Optimal contact definition for reconstruction of Contact Maps
BACKGROUND: Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simpli...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583236/ https://www.ncbi.nlm.nih.gov/pubmed/20507547 http://dx.doi.org/10.1186/1471-2105-11-283 |
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author | Duarte, Jose M Sathyapriya, Rajagopal Stehr, Henning Filippis, Ioannis Lappe, Michael |
author_facet | Duarte, Jose M Sathyapriya, Rajagopal Stehr, Henning Filippis, Ioannis Lappe, Michael |
author_sort | Duarte, Jose M |
collection | PubMed |
description | BACKGROUND: Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. RESULTS: We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the C(β )atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. CONCLUSIONS: Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap. |
format | Online Article Text |
id | pubmed-3583236 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35832362013-02-28 Optimal contact definition for reconstruction of Contact Maps Duarte, Jose M Sathyapriya, Rajagopal Stehr, Henning Filippis, Ioannis Lappe, Michael BMC Bioinformatics Research Article BACKGROUND: Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. RESULTS: We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the C(β )atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. CONCLUSIONS: Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap. BioMed Central 2010-05-27 /pmc/articles/PMC3583236/ /pubmed/20507547 http://dx.doi.org/10.1186/1471-2105-11-283 Text en Copyright ©2010 Duarte et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Duarte, Jose M Sathyapriya, Rajagopal Stehr, Henning Filippis, Ioannis Lappe, Michael Optimal contact definition for reconstruction of Contact Maps |
title | Optimal contact definition for reconstruction of Contact Maps |
title_full | Optimal contact definition for reconstruction of Contact Maps |
title_fullStr | Optimal contact definition for reconstruction of Contact Maps |
title_full_unstemmed | Optimal contact definition for reconstruction of Contact Maps |
title_short | Optimal contact definition for reconstruction of Contact Maps |
title_sort | optimal contact definition for reconstruction of contact maps |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583236/ https://www.ncbi.nlm.nih.gov/pubmed/20507547 http://dx.doi.org/10.1186/1471-2105-11-283 |
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