An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel
In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that ca...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2018-09-01
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| Series: | Molecules |
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| Online Access: | http://www.mdpi.com/1420-3049/23/10/2459 |
| _version_ | 1819212565091188736 |
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| author | Udeok Seo Ku-Jin Kim Beom Sik Kang |
| author_facet | Udeok Seo Ku-Jin Kim Beom Sik Kang |
| author_sort | Udeok Seo |
| collection | DOAJ |
| description | In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds. |
| first_indexed | 2024-12-23T06:44:59Z |
| format | Article |
| id | doaj.art-58f429b054244fc58c013c7a97727b52 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-23T06:44:59Z |
| publishDate | 2018-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-58f429b054244fc58c013c7a97727b522022-12-21T17:56:35ZengMDPI AGMolecules1420-30492018-09-012310245910.3390/molecules23102459molecules23102459An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/ChannelUdeok Seo0Ku-Jin Kim1Beom Sik Kang23D Convergence Technology Center, 70 Dongnaero, Donggu, Daegu 41061, KoreaSchool of Computer Science & Engineering, College of IT Engineering, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, KoreaSchool of Life Sciences and Biotechnology, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, KoreaIn this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.http://www.mdpi.com/1420-3049/23/10/2459protein moleculeside chain rotamerconformationtunnelchannelflexibilityvisualization |
| spellingShingle | Udeok Seo Ku-Jin Kim Beom Sik Kang An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel Molecules protein molecule side chain rotamer conformation tunnel channel flexibility visualization |
| title | An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel |
| title_full | An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel |
| title_fullStr | An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel |
| title_full_unstemmed | An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel |
| title_short | An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel |
| title_sort | algorithm for computing side chain conformational variations of a protein tunnel channel |
| topic | protein molecule side chain rotamer conformation tunnel channel flexibility visualization |
| url | http://www.mdpi.com/1420-3049/23/10/2459 |
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