MDBind 5ypo

Open

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

MD-A00647

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 5ypo pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 5YPOPDB 5YPO(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 chain2,952 atoms183 residues
OtherOther237 atoms
Total3,189 atoms184 residues
Box dimensions: a6.417nm
b6.858nm
c7.284nm

Sequences

Sequence 1Protein · 183 residues

VHYARPIIIL GPTKDRANDD LLSEFPDKFG SCVPHTTRPK REYEIDGRDY HFVSSREKME KDIQAHKFIE AGQYNSHLYG TSVQSVREVA EQGKHCILDV SANAVRRLQA AHLHPIAIFI RPRSLENVLE INKRITEEQA RKAFDRATKL EQEFTECFSA IVEGDSFEEI YHKVKRVIED LSG

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

32 files · 49.9 MB

All files49.9 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