Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity
Identifieur interne : 000093 ( PascalFrancis/Corpus ); précédent : 000092; suivant : 000094Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity
Auteurs : David W. Ritchie ; Anisah W. Ghoorah ; Lazaros Mavridis ; Vishwesh VenkatramanSource :
- Bioinformatics : (Oxford. Print) [ 1367-4803 ] ; 2012.
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- Pascal (Inist)
English descriptors
- KwdEn :
Abstract
Motivation: Aligning and comparing protein structures is important for understanding their evolutionary and functional relationships. With the rapid growth of protein structure databases in recent years, the need to align, superpose and compare protein structures rapidly and accurately has never been greater. Many structural alignment algorithms have been described in the past 20 years. However, achieving an algorithm that is both accurate and fast remains a considerable challenge. Results: We have developed a novel protein structure alignment algorithm called 'Kpax', which exploits the highly predictable covalent geometry of Cα atoms to define multiple local coordinate frames in which backbone peptide fragments may be oriented and compared using sensitive Gaussian overlap scoring functions. A global alignment and hence a structural superposition may then be found rapidly using dynamic programming with secondary structure-specific gap penalties. When superposing pairs of structures, Kpax tends to give tighter secondary structure overlays than several popular structure alignment algorithms. When searching the CATH database, Kpax is faster and more accurate than the very efficient Yakusa algorithm, and it gives almost the same high level of fold recognition as TM-Align while being more than 100 times faster.
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| NO : | PASCAL 13-0022044 INIST |
|---|---|
| ET : | Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity |
| AU : | RITCHIE (David W.); GHOORAH (Anisah W.); MAVRIDIS (Lazaros); VENKATRAMAN (Vishwesh) |
| AF : | Inria Nancy, 615 Rue du Jardin Botanique/54600 Villers-lès-Nancy/France (1 aut., 2 aut.); Université de Lorraine, LORIA/54506 Nancy/France (2 aut.); University of St. Andrews/St. Andrews KY16 9AJ, Scotland/Royaume-Uni (3 aut.); Norwegian University of Science and Technology, Høgskoleringen 5/Trondheim/Norvège (4 aut.) |
| DT : | Publication en série; Niveau analytique |
| SO : | Bioinformatics : (Oxford. Print); ISSN 1367-4803; Royaume-Uni; Da. 2012; Vol. 28; No. 24; Pp. 3274-3281; Bibl. 1 p.1/4 |
| LA : | Anglais |
| EA : | Motivation: Aligning and comparing protein structures is important for understanding their evolutionary and functional relationships. With the rapid growth of protein structure databases in recent years, the need to align, superpose and compare protein structures rapidly and accurately has never been greater. Many structural alignment algorithms have been described in the past 20 years. However, achieving an algorithm that is both accurate and fast remains a considerable challenge. Results: We have developed a novel protein structure alignment algorithm called 'Kpax', which exploits the highly predictable covalent geometry of Cα atoms to define multiple local coordinate frames in which backbone peptide fragments may be oriented and compared using sensitive Gaussian overlap scoring functions. A global alignment and hence a structural superposition may then be found rapidly using dynamic programming with secondary structure-specific gap penalties. When superposing pairs of structures, Kpax tends to give tighter secondary structure overlays than several popular structure alignment algorithms. When searching the CATH database, Kpax is faster and more accurate than the very efficient Yakusa algorithm, and it gives almost the same high level of fold recognition as TM-Align while being more than 100 times faster. |
| CC : | 002A01B |
