DOI: 10.1093/bioinformatics/btn507. Searching protein structure databases with DaliLite v.3

Searching protein structure databases with DaliLite v.3

10.1093/bioinformatics/btn507

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

Abstract 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

Bibliography

Holm, L., KÃ¤Ã¤riÃ¤inen, S., RosenstrÃ¶m, P., & Schenkel, A. (2008). Searching protein structure databases with DaliLite v.3. Bioinformatics, 24(23), 2780â2781.

Authors 4

L. Holm (first)
S. Kääriäinen (additional)
P. Rosenström (additional)
A. Schenkel (additional)

References 7 Referenced 900

10.1093/bioinformatics/btm358 / Bioinformatics / The global trace graph, a novel paradigm for searching protein sequence databases by Heger (2007)
10.1093/bioinformatics/16.6.566 / Bioinformatics / DaliLite workbench for protein structure comparison by Holm (2000)
10.1002/prot.340190302 / Proteins / Searching protein structure databases has come of age by Holm (1994)
10.1093/bioinformatics/btl158 / Bioinformatics / Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences by Li (2006)
10.1016/S0022-2836(05)80134-2 / J. Mol. Biol. / SCOP: a structural classification of proteins database for the investigation of sequences and structures by Murzin (1995)
{'key': '2023020212234187600_B6', 'first-page': '2256', 'article-title': 'Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions', 'volume-title': 'Acta Cryst.', 'author': 'Krissinel', 'year': '2004'} / Acta Cryst. / Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions by Krissinel (2004)
10.1110/ps.03328504 / Protein Sci. / Sensitivity and selectivity in protein structure comparison by Sierk (2004)

Dates

Type	When
Created	16 years, 11 months ago (Sept. 25, 2008, 8:13 p.m.)
Deposited	2 years, 6 months ago (Feb. 2, 2023, 9:53 a.m.)
Indexed	4 days, 3 hours ago (Aug. 23, 2025, 1:04 a.m.)
Issued	16 years, 11 months ago (Sept. 25, 2008)
Published	16 years, 11 months ago (Sept. 25, 2008)
Published Online	16 years, 11 months ago (Sept. 25, 2008)
Published Print	16 years, 8 months ago (Dec. 1, 2008)

Funders 0

None

BibTeX

@article{Holm_2008, title={Searching protein structure databases with DaliLite v.3}, volume={24}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btn507}, DOI={10.1093/bioinformatics/btn507}, number={23}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Holm, L. and Kääriäinen, S. and Rosenström, P. and Schenkel, A.}, year={2008}, month=sep, pages={2780–2781} }

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