MDBind 5e8f

Open

Pierre-yves Libouban;Pascal Bonnet;Samia Aci-Sèche;

MD-A0062W

Created: 17 Feb 2026
License: This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License (opens in a new tab)

Description

10 ns simulation of 5e8f pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 5E8FPDB 5E8F(opens in a new tab)
Force field: Amber ff14SB, GAFFTIP3P
Engine: Amber 20
Method: Classical MD
Timestep: 2 fs
Frames: 500
Composition: Molecules of interest
ProteinProtein · 1 chain2,410 atoms147 residues
OtherOther87 atoms
Total2,497 atoms148 residues
Box dimensions: a6.397nm
b5.754nm
c6.82nm

Sequences

Sequence 1Protein · 147 residues

KDERAREILR GFKLNWMNLR DAETGKILWQ GTEDLSVPGV EHEARVPKKI LKCKAVSREL NFSSTEQMEK FRLEQKVYFK GQCLEEWFFE FGFVIPNSTN TWQSLIEAAP ESQMMPASVL TGNVIIETKF FDDDLLVSTS RVRLFYV

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3	Trajectory Analyses
replica 4	Trajectory Analyses
replica 5	Trajectory Analyses
replica 6	Trajectory Analyses
replica 7	Trajectory Analyses
replica 8	Trajectory Analyses
replica 9	Trajectory Analyses
replica 10	Trajectory Analyses

Files

31 files · 45.5 MB

All files45.5 MB

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Contributors

Research groups: Institute of Organic and Analytical chemistry, Orleans, FranceJanssen/Johnson & Johnson
Contact: For any questions please send a mail to plibouba@its.jnj.com