Dynarepo 5TIH | MDRepo

Description

PPIs from test53, Classical MD simulations, 3 replicates of 500 ns

Molecular system

Starting structure: 5TIHPDB 5TIH(opens in a new tab)
Force field: CHARMM36mTIP3P
Engine: GROMACS 2024.2
Method: Classical MD
Ensemble: NPT
Temperature: 310 K
Timestep: 2 fs
Composition: Molecules of interest
ProteinProtein · 3 chains11,904 atoms759 residues
Total11,904 atoms759 residues
Box dimensions: Dodecahedron
a15.04nm
b15.04nm
c10.636nm

Sequences

Sequence 1Protein · 212 residues

DIQMTQSPSS LSASLGERVS LTCRASQEIS GYLSWLQRKP DGTIKRLIYT ASTVDSGVPN RFSGSRSGSD YSLTISSLES EDFADYYCLQ YDTYPWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RN

Sequence 2Protein · 332 residues

RHVFIRTELS FIKNNVPCIR DMFFIYKREL YNICLDDLKG EEDETHIYVQ KKVKDSWITL NDLFKETDLT GRPHIFAYVD VEEIIILLCE DEEFSNRKKD MTCHRFYSND GKEYNNAEIT ISDYILKDKL LSSYVSLPLK IENREYFLIC GVSPYKFKDD NKKDDILCMA SHDKGETWGT KIVIKYDNYK LGVQYFFLRP YISKNDLSFH FYVGDNINNV KNVNFIECTH EKDLEFVCSN RDFLKDNKVL QDVSTLