Searching protein structure databases with DaliLite v.3

By Liisa Holm, S. Kääriäinen, Päivi Rosenström, Alain Schenkel. Bioinform., 2008

1,046 citations recorded by the source corpus.

The Red Queen said, ‘It takes all the running you can do, to keep in the same place.’ Lewis Carrol Motivation: Newly solved protein structures are routinely scanned against structures already in the Protein Data Bank (PDB) using Internet servers. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The number of known structures continues to grow exponentially. Sensitive—thorough but slow—search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the PDB than seconds in a day. The brute-force solution would be to distribute the individual comparisons on a massively parallel computer. A frugal solution, as implemented in the Dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. This note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a PC. Availability: The Dali server for protein structure database searching at http://ekhidna.biocenter.helsinki.fi/dali_server is running DaliLite v.3. The software can be downloaded for academic use from http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3. Contact: liisa.holm@helsinki.fi

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b9c2d0d60a98bb12045efa70569b003a6497ed88

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Citations in the corpus

Structural basis for a bacterial Pip system plant effector recognition protein (2021, background): “A Dali search (20) of the Protein Data Bank identified >40 similar structures (Z-scores >20; average rms distance, 2.”
Structural ties between cholesterol transport and morphogen signaling. (2009, background): “The Dali program for superimposing protein structures (Holm et al., 2008) reveals a highly significant structural homology between the similar length chains of NPC1 and RBP (224 and 212 amino acids, respectively; Z score = 7.6, rmsd = 3.7 Å over 135 aligned residues with 20% identity).”
Dali server: structural unification of protein families (2022, neutral): “The Dali server applies a heuristic strategy to search the PDB exploiting a network of known structural similarities that has been built up incrementally for decades (35).”
CASP9 Target Classification (2011, background): “12 Several cases of unusual structural differences revealed in this inspection between the targets and templates with detectable sequence similarities are discussed below.”
Advances and pitfalls of protein structural alignment. (2009, background): “Þ (to be minimized) Similarity index (SI) [11] Norm 1 (cid:4) 1 þ N e ð 1 þ rmsd = 1 : 5 Þð 1 þ min ð N A ; N B ÞÞ Match index (MI) [11] Norm max u 2 PUU ð A Þ ; 2 PUU ð B Þ 0 : 5 Dali’s empirical Z -score.”
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).”
PROTEIN STRUCTURE PREDICTION CENTER IN CASP8 (2009, background): “Registrations were possible in several participation roles, including (1) a human-expert group; (2) a server group; (3) an extended timeframe group (for participants relying on computationally intensive prediction methods); (4) a member of a prediction group; or (5) an observer.”
Dali server: conservation mapping in 3D (2010, methodology): “The Dali server has been around for 15 years in various incar-nations (2,8).”
Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA (2016, background): “Only five structural homologs of the FPA SPOC domain were found in the Protein Data Bank with the DaliLite server [17], suggesting that the SPOC domain structure is relatively unique.”
mTM-align: a server for fast protein structure database search and multiple protein structure alignment (2018, methodology): “If hits are found, a procedure called ‘walk’ (please note that the name and the idea of walk were from the Dali server papers (2,13)) is used to find more similar structures in NRDB (introduced in the next para-graph).”