Real time structural search of the Protein Data Bank.
Detection of protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structu...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-07-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007970&type=printable |
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| author | Dmytro Guzenko Stephen K Burley Jose M Duarte |
| author_facet | Dmytro Guzenko Stephen K Burley Jose M Duarte |
| author_sort | Dmytro Guzenko |
| collection | DOAJ |
| description | Detection of protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. Traditional methods use atom level information, which can be complicated by the presence of topological permutations within a polypeptide chain and/or subunit rearrangements. These challenges can be overcome by comparing electron density volumes directly. But, brute force alignment of 3D data is a compute intensive search problem. We developed a 3D Zernike moment normalization procedure to orient electron density volumes and assess similarity with unprecedented speed. Similarity searching with this approach enables real-time retrieval of proteins/protein assemblies resembling a target, from PDB or user input, together with resulting alignments (http://shape.rcsb.org). |
| format | Article |
| id | doaj-art-b567fa7776604fe1aa12e25bb981f82a |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2020-07-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-b567fa7776604fe1aa12e25bb981f82a2025-08-20T02:17:05ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582020-07-01167e100797010.1371/journal.pcbi.1007970Real time structural search of the Protein Data Bank.Dmytro GuzenkoStephen K BurleyJose M DuarteDetection of protein structure similarity is a central challenge in structural bioinformatics. Comparisons are usually performed at the polypeptide chain level, however the functional form of a protein within the cell is often an oligomer. This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval. Traditional methods use atom level information, which can be complicated by the presence of topological permutations within a polypeptide chain and/or subunit rearrangements. These challenges can be overcome by comparing electron density volumes directly. But, brute force alignment of 3D data is a compute intensive search problem. We developed a 3D Zernike moment normalization procedure to orient electron density volumes and assess similarity with unprecedented speed. Similarity searching with this approach enables real-time retrieval of proteins/protein assemblies resembling a target, from PDB or user input, together with resulting alignments (http://shape.rcsb.org).https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007970&type=printable |
| spellingShingle | Dmytro Guzenko Stephen K Burley Jose M Duarte Real time structural search of the Protein Data Bank. PLoS Computational Biology |
| title | Real time structural search of the Protein Data Bank. |
| title_full | Real time structural search of the Protein Data Bank. |
| title_fullStr | Real time structural search of the Protein Data Bank. |
| title_full_unstemmed | Real time structural search of the Protein Data Bank. |
| title_short | Real time structural search of the Protein Data Bank. |
| title_sort | real time structural search of the protein data bank |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007970&type=printable |
| work_keys_str_mv | AT dmytroguzenko realtimestructuralsearchoftheproteindatabank AT stephenkburley realtimestructuralsearchoftheproteindatabank AT josemduarte realtimestructuralsearchoftheproteindatabank |