MDBind 5uff

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

Created 20 Feb 2026Updated 29 Jun 2026This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License

MD-A00673

Description

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

Molecular system

Starting structure: 5UFFPDB 5UFF(opens in a new tab)
Program: Amber 20
Force field: Amber ff14SB, GAFF
Water model: TIP3P
Method: Classical MD
Timestep: 2 fs
Frames: 500
Size: 3,370 atoms

Sequences

Sequence 1Protein · 216 residues

CPSQCSCSGT TVDCRSKRHA SVPAGIPTNA QILYLHDNQI TKLEPGVFDS LINLKELYLG SNQLGALPVG VFDSLTQLTV LDLGTNQLTV LPSAVFDRLV HLKELFMCCN KLTELPRGIE RLTHLTHLAL DQNQLKSIPH GAFDRLSSLT HAYLFGNPWD CECRDIMYLR NWVADHTSIA MRWDGKAVND PDSAKCAGTN TPVRAVTEAS TSPSKC

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

39 files · 67.5 MB

All files67.5 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