MDBind 5ajo

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

Molecular system

Starting structure: 5AJOPDB 5AJO(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 chain7,861 atoms495 residues
OtherOther201 atoms
Total8,062 atoms496 residues
Box dimensions: a10.138nm
b8.554nm
c9.076nm

Sequences

Sequence 1Protein · 495 residues

KVRWPDFNQE AYVGGTMVRS GQDPYARNKF NQVESDKLRM DRAIPDTRHD QCQRKQWRVD LPATSVVITF HNEARSALLR TVVSVLKKSP PHLIKEIILV DDYSNDPEDG ALLGKIEKVR VLRNDRREGL MRSRVRGADA AQAKVLTFLD SHCECNEHWL EPLLERVAED RTRVVSPIID VINMDNFQYV GASADLKGGF DWNLVFKWDY MTPEQRRSRQ GNPVAPIKTP MIAGGLFVMD KFYFEELGKY DMMMDVWGGE NLEISFRVWQ CGGSLEIIPC SRVGHVFRKQ HPYTFPGGSG TVFARNTRRA AEVWMDEYKN FYYAAVPSAR NVPYGNIQSR LELRKKLSCK PFKWYLENVY PELRVPDHQD IAFGALQQGT NCLDTLGHFA DGVVGVYECH NAGGNQEWAL TKEKSVKHMD LCLTVVDRAP GSLIKLQGCR EDDSRQKWEQ IEGNSKLRHV GSNLCLDSRT AKSGGLSVEV CGPALSQQWK FTLNL

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

25 files · 106 MB

All files106 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