MDBind 5huy

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

Molecular system

Starting structure: 5HUYPDB 5HUY(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 chain6,531 atoms423 residues
OtherOther169 atoms
Total6,700 atoms424 residues
Box dimensions: a6.833nm
b10.407nm
c9.692nm

Sequences

Sequence 1Protein · 423 residues

NWSVEDIVKG INSNNLESQL QATQAARKLL SREKQPPIDN IIRAGLIPKF VSFLGKTDCS PIQFESAWAL TNIASGTSEQ TKAVVDGGAI PAFISLLASP HAHISEQAVW ALGNIAGDGS AFRDLVIKHG AIDPLLALLA VPDLSTLACG YLRNLTWTLS NLCRNKNPAP PLDAVEQILP TLVRLLHHND PEVLADSCWA ISYLTDGPNE RIEMVVKKGV VPQLVKLLGA TELPIVTPAL RAIGNIVTGT DEQTQKVIDA GALAVFPSLL TNPKTNIQKE ATWTMSNITA GRQDQIQQVV NHGLVPFLVG VLSKADFKTQ KEAAWAITNY TSGGTVEQIV YLVHCGIIEP LMNLLSAKDT KIIQVILDAI SNIFQAAEKL GETEKLSIMI EECGGLDKIE ALQRHENESV YKASLNLIEK YFS

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

27 files · 99.7 MB

All files99.7 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

Description

Molecular system

Sequences

Experiments

Files

Contributors