Accurate prediction of protein catalytic residues by side chain orientation and residue contact density.
Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure informati...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3480458?pdf=render |
| _version_ | 1818130657491025920 |
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| author | Yu-Tung Chien Shao-Wei Huang |
| author_facet | Yu-Tung Chien Shao-Wei Huang |
| author_sort | Yu-Tung Chien |
| collection | DOAJ |
| description | Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures. |
| first_indexed | 2024-12-11T08:08:31Z |
| format | Article |
| id | doaj.art-5265f938b7fa44a8a906bdae8851e91d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T08:08:31Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5265f938b7fa44a8a906bdae8851e91d2022-12-22T01:14:56ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-01710e4795110.1371/journal.pone.0047951Accurate prediction of protein catalytic residues by side chain orientation and residue contact density.Yu-Tung ChienShao-Wei HuangPrediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.http://europepmc.org/articles/PMC3480458?pdf=render |
| spellingShingle | Yu-Tung Chien Shao-Wei Huang Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. PLoS ONE |
| title | Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. |
| title_full | Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. |
| title_fullStr | Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. |
| title_full_unstemmed | Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. |
| title_short | Accurate prediction of protein catalytic residues by side chain orientation and residue contact density. |
| title_sort | accurate prediction of protein catalytic residues by side chain orientation and residue contact density |
| url | http://europepmc.org/articles/PMC3480458?pdf=render |
| work_keys_str_mv | AT yutungchien accuratepredictionofproteincatalyticresiduesbysidechainorientationandresiduecontactdensity AT shaoweihuang accuratepredictionofproteincatalyticresiduesbysidechainorientationandresiduecontactdensity |