CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations
文献类型：期刊论文
| 作者 | Qi, Yifei1; Lee, Jumin2,3; Cheng, Xi4; Shen, Rong5,6; Islam, Shahidul M.7; Roux, Benoit5,6; Im, Wonpil2,3 |
| 刊名 | JOURNAL OF COMPUTATIONAL CHEMISTRY
 |
| 出版日期 | 2019-07-22 |
| 页码 | 6 |
| ISSN号 | 0192-8651 |
| 关键词 | MDDS simulation reMD simulation spin label EPR DEER CHARMM-GUI |
| DOI | 10.1002/jcc.26032 |
| 通讯作者 | Qi, Yifei(yfqi@chem.ecnu.edu.cn) ; Islam, Shahidul M.(mshahidi@uic.edu) ; Roux, Benoit(roux@uchicago.edu) ; Im, Wonpil(wonpil@lehigh.edu) |
| 英文摘要 | The double electron-electron resonance (DEER) is a powerful structural biology technique to obtain distance information in the range of 18 to 80 a by measuring the dipolar coupling between two unpaired electron spins. The distance distributions obtained from the experiment provide valuable structural information about the protein in its native environment that can be exploited using restrained ensemble molecular dynamics (reMD) simulations. We present a new tool DEER Facilitator in CHARMM-GUI that consists of two modules Spin-Pair Distributor and reMD Prepper to setup simulations that utilize information from DEER experiments. Spin-Pair Distributor provides a web-based interface to calculate the spin-pair distance distribution of labeled sites in a protein using MD simulations. The calculated distribution can be used to guide the selection of the labeling sites in experiments as well as validate different protein structure models. reMD Prepper facilities the setup of reMD simulations using different types of spin labels in four different environments including vacuum, solution, micelle, and bilayer. The applications of these two modules are demonstrated with several test cases. Spin-Pair Distributor and reMD Prepper are available at and . DEER Facilitator is expected to facilitate advanced biomolecular modeling and simulation, thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems based on experimental DEER data. (c) 2019 Wiley Periodicals, Inc. |
| WOS关键词 | ALTERNATING ACCESS ; MEMBRANE-BUILDER ; ALGORITHMS ; INTERFACE ; MECHANISM ; PROTEINS ; PARALLEL ; CHANNEL ; LABELS ; AMBER |
| 资助项目 | NIH[U54GM087519] ; National Natural Science Foundation of China[31700646] ; Natural Science Foundation of Shanghai[19ZR1473600] |
| WOS研究方向 | Chemistry |
| 语种 | 英语 |
| 出版者 | WILEY |
| WOS记录号 | WOS:000477203000001 |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/289181]  |
| 专题 | 新药研究国家重点实验室 |
| 通讯作者 | Qi, Yifei; Islam, Shahidul M.; Roux, Benoit; Im, Wonpil |
| 作者单位 | 1.East China Normal Univ, Shanghai Engn Res Ctr Mol Therapeut & New Drug De, Sch Chem & Mol Engn, Shanghai 200062, Peoples R China 2.Lehigh Univ, Dept Biol Sci, Bethlehem, PA 18015 USA 3.Lehigh Univ, Dept Bioengn, Bethlehem, PA 18015 USA 4.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China 5.Univ Chicago, Dept Biochem & Mol Biol, 920 E 58Th St, Chicago, IL 60637 USA 6.Univ Chicago, Dept Chem, 5735 S Ellis Ave, Chicago, IL 60637 USA 7.Univ Illinois, Dept Chem, Chicago, IL 60607 USA |
| 推荐引用方式 GB/T 7714 | Qi, Yifei,Lee, Jumin,Cheng, Xi,et al. CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY,2019:6. |
| APA | Qi, Yifei.,Lee, Jumin.,Cheng, Xi.,Shen, Rong.,Islam, Shahidul M..,...&Im, Wonpil.(2019).CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations.JOURNAL OF COMPUTATIONAL CHEMISTRY,6. |
| MLA | Qi, Yifei,et al."CHARMM-GUI DEER facilitator for spin-pair distance distribution calculations and preparation of restrained-ensemble molecular dynamics simulations".JOURNAL OF COMPUTATIONAL CHEMISTRY (2019):6. |
入库方式： OAI收割
来源：上海药物研究所
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