Dataset for modified heated molecular dynamics for anti-human CXCR2 fragment variable vH-vL interface simulation

Dataset for modified heated molecular dynamics for anti-human CXCR2 fragment variable vH-vL interface simulation --------------------------------------------------------------------------------------------------------------------------------- This dataset contains raw and analysed data of modified heated molecular dynamics (MD) simulation of fragment variable (Fv) vH-vL interface of anti-human CXCR2, HY29-1 antibody. Patent disclosed Fv sequences of heavy (vH) and light (vL) chains of HY29-1 was modelled using Alpha Fold and SAbPred webservers. Pairs of vH and vL 3D homology models were docked by using ClusPro and LZerD docking suites and screened for the best docking pose. Modified heated MD simulation was performed at gradual increasing temperature for coupling: 300K, 330K, 360K and 390K throughout 70ns. The root-mean-square-deviation of interface (RMSDi) was calculated from the simulation trajectories of coarse-grain backbone (BB) with the least-squares fit to the BB of the initial (docked pose model) as reference. The dataset consists of raw data (structure, trajectory and other associated files in Input & Output folders), analysed data (RMSDi data in Analysis folder) in three replicates and RMSDi compilation data in MS Excel spreadsheet (Compilation of RMSDi data of modified heated MD.xlsx).# 抗人CXCR2抗体可变区vH-vL界面改性加热分子动力学模拟数据集 本数据集收录了抗人CXCR2抗体HY29-1的可变区片段（fragment variable, Fv）vH-vL界面的改性加热分子动力学（Molecular Dynamics, MD）模拟原始数据与分析数据。HY29-1抗体重链可变区（variable heavy, vH）与轻链可变区（variable light, vL）的Fv序列已由专利公开，本研究借助AlphaFold与SAbPred在线服务器构建其三维同源模型。利用ClusPro与LZerD对接套件对vH与vL的三维同源模型进行配对对接，并筛选得到最优对接构象。随后以逐步升温的控温耦合方式实施改性加热MD模拟，模拟温度梯度为300K、330K、360K与390K，总模拟时长为70纳秒（nanosecond, ns）。本研究以初始对接构象模型的主链（backbone, BB）为参考，通过最小二乘拟合粗粒度主链的模拟轨迹，计算得到界面均方根偏差（root-mean-square-deviation of interface, RMSDi）。 本数据集包含三类数据：Input & Output文件夹内的原始数据（结构文件、轨迹文件及其他关联文件）、三次重复实验的分析数据（Analysis文件夹内的RMSDi数据），以及MS Excel格式的RMSDi汇总数据文件"Compilation of RMSDi data of modified heated MD.xlsx"。