Department of Chemistry and *Graduate Program of Comparative Biochemistry, University of California, Berkeley, CA 94720; and tBerkeley Structural Gertomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Global mapping of the protein structure space and application in structure-based inference of protein function.
Saved in:
| Title: | Department of Chemistry and *Graduate Program of Comparative Biochemistry, University of California, Berkeley, CA 94720; and tBerkeley Structural Gertomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Global mapping of the protein structure space and application in structure-based inference of protein function. |
|---|---|
| Authors: | Jingtong Hou1, Se-Ran Jun2, Chao Zhang3, Sung-Hou Kim1,2,3 shkim@cchem.berkeIey.edu |
| Source: | Proceedings of the National Academy of Sciences of the United States of America. 3/8/2005, Vol. 102 Issue 10, p3651-3656. 6p. |
| Subjects: | Protein conformation, Biochemistry, Biomolecules, Protein folding, Medical sciences, Universities & colleges |
| Abstract: | We have constructed a map of the "protein structure space" by using the pairwise structural similarity scores calculated for all nonredundant protein structures determined experimentally. As expected, proteins with similar structures clustered together in the map and the overall distribution of structural classes of this map followed closely that of the map of the "protein fold space" we have reported previously. Consequently, proteins sharing similar molecular functions also were found to colocalize in the protein structure space map, pointing toward a previously undescribed scheme for structure-based functional inference for remote homologues based on the proximity in the map of the protein structure space. We found that this scheme consistently outperformed other predictions made by using either the raw scores or normalized Z-scores of pairwise DALI structure alignment. [ABSTRACT FROM AUTHOR] |
| Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
|---|---|
| Header | DbId: egs DbLabel: Engineering Source An: 16554958 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Department of Chemistry and *Graduate Program of Comparative Biochemistry, University of California, Berkeley, CA 94720; and tBerkeley Structural Gertomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Global mapping of the protein structure space and application in structure-based inference of protein function. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Jingtong+Hou%22">Jingtong Hou</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Se-Ran+Jun%22">Se-Ran Jun</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Chao+Zhang%22">Chao Zhang</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Sung-Hou+Kim%22">Sung-Hou Kim</searchLink><relatesTo>1,2,3</relatesTo><i> shkim@cchem.berkeIey.edu</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Proceedings+of+the+National+Academy+of+Sciences+of+the+United+States+of+America%22">Proceedings of the National Academy of Sciences of the United States of America</searchLink>. 3/8/2005, Vol. 102 Issue 10, p3651-3656. 6p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Protein+conformation%22">Protein conformation</searchLink><br /><searchLink fieldCode="DE" term="%22Biochemistry%22">Biochemistry</searchLink><br /><searchLink fieldCode="DE" term="%22Biomolecules%22">Biomolecules</searchLink><br /><searchLink fieldCode="DE" term="%22Protein+folding%22">Protein folding</searchLink><br /><searchLink fieldCode="DE" term="%22Medical+sciences%22">Medical sciences</searchLink><br /><searchLink fieldCode="DE" term="%22Universities+%26+colleges%22">Universities & colleges</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: We have constructed a map of the "protein structure space" by using the pairwise structural similarity scores calculated for all nonredundant protein structures determined experimentally. As expected, proteins with similar structures clustered together in the map and the overall distribution of structural classes of this map followed closely that of the map of the "protein fold space" we have reported previously. Consequently, proteins sharing similar molecular functions also were found to colocalize in the protein structure space map, pointing toward a previously undescribed scheme for structure-based functional inference for remote homologues based on the proximity in the map of the protein structure space. We found that this scheme consistently outperformed other predictions made by using either the raw scores or normalized Z-scores of pairwise DALI structure alignment. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Proceedings of the National Academy of Sciences of the United States of America is the property of National Academy of Sciences and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=16554958 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1073/pnas.0409772102 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 6 StartPage: 3651 Subjects: – SubjectFull: Protein conformation Type: general – SubjectFull: Biochemistry Type: general – SubjectFull: Biomolecules Type: general – SubjectFull: Protein folding Type: general – SubjectFull: Medical sciences Type: general – SubjectFull: Universities & colleges Type: general Titles: – TitleFull: Department of Chemistry and *Graduate Program of Comparative Biochemistry, University of California, Berkeley, CA 94720; and tBerkeley Structural Gertomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Global mapping of the protein structure space and application in structure-based inference of protein function. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Jingtong Hou – PersonEntity: Name: NameFull: Se-Ran Jun – PersonEntity: Name: NameFull: Chao Zhang – PersonEntity: Name: NameFull: Sung-Hou Kim IsPartOfRelationships: – BibEntity: Dates: – D: 08 M: 03 Text: 3/8/2005 Type: published Y: 2005 Identifiers: – Type: issn-print Value: 00278424 Numbering: – Type: volume Value: 102 – Type: issue Value: 10 Titles: – TitleFull: Proceedings of the National Academy of Sciences of the United States of America Type: main |
| ResultId | 1 |
