Protein folding in HP model on hexagonal lattices with diagonals
Three dimensional structure prediction of a protein from its amino acid sequence, known as protein folding, is one of the most studied computational problem in bioinformatics and computational biology. Since, this is a hard problem, a number of simplified models have been proposed in literature to c...
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| Veröffentlicht in: | BMC bioinformatics 2014, Vol.15 Suppl 2 (S2), p.S7-S7, Article S7 |
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| creator | Shaw, Dipan Shohidull Islam, A S M Sohel Rahman, M Hasan, Masud |
| description | Three dimensional structure prediction of a protein from its amino acid sequence, known as protein folding, is one of the most studied computational problem in bioinformatics and computational biology. Since, this is a hard problem, a number of simplified models have been proposed in literature to capture the essential properties of this problem. In this paper we introduce the hexagonal lattices with diagonals to handle the protein folding problem considering the well researched HP model. We give two approximation algorithms for protein folding on this lattice. Our first algorithm is a 5/3-approximation algorithm, which is based on the strategy of partitioning the entire protein sequence into two pieces. Our next algorithm is also based on partitioning approaches and improves upon the first algorithm. |
| doi_str_mv | 10.1186/1471-2105-15-S2-S7 |
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Since, this is a hard problem, a number of simplified models have been proposed in literature to capture the essential properties of this problem. In this paper we introduce the hexagonal lattices with diagonals to handle the protein folding problem considering the well researched HP model. We give two approximation algorithms for protein folding on this lattice. Our first algorithm is a 5/3-approximation algorithm, which is based on the strategy of partitioning the entire protein sequence into two pieces. 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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</rights><rights>Copyright © 2014 Shaw et al.; licensee BioMed Central Ltd. 2014 Shaw et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b525t-c0be64ab00eba2f8eb832b70e2812a974bb5b49f4be8251cbd9c0068b354699c3</citedby><cites>FETCH-LOGICAL-b525t-c0be64ab00eba2f8eb832b70e2812a974bb5b49f4be8251cbd9c0068b354699c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016602/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016602/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,4021,27921,27922,27923,53789,53791</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24564789$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shaw, Dipan</creatorcontrib><creatorcontrib>Shohidull Islam, A S M</creatorcontrib><creatorcontrib>Sohel Rahman, M</creatorcontrib><creatorcontrib>Hasan, Masud</creatorcontrib><title>Protein folding in HP model on hexagonal lattices with diagonals</title><title>BMC bioinformatics</title><addtitle>BMC Bioinformatics</addtitle><description>Three dimensional structure prediction of a protein from its amino acid sequence, known as protein folding, is one of the most studied computational problem in bioinformatics and computational biology. 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| subjects | Algorithms Bioinformatics Computational Biology - methods Computer science Genetic algorithms Models, Biological Proceedings Protein Folding Protein Structure, Tertiary Sequence Analysis, Protein |
| title | Protein folding in HP model on hexagonal lattices with diagonals |
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