May 30, 2006; 127(6): 755 - 766. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. A. Price, G. E. Crooks, R. E. Green, and S. E. Brenner Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap Bioinformatics, October 15, 2005; 21(20): 3824 - 3831. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Kolodny, L. Guibas, M. Levitt, and P. Koehl Inverse Kinematics in Biology: The Protein Loop Closure Problem The International Journal of Robotics Research, February 1, 2005; 24(2-3): 151 - 163. [Abstract] [PDF]
|
|
|
|
|
|
R. I. Dima and D. Thirumalai Probing the instabilities in the dynamics of helical fragments from mouse PrPC PNAS, October 26, 2004; 101(43): 15335 - 15340. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I.-G. Choi, J. Kwon, and S.-H. Kim Local feature frequency profile: A method to measure structural similarity in proteins PNAS, March 16, 2004; 101(11): 3797 - 3802. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-M. Chandonia, G. Hon, N. S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S. E. Brenner The ASTRAL Compendium in 2004 Nucleic Acids Res., January 1, 2004; 32(90001): D189 - 192. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Fleming, A. Muller, R. M. MacCallum, and M. J. E. Sternberg 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes Nucleic Acids Res., January 1, 2004; 32(90001): D245 - 250. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Vogel, S. A. Teichmann, and C. Chothia The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity Development, December 22, 2003; 130(25): 6317 - 6328. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Bienkowska, H. Hartman, and T. F. Smith A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells? Protein Eng. Des. Sel., December 1, 2003; 16(12): 897 - 904. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. M. Babu NCI: a server to identify non-canonical interactions in protein structures Nucleic Acids Res., July 1, 2003; 31(13): 3345 - 3348. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Linding, R. B. Russell, V. Neduva, and T. J. Gibson GlobPlot: exploring protein sequences for globularity and disorder Nucleic Acids Res., July 1, 2003; 31(13): 3701 - 3708. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Du, M. Andrec, and R. M. Levy Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update Protein Eng. Des. Sel., June 1, 2003; 16(6): 407 - 414. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lo Conte, S. E. Brenner, T. J. P. Hubbard, C. Chothia, and A. G. Murzin SCOP database in 2002: refinements accommodate structural genomics Nucleic Acids Res., January 1, 2002; 30(1): 264 - 267. [Abstract] [Full Text] [PDF]
|
|