Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement
Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the...
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| Format: | Article |
| Language: | English |
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Wiley
2006-01-01
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| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1100/tsw.2006.250 |
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| _version_ | 1849691022004584448 |
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| author | V. Kairys M.K. Gilson Miguel Xavier Fernandes |
| author_facet | V. Kairys M.K. Gilson Miguel Xavier Fernandes |
| author_sort | V. Kairys |
| collection | DOAJ |
| description | Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models. |
| format | Article |
| id | doaj-art-e91fdc8718a04ba0a6e4d453cf1fdf4c |
| institution | DOAJ |
| issn | 1537-744X |
| language | English |
| publishDate | 2006-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-e91fdc8718a04ba0a6e4d453cf1fdf4c2025-08-20T03:21:09ZengWileyThe Scientific World Journal1537-744X2006-01-0161542155410.1100/tsw.2006.250Using Protein Homology Models for Structure-Based Studies: Approaches to Model RefinementV. Kairys0M.K. Gilson1Miguel Xavier Fernandes2Centro de Química da Madeira, Departamento de Química da Universidade da Madeira, Campus da Penteada, 9000-390 Funchal, PortugalCenter for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USACentro de Química da Madeira, Departamento de Química da Universidade da Madeira, Campus da Penteada, 9000-390 Funchal, PortugalHomology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models.http://dx.doi.org/10.1100/tsw.2006.250 |
| spellingShingle | V. Kairys M.K. Gilson Miguel Xavier Fernandes Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement The Scientific World Journal |
| title | Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement |
| title_full | Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement |
| title_fullStr | Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement |
| title_full_unstemmed | Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement |
| title_short | Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement |
| title_sort | using protein homology models for structure based studies approaches to model refinement |
| url | http://dx.doi.org/10.1100/tsw.2006.250 |
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