MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD
文献类型：期刊论文
| 作者 | Gao, Kaifu1,2; Yang, Minghui1 |
| 刊名 | JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
 |
| 出版日期 | 2012-12-01 |
| 卷号 | 11期号:6页码:1201-1215 |
| 关键词 | Protein folding coarse-graining UNRES force field GPU |
| 英文摘要 | We have investigated the folding of two helix-bundle proteins, 36-residue Villin headpiece and 56-residue E-domain of Staphylococcal protein A, by combining molecular dynamics (MD) simulations with Coarse-Grained United-Residue (UNRES) Force Field and all-atom force field. Starting from extended structures, each of the proteins was folded to a stable structure within a short time frame using the UNRES model. However, the secondary structures of helices were not well formed. Further refinement using MD simulations with the all-atom force field was able to fold the protein structure into the native-like state with the smallest main-chain root-mean-square deviation of around 3 angstrom. Detailed analysis of the folding trajectories was presented and the performance of GPU-based MD simulations was also discussed. |
| WOS标题词 | Science & Technology ; Physical Sciences |
| 类目[WOS] | Chemistry, Multidisciplinary |
| 研究领域[WOS] | Chemistry |
| 关键词[WOS] | VILLIN HEADPIECE SUBDOMAIN ; POTENTIAL-ENERGY LANDSCAPE ; FOLDING SIMULATIONS ; HIERARCHICAL DESIGN ; E-DOMAIN ; SPEED LIMIT ; MEAN FORCE ; GRAPHICS ; OPTIMIZATION ; TESTS |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000313425700004 |
| 公开日期 | 2015-07-14 |
| 源URL | [http://ir.wipm.ac.cn/handle/112942/1601]  |
| 专题 | 武汉物理与数学研究所_理论与交叉研究部 |
| 作者单位 | 1.Chinese Acad Sci, Wuhan Inst Phys & Math, Wuhan Ctr Magnet Resonance, State Key Lab Magnet Resonance & Atom & Mol Phys, Wuhan 430071, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China |
| 推荐引用方式 GB/T 7714 | Gao, Kaifu,Yang, Minghui. MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD[J]. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY,2012,11(6):1201-1215. |
| APA | Gao, Kaifu,&Yang, Minghui.(2012).MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD.JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY,11(6),1201-1215. |
| MLA | Gao, Kaifu,et al."MOLECULAR DYNAMICS SIMULATIONS OF HELIX BUNDLE PROTEINS USING UNRES FORCE FIELD AND ALL-ATOM FORCE FIELD".JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 11.6(2012):1201-1215. |
入库方式： OAI收割
来源：武汉物理与数学研究所
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