Dataset for modified heated molecular dynamics for anti-human CXCR2 fragment variable vH-vL interface simulation
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Date
2022-12-10
Authors
Muhamad Alif Che Nordin
Mohammad Tasyriq Che Omar
Journal Title
Journal ISSN
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Publisher
Mendeley
Abstract
Description
Dataset for modified heated molecular dynamics for anti-human CXCR2 fragment variable vH-vL interface simulation
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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).
Link to data: http://dx.doi.org/10.17632/rkjnh77kd2.2