Searching protein structure databases with DaliLite v.3
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 reve...
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| Published in | Bioinformatics Vol. 24; no. 23; pp. 2780 - 2781 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
01.12.2008
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/btn507 |
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| 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 |
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| AbstractList | 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 The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis CarrolMotivation: 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. 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 The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis CarrolUNLABELLEDThe Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis CarrolNewly 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.MOTIVATIONNewly 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.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.AVAILABILITYThe 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. The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis Carrol 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. 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. 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 |
| Author | Rosenström, P. Schenkel, A. Holm, L. Kääriäinen, S. |
| AuthorAffiliation | 1 Department of Biological and Environmental Sciences, and 2 Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland |
| AuthorAffiliation_xml | – name: 1 Department of Biological and Environmental Sciences, and 2 Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland |
| Author_xml | – sequence: 1 givenname: L. surname: Holm fullname: Holm, L. organization: Department of Biological and Environmental Sciences, and Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland – sequence: 2 givenname: S. surname: Kääriäinen fullname: Kääriäinen, S. organization: Department of Biological and Environmental Sciences, and Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland – sequence: 3 givenname: P. surname: Rosenström fullname: Rosenström, P. organization: Department of Biological and Environmental Sciences, and Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland – sequence: 4 givenname: A. surname: Schenkel fullname: Schenkel, A. organization: Department of Biological and Environmental Sciences, and Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20875954$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/18818215$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/bioinformatics/btm358 10.1110/ps.03328504 10.1002/prot.340190302 10.1016/S0022-2836(05)80134-2 10.1093/bioinformatics/16.6.566 10.1093/bioinformatics/btl158 |
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| References | Sierk (2023020212234187600_B7) 2004; 13 Holm (2023020212234187600_B2) 2000; 16 Murzin (2023020212234187600_B5) 1995; 247 Heger (2023020212234187600_B1) 2007; 23 Holm (2023020212234187600_B3) 1994; 19 Krissinel (2023020212234187600_B6) 2004 Li (2023020212234187600_B4) 2006; 22 10980157 - Bioinformatics. 2000 Jun;16(6):566-7 7937731 - Proteins. 1994 Jul;19(3):165-73 14978311 - Protein Sci. 2004 Mar;13(3):773-85 7723011 - J Mol Biol. 1995 Apr 7;247(4):536-40 16731699 - Bioinformatics. 2006 Jul 1;22(13):1658-9 15572779 - Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68 17823134 - Bioinformatics. 2007 Sep 15;23(18):2361-7 |
| References_xml | – volume: 23 start-page: 2361 year: 2007 ident: 2023020212234187600_B1 article-title: The global trace graph, a novel paradigm for searching protein sequence databases publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm358 – volume: 13 start-page: 773 year: 2004 ident: 2023020212234187600_B7 article-title: Sensitivity and selectivity in protein structure comparison publication-title: Protein Sci. doi: 10.1110/ps.03328504 – start-page: 2256 volume-title: Acta Cryst. year: 2004 ident: 2023020212234187600_B6 article-title: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions – volume: 19 start-page: 165 year: 1994 ident: 2023020212234187600_B3 article-title: Searching protein structure databases has come of age publication-title: Proteins doi: 10.1002/prot.340190302 – volume: 247 start-page: 536 year: 1995 ident: 2023020212234187600_B5 article-title: SCOP: a structural classification of proteins database for the investigation of sequences and structures publication-title: J. Mol. Biol. doi: 10.1016/S0022-2836(05)80134-2 – volume: 16 start-page: 566 year: 2000 ident: 2023020212234187600_B2 article-title: DaliLite workbench for protein structure comparison publication-title: Bioinformatics doi: 10.1093/bioinformatics/16.6.566 – volume: 22 start-page: 1658 year: 2006 ident: 2023020212234187600_B4 article-title: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl158 – reference: 17823134 - Bioinformatics. 2007 Sep 15;23(18):2361-7 – reference: 10980157 - Bioinformatics. 2000 Jun;16(6):566-7 – reference: 7723011 - J Mol Biol. 1995 Apr 7;247(4):536-40 – reference: 16731699 - Bioinformatics. 2006 Jul 1;22(13):1658-9 – reference: 14978311 - Protein Sci. 2004 Mar;13(3):773-85 – reference: 7937731 - Proteins. 1994 Jul;19(3):165-73 – reference: 15572779 - Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2256-68 |
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| Snippet | 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... 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... 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... The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis Carrol Newly solved protein structures are routinely scanned... 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... The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis CarrolMotivation: Newly solved protein structures are routinely... The Red Queen said, 'It takes all the running you can do, to keep in the same place.' Lewis CarrolUNLABELLEDThe Red Queen said, 'It takes all the running you... |
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| SubjectTerms | Algorithms Applications Note Biological and medical sciences Database searching Databases, Protein Fundamental and applied biological sciences. Psychology General aspects Internet Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Proteins - chemistry Sequence Analysis, Protein Software |
| Title | Searching protein structure databases with DaliLite v.3 |
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