Non-sequential protein structure alignment by conformational space annealing and local refinement
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| Publicat a: | PLoS One vol. 14, no. 1 (Jan 2019), p. e0210177 |
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| Altres autors: | , , |
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Public Library of Science
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| 024 | 7 | |a 10.1371/journal.pone.0210177 |2 doi | |
| 035 | |a 2173760829 | ||
| 045 | 2 | |b d20190101 |b d20190131 | |
| 084 | |a 174835 |2 nlm | ||
| 100 | 1 | |a Joung, InSuk | |
| 245 | 1 | |a Non-sequential protein structure alignment by conformational space annealing and local refinement | |
| 260 | |b Public Library of Science |c Jan 2019 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a Protein structure alignment is an important tool for studying evolutionary biology and protein modeling. A tool which intensively searches for the globally optimal non-sequential alignments is rarely found. We propose ALIGN-CSA which shows improvement in scores, such as DALI-score, SP-score, SO-score and TM-score over the benchmark set including 286 cases. We performed benchmarking of existing popular alignment scoring functions, where the dependence of the search algorithm was effectively eliminated by using ALIGN-CSA. For the benchmarking, we set the minimum block size to 4 to prevent much fragmented alignments where the biological relevance of small alignment blocks is hard to interpret. With this condition, globally optimal alignments were searched by ALIGN-CSA using the four scoring functions listed above, and TM-score is found to be the most effective in generating alignments with longer match lengths and smaller RMSD values. However, DALI-score is the most effective in generating alignments similar to the manually curated reference alignments, which implies that DALI-score is more biologically relevant score. Due to the high demand on computational resources of ALIGN-CSA, we also propose a relatively fast local refinement method, which can control the minimum block size and whether to allow the reverse alignment. ALIGN-CSA can be used to obtain much improved alignment at the cost of relatively more extensive computation. For faster alignment, we propose a refinement protocol that improves the score of a given alignment obtained by various external tools. All programs are available from http://lee.kias.re.kr. | |
| 653 | |a Proteins | ||
| 653 | |a Alignment | ||
| 653 | |a Protocol (computers) | ||
| 653 | |a Bioinformatics | ||
| 653 | |a Biological evolution | ||
| 653 | |a Search algorithms | ||
| 653 | |a Computer applications | ||
| 653 | |a Protein structure | ||
| 653 | |a Algorithms | ||
| 653 | |a Dependence | ||
| 653 | |a Benchmarks | ||
| 700 | 1 | |a Jong Yun Kim | |
| 700 | 1 | |a Joo, Keehyoung | |
| 700 | 1 | |a Jooyoung Lee ⨯ | |
| 773 | 0 | |t PLoS One |g vol. 14, no. 1 (Jan 2019), p. e0210177 | |
| 786 | 0 | |d ProQuest |t Health & Medical Collection | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/2173760829/abstract/embedded/6A8EOT78XXH2IG52?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/2173760829/fulltext/embedded/6A8EOT78XXH2IG52?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/2173760829/fulltextPDF/embedded/6A8EOT78XXH2IG52?source=fedsrch |