DaliLite workbench for protein structure comparison

By Liisa Holm, Jong H. Park. 2000

929 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Molecular Biology

Citations in the corpus

Dali server update (2016, methodology): “There have been no major changes to the algorithms for structural alignment ((12,21,22); a full bibliography of methods is available from the Dali server web site).”
Analysis of CASP8 targets, predictions and assessment methods (2009, methodology): “Additionally, DALI (23) finds partial, but quite significant ( Z -score > 5) similarity to the cyclin fold, matching four out of five cyclin helices.”
Searching protein structure databases with DaliLite v.3 (2008, methodology): “The database search option DaliLite –quick compares a query structure to all structures in the PDB, as organized in the structural similarity graph.”
Structure of the Plasmodium 6-cysteine s48/45 domain (2012, methodology): “Structure similarity searches using the DaliLite (43) program indicate that the β-sandwich fold shared by s48/45 and the SRS superfamily is further related to comparable β-sandwich domains found in a diverse array of cellsurface molecules from various organisms (z > 4 in reciprocal structure similar”
ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. (2003, background): “In fact, a variety of methods exist for the structure-to-structure alignment of proteins (Holm and Park, 2000; Holm and Sander, 1996; Russell and Barton, 1992).”
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison (2002, methodology): “We have studied here both the Z-score (dali) and the percentage of superimposed residues (dali-sup) provided by the DaliLite package (Holm and Park 2000).”
Structural and Biochemical Characterization of Plasmodium falciparum 12 (Pf12) Reveals a Unique Interdomain Organization and the Potential for an Antiparallel Arrangement with Pf41* (2013, background): “Evolutionary Divergence between D1 and D2—To investigate the similarity of Pf12 to other structurally characterized proteins, a DaliLite search (63) was performed for Pf12 D1 and D2 separately.”