| FD : | Protéine; Structure; Chevauchement; Sonorisation (film); Fragment peptidique; Peptide; Similitude; Alignement structure |
| ED : | Protein; Structure; Overlap; Scoring; Peptide fragment; Peptides; Similarity |
| SD : | Proteína; Estructura; Imbricación; Sonorización (pelicula); Fragmento peptídico; Péptido; Similitud |
| LO : | INIST-21331.354000505476120160 |
| ID : | 13-0022044 |
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Pascal:13-0022044Le document en format XML
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Ritchie</name><affiliation><inist:fA14 i1="01"><s1>Inria Nancy, 615 Rue du Jardin Botanique</s1><s2>54600 Villers-lès-Nancy</s2><s3>FRA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ></inist:fA14></affiliation></author><author><name sortKey="Ghoorah, Anisah W" sort="Ghoorah, Anisah W" uniqKey="Ghoorah A" first="Anisah W." last="Ghoorah">Anisah W. Ghoorah</name><affiliation><inist:fA14 i1="01"><s1>Inria Nancy, 615 Rue du Jardin Botanique</s1><s2>54600 Villers-lès-Nancy</s2><s3>FRA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ></inist:fA14></affiliation><affiliation><inist:fA14 i1="02"><s1>Université de Lorraine, LORIA</s1><s2>54506 Nancy</s2><s3>FRA</s3><sZ>2 aut.</sZ></inist:fA14></affiliation></author><author><name sortKey="Mavridis, Lazaros" sort="Mavridis, Lazaros" uniqKey="Mavridis L" first="Lazaros" last="Mavridis">Lazaros Mavridis</name><affiliation><inist:fA14 i1="03"><s1>University of St. Andrews</s1><s2>St. Andrews KY16 9AJ, Scotland</s2><s3>GBR</s3><sZ>3 aut.</sZ></inist:fA14></affiliation></author><author><name sortKey="Venkatraman, Vishwesh" sort="Venkatraman, Vishwesh" uniqKey="Venkatraman V" first="Vishwesh" last="Venkatraman">Vishwesh Venkatraman</name><affiliation><inist:fA14 i1="04"><s1>Norwegian University of Science and Technology, Høgskoleringen 5</s1><s2>Trondheim</s2><s3>NOR</s3><sZ>4 aut.</sZ></inist:fA14></affiliation></author></analytic><series><title level="j" type="main">Bioinformatics : (Oxford. 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With the rapid growth of protein structure databases in recent years, the need to align, superpose and compare protein structures rapidly and accurately has never been greater. Many structural alignment algorithms have been described in the past 20 years. However, achieving an algorithm that is both accurate and fast remains a considerable challenge. Results: We have developed a novel protein structure alignment algorithm called 'Kpax', which exploits the highly predictable covalent geometry of C<sub>α</sub> atoms to define multiple local coordinate frames in which backbone peptide fragments may be oriented and compared using sensitive Gaussian overlap scoring functions. A global alignment and hence a structural superposition may then be found rapidly using dynamic programming with secondary structure-specific gap penalties. When superposing pairs of structures, Kpax tends to give tighter secondary structure overlays than several popular structure alignment algorithms. When searching the CATH database, Kpax is faster and more accurate than the very efficient Yakusa algorithm, and it gives almost the same high level of fold recognition as TM-Align while being more than 100 times faster.</div></front></TEI><inist><standard h6="B"><pA><fA01 i1="01" i2="1"><s0>1367-4803</s0></fA01><fA03 i2="1"><s0>Bioinformatics : (Oxf., Print)</s0></fA03><fA05><s2>28</s2></fA05><fA06><s2>24</s2></fA06><fA08 i1="01" i2="1" l="ENG"><s1>Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity</s1></fA08><fA11 i1="01" i2="1"><s1>RITCHIE (David W.)</s1></fA11><fA11 i1="02" i2="1"><s1>GHOORAH (Anisah W.)</s1></fA11><fA11 i1="03" i2="1"><s1>MAVRIDIS (Lazaros)</s1></fA11><fA11 i1="04" i2="1"><s1>VENKATRAMAN (Vishwesh)</s1></fA11><fA14 i1="01"><s1>Inria Nancy, 615 Rue du Jardin Botanique</s1><s2>54600 Villers-lès-Nancy</s2><s3>FRA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ></fA14><fA14 i1="02"><s1>Université de Lorraine, LORIA</s1><s2>54506 Nancy</s2><s3>FRA</s3><sZ>2 aut.