EGSCyP_REMD_20_cyclic_pentapeptides

IMPMC, Sorbonne University, Paris, France<br> LAAS-CNRS, University of Toulouse, France 16 july 2020 This zenodo-repository contains the data presented in the article: Maud Jusot, Jaysen Sawmynaden, Juan Cortes, Jacques Chomilier, Dirk Stratmann<br> "How chemical modifications affect the conformation landscape of small cyclic peptides"<br> July 2020, bioRxiv.org There are two tar archives in the repository:<br> EGSCyP.tar<br> REMD.tar EGSCyP.tar contains the data generated with the EGSCyP method that has been published previously:<br> https://doi.org/10.1021/acs.jcim.8b00375 REMD.tar contains the data generated with replica-exchange molecular dynamics simulations (REMD)<br> in implicit solvent using 8 replicas from 300K to 450K generated with GROMACS 5.1.4 Both archives contain the data of 20 cyclic penta-peptides, as presented in the article cited above.<br> One sub-directory per peptide. For the EGSCyP data:<br> Generated 3D structures where assembled in a single xtc file, which is not a standard trajectory here,<br> just one frame per generated structure.<br> To be able to read the xtc file, an arbitrary structure is given in a PDB file. For the REMD data:<br> Each number correspond to a replica: 0 for 300K to 7 for 450K.<br> Trajectories are either available as trr or xtc files. Coordinates are available in a gro file. <br> Contact: [e-mail]<br> [e-mail]<br> [e-mail]，索邦大学，法国巴黎；LAAS-CNRS，图卢兹大学，法国，2020年7月16日 本zenodo（Zenodo）仓库包含下述论文的配套数据：作者为Maud Jusot、Jaysen Sawmynaden、Juan Cortes、Jacques Chomilier、Dirk Stratmann，论文标题为《化学修饰如何影响小型环肽的构象景观》，于2020年7月发布于bioRxiv.org 本仓库包含两个tar压缩归档文件：EGSCyP.tar与REMD.tar EGSCyP.tar包含此前已发表的EGSCyP方法生成的实验数据，相关研究的DOI链接为：https://doi.org/10.1021/acs.jcim.8b00375 REMD.tar包含使用副本交换分子动力学（replica-exchange molecular dynamics, REMD）模拟生成的数据，模拟采用隐式溶剂模型，使用8个温度副本，温度范围覆盖300K至450K，模拟程序为GROMACS 5.1.4 两个归档文件均包含上述引用论文中提及的20种环五肽的相关数据，每个肽对应一个独立子目录 针对EGSCyP数据集：生成的三维结构被整合为单个xtc格式文件，此处该文件并非标准轨迹文件，每个生成的结构仅对应一帧。若需读取该xtc文件，需在PDB（Protein Data Bank）格式文件中提供一个任意参考结构 针对REMD数据集：每个编号对应一个温度副本，编号0对应300K，编号7对应450K。轨迹文件可采用trr或xtc格式存储，坐标信息存储于gro格式文件中 联系方式：[e-mail]、[e-mail]、[e-mail]