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CLICK—topology-independent comparison of biomolecular 3D structures
Our server, CLICK: http://mspc.bii.a-star.edu.sg/click, is capable of superimposing the 3D structures of any pair of biomolecules (proteins, DNA, RNA, etc.). The server makes use of the Cartesian coordinates of the molecules with the option of using other structural features such as secondary struct...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125785/ https://www.ncbi.nlm.nih.gov/pubmed/21602266 http://dx.doi.org/10.1093/nar/gkr393 |
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author | Nguyen, M. N. Tan, K. P. Madhusudhan, M. S. |
author_facet | Nguyen, M. N. Tan, K. P. Madhusudhan, M. S. |
author_sort | Nguyen, M. N. |
collection | PubMed |
description | Our server, CLICK: http://mspc.bii.a-star.edu.sg/click, is capable of superimposing the 3D structures of any pair of biomolecules (proteins, DNA, RNA, etc.). The server makes use of the Cartesian coordinates of the molecules with the option of using other structural features such as secondary structure, solvent accessible surface area and residue depth to guide the alignment. CLICK first looks for cliques of points (3–7 residues) that are structurally similar in the pair of structures to be aligned. Using these local similarities, a one-to-one equivalence is charted between the residues of the two structures. A least square fit then superimposes the two structures. Our method is especially powerful in establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants. CLICK has been extensively benchmarked and compared with other popular methods for protein and RNA structural alignments. In most cases, CLICK alignments were statistically significantly better in terms of structure overlap. The method also recognizes conformational changes that may have occurred in structural domains or subdomains in one structure with respect to the other. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server. |
format | Online Article Text |
id | pubmed-3125785 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31257852011-07-05 CLICK—topology-independent comparison of biomolecular 3D structures Nguyen, M. N. Tan, K. P. Madhusudhan, M. S. Nucleic Acids Res Articles Our server, CLICK: http://mspc.bii.a-star.edu.sg/click, is capable of superimposing the 3D structures of any pair of biomolecules (proteins, DNA, RNA, etc.). The server makes use of the Cartesian coordinates of the molecules with the option of using other structural features such as secondary structure, solvent accessible surface area and residue depth to guide the alignment. CLICK first looks for cliques of points (3–7 residues) that are structurally similar in the pair of structures to be aligned. Using these local similarities, a one-to-one equivalence is charted between the residues of the two structures. A least square fit then superimposes the two structures. Our method is especially powerful in establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants. CLICK has been extensively benchmarked and compared with other popular methods for protein and RNA structural alignments. In most cases, CLICK alignments were statistically significantly better in terms of structure overlap. The method also recognizes conformational changes that may have occurred in structural domains or subdomains in one structure with respect to the other. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server. Oxford University Press 2011-07-01 2011-05-20 /pmc/articles/PMC3125785/ /pubmed/21602266 http://dx.doi.org/10.1093/nar/gkr393 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Nguyen, M. N. Tan, K. P. Madhusudhan, M. S. CLICK—topology-independent comparison of biomolecular 3D structures |
title | CLICK—topology-independent comparison of biomolecular 3D structures |
title_full | CLICK—topology-independent comparison of biomolecular 3D structures |
title_fullStr | CLICK—topology-independent comparison of biomolecular 3D structures |
title_full_unstemmed | CLICK—topology-independent comparison of biomolecular 3D structures |
title_short | CLICK—topology-independent comparison of biomolecular 3D structures |
title_sort | click—topology-independent comparison of biomolecular 3d structures |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125785/ https://www.ncbi.nlm.nih.gov/pubmed/21602266 http://dx.doi.org/10.1093/nar/gkr393 |
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