</sZ></fA14><fA14 i1="03"><s1>University of St. Andrews</s1><s2>St. Andrews KY16 9AJ, Scotland</s2><s3>GBR</s3><sZ>3 aut.</sZ></fA14><fA14 i1="04"><s1>Norwegian University of Science and Technology, Høgskoleringen 5</s1><s2>Trondheim</s2><s3>NOR</s3><sZ>4 aut.</sZ></fA14><fA20><s1>3274-3281</s1></fA20><fA21><s1>2012</s1></fA21><fA23 i1="01"><s0>ENG</s0></fA23><fA43 i1="01"><s1>INIST</s1><s2>21331</s2><s5>354000505476120160</s5></fA43><fA44><s0>0000</s0><s1>© 2013 INIST-CNRS. All rights reserved.</s1></fA44><fA45><s0>1 p.1/4</s0></fA45><fA47 i1="01" i2="1"><s0>13-0022044</s0></fA47><fA60><s1>P</s1></fA60><fA61><s0>A</s0></fA61><fA64 i1="01" i2="1"><s0>Bioinformatics : (Oxford. Print)</s0></fA64><fA66 i1="01"><s0>GBR</s0></fA66><fC01 i1="01" l="ENG"><s0>Motivation: Aligning and comparing protein structures is important for understanding their evolutionary and functional relationships. With the rapid growth of protein structure databases in recent years, the need to align, superpose and compare protein structures rapidly and accurately has never been greater. Many structural alignment algorithms have been described in the past 20 years. However, achieving an algorithm that is both accurate and fast remains a considerable challenge. Results: We have developed a novel protein structure alignment algorithm called 'Kpax', which exploits the highly predictable covalent geometry of C<sub>α</sub> atoms to define multiple local coordinate frames in which backbone peptide fragments may be oriented and compared using sensitive Gaussian overlap scoring functions. A global alignment and hence a structural superposition may then be found rapidly using dynamic programming with secondary structure-specific gap penalties. When superposing pairs of structures, Kpax tends to give tighter secondary structure overlays than several popular structure alignment algorithms. 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Print); ISSN 1367-4803; Royaume-Uni; Da. 2012; Vol. 28; No. 24; Pp. 3274-3281; Bibl. 1 p.1/4</SO><LA>Anglais</LA><EA>Motivation: Aligning and comparing protein structures is important for understanding their evolutionary and functional relationships. With the rapid growth of protein structure databases in recent years, the need to align, superpose and compare protein structures rapidly and accurately has never been greater. Many structural alignment algorithms have been described in the past 20 years. However, achieving an algorithm that is both accurate and fast remains a considerable challenge. Results: We have developed a novel protein structure alignment algorithm called 'Kpax', which exploits the highly predictable covalent geometry of C<sub>α</sub> atoms to define multiple local coordinate frames in which backbone peptide fragments may be oriented and compared using sensitive Gaussian overlap scoring functions. A global alignment and hence a structural superposition may then be found rapidly using dynamic programming with secondary structure-specific gap penalties. When superposing pairs of structures, Kpax tends to give tighter secondary structure overlays than several popular structure alignment algorithms. When searching the CATH database, Kpax is faster and more accurate than the very efficient Yakusa algorithm, and it gives almost the same high level of fold recognition as TM-Align while being more than 100 times faster.</EA><CC>002A01B</CC><FD>Protéine; Structure; Chevauchement; Sonorisation (film); Fragment peptidique; Peptide; Similitude; Alignement structure</FD><ED>Protein; Structure; Overlap; Scoring; Peptide fragment; Peptides; Similarity</ED><SD>Proteína; Estructura; Imbricación; Sonorización (pelicula); Fragmento peptídico; Péptido; Similitud</SD><LO>INIST-21331.354000505476120160</LO><ID>13-0022044</ID></server></inist></record>Pour manipuler ce document sous Unix (Dilib)
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