The ASTRAL Compendium in 2004

By John-Marc Chandonia, Gary Chung Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner. 2003

574 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Data growth and its impact on the SCOP database: new developments (2007, methodology): “The sequences and structures of SCOP domains are available from the ASTRAL compendium ( 4 ), and hidden Markov models of SCOP domains are available from the SUPERFAMILY database (5).”
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison (2010, methodology): “Here, we used SCOP [24] (1.71) protein structures and corresponding ASTRAL [13] sequences.”
PROMALS3D: a tool for multiple protein sequence and structure alignments (2008, methodology): “To identify homologs with known structures for target sequences, we used the ASTRAL SCOP40 structural domain database ( 14 ,15) (version 1.69, 7290 domains, with <40% sequence identity to each other).”
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations (2014, methodology): “66% of the dataset was not evaluated by nsSNPAnalyzer due to a requirement for the existence of a homologous protein to the investigated sequence in the ASTRAL database [53], a condition which was not fulfilled by many protein sequences in PredictSNP benchmark dataset.”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, methodology): “If there is no existing assignment, then the sequences will be compared with the SCOP domain sequences from ASTRAL ( 4 ) using BLAST (5).”
Clustered Sequence Representation for Fast Homology Search (2007, unknown): “For our assessments, we used version 1.65 of the ASTRAL Compendium (Chandonia et al., 2004) that uses information from the SCOP database (Murzin et al., 1995; Andreeva et al., 2004) to classify sequences with fold, superfamily, and family information.”
TALE: A Tool for Approximate Large Graph Matching (2008, methodology): “The number of protein structures (graphs) in the ASTRAL database [8] has increased more than 3 folds since 2002.”
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures (2019, methodology): “Previously, the SCOP domain sequences were derived from the PDB files and together with the representative subsets were provided by Astral (9).”
Fast Multiple Alignment of Protein Structures Using Conformational Letter Blocks (2009, methodology): “ASTRAL40 is extracted from %40 percentage identity filtered ASTRAL SCOP genetic domain sequence subsets [34].”
SCOP database in 2004: refinements integrate structure and sequence family data (2004, methodology): “The sequences and structures of SCOP domains are available from the ASTRAL compendium ( 6 ), and hidden Markov models of SCOP domains are available from the SUPERFAMILY database (7).”
PDBselect 1992–2009 and PDBfilter-select (2009, methodology): “One of the successors of PDBselect, ASTRAL ( 3 ), uses a similar measure supplemented by stereochemical checks from PROCHECK (4) and WHAT_CHECK (5).”
The ProDom database of protein domain families: more emphasis on 3D (2004, methodology): “Among these families, 21 families were derived from in-house expertise and 1352 structural domain families were selected from SCOP release 1.63 (9) using the ASTRAL compendium ( 10 ) on the basis of the following criteria: (i) length homogeneity (the shortest sequence should be at most 25% shorter t”