MDBind 3d9m

Open

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

MD-A00609

Created: 16 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 3d9m pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 3D9MPDB 3D9M(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 chain2,323 atoms140 residues
OtherOther102 atoms
Total2,425 atoms141 residues
Box dimensions: a5.791nm
b6.412nm
c6.913nm

Sequences

Sequence 1Protein · 140 residues

MEAVKTFNSE LYSLNDYKPP ISKAKMTQIT KAAIKAIKFY KHVVQSVEKF IQKCKPEYKV PGLYVIDSIV RQSRHQFGQE KDVFAPRFSN NIISTFQNLY RCPGDDKSKI VRVLNLWQKN NVFKSEIIQP LLDMAAALEH

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

36 files · 40.4 MB

All files40.4 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