Representing and comparing protein structures as paths in three-dimensional space
<p>Abstract</p> <p>Background</p> <p>Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction.</p> <p>Results<...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2006-10-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/7/460 |
| _version_ | 1818835851922112512 |
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| author | Pevzner Pavel Cao Haibo Krishna S Sri Zhi Degui Godzik Adam |
| author_facet | Pevzner Pavel Cao Haibo Krishna S Sri Zhi Degui Godzik Adam |
| author_sort | Pevzner Pavel |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction.</p> <p>Results</p> <p>We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure.</p> <p>Conclusion</p> <p>Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver.</p> |
| first_indexed | 2024-12-19T02:57:17Z |
| format | Article |
| id | doaj.art-e461289879ea492d94e996f6c0c9bb12 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-19T02:57:17Z |
| publishDate | 2006-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e461289879ea492d94e996f6c0c9bb122022-12-21T20:38:19ZengBMCBMC Bioinformatics1471-21052006-10-017146010.1186/1471-2105-7-460Representing and comparing protein structures as paths in three-dimensional spacePevzner PavelCao HaiboKrishna S SriZhi DeguiGodzik Adam<p>Abstract</p> <p>Background</p> <p>Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction.</p> <p>Results</p> <p>We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure.</p> <p>Conclusion</p> <p>Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver.</p>http://www.biomedcentral.com/1471-2105/7/460 |
| spellingShingle | Pevzner Pavel Cao Haibo Krishna S Sri Zhi Degui Godzik Adam Representing and comparing protein structures as paths in three-dimensional space BMC Bioinformatics |
| title | Representing and comparing protein structures as paths in three-dimensional space |
| title_full | Representing and comparing protein structures as paths in three-dimensional space |
| title_fullStr | Representing and comparing protein structures as paths in three-dimensional space |
| title_full_unstemmed | Representing and comparing protein structures as paths in three-dimensional space |
| title_short | Representing and comparing protein structures as paths in three-dimensional space |
| title_sort | representing and comparing protein structures as paths in three dimensional space |
| url | http://www.biomedcentral.com/1471-2105/7/460 |
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