Surprising similarities in structure comparison.

By Jean-François Gibrat, T. Madej, Stephen H. Bryant. 1996

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Citations in the corpus

Assessment of CASP10 contact‐assisted predictions (2014, methodology): “22–25) and have been To measure community-wide improvement, we performed t -tests for each target on all, not just the best, aided predictions versus all unaided predictions from those groups who submitted both predictions.”
Database resources of the National Center for Biotechnology Information: update (2004, methodology): “MMDB provides structural neighbors for each record based on similarities computed by the VAST algorithm between compact structural domains within protein structures (43, 44) .”
Rapid 3D protein structure database searching using information retrieval techniques (2004, unknown): “The classical pairwise comparison methods include SSAP (Orengo and Taylor, 1996), DALI (Holm and Sander, 1993), VAST (Gibrat et al., 1996) and CE (Shindyalov and Bourne, 1998).”
Tools for integrated sequence-structure analysis with UCSF Chimera (2006, methodology): “Cn3D [22] aligns structures using VAST (Vector Alignment Search Tool) [30], which pairs secondary structure elements of similar types, orientations, and connec-tivities.”
Database resources of the National Center for Biotechnology Information (2009, methodology): “The NCBI MMDB (46) contains experimentally determined coordinate sets from the Protein Data Bank (47), augmented with domain annotations and links to relevant literature, protein and nucleotide sequences, chemicals (PDB heterogens) and conserved domains in CDD (48) as well as structural neighbors co”
Sequence and structural analysis of BTB domain proteins (2005, methodology): “Materials and methods Structure alignment Twenty-five entries comprising nine unique BTB structures were retrieved from the PDB with DALI [116], CE [117] and VAST [118] structure superposition searches.”
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison (2002, methodology): “MAMMOTH provides structural alignments similar to those obtained by other approaches such as Dali (Holm and Sander 1993), Vast (Madej et al. 1995; Gibrat et al. 1996), ProSup (Lackner et al.”
HorA web server to infer homology between proteins using sequence and structural similarity (2009, unknown): “DALI (10), VAST (11), CE (12), SSM (13), MATRAS (14) and 3D-BLAST (15).”
Finding weak similarities between proteins by sequence profile comparison. (2003, methodology): “The list of structure neighbors is distributed with Entrez and structure±structure alignments in this set are computed by the VAST algorithm (24,25) based on complete chains or domains.”
The Use of a Conformational Alphabet for Fast Alignment of Protein Structures (2008, background): “…DALI identifies interaction patterns of fragment pairs (Holm and Sander, 1997), VAST describes secondary structure elements (SSEs) as a set of vectors (Gibrat et al., 1996) while CE designates short similar fragment pairs (SFPs) of local structural similarities (Shindyalov and Bourne, 1998).”
Database resources of the National Center for Biotechnology Information (2010, methodology): “Compact structural domains within protein structures are stored in the 3D Domains database, and structural neighbors computed by the VAST algorithm (59,60) are available for structures containing these domains.”
A study of quality measures for protein threading models (2001, methodology): “(cid:127) covr CASP2 The coverage reports the fraction of the reconstructed model alignment that has been aligned as well by VAST [27], expressed as a percentage.”