MDBind 6cdm 1 | MDRepo

Description

10 ns simulation of 6cdm pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 6CDMPDB 6CDM(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 · 2 chains6,598 atoms436 residues
OtherOther72 atoms
Total6,670 atoms437 residues
Box dimensions: a9.739nm
b6.896nm
c7.511nm

Sequences

Sequence 1Protein · 218 residues

QVQLQQSGAE LVRPGASVTL SCKASGYTFT DYEMHWVKQT PVHGLEWIGA IVPETGFTAY TQKFKGKAML TADKSSSTAY MELRSLTSED SAVYFCSRLR LYWYFDVWGT GTTVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEP

Sequence 2Protein · 218 residues

GVLMTQTPLS LPVRLGDQAS ISCRSSQSIV YSNGNTYLEW YLQRPGQSPK LLIYKVSNRF SGVPDRVSGS GSGTDFTLKI SRVEAEDLGV YYCFQGSHVP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ SGNSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGE

Experiments

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3

Files

27 files · 108 MB

All files108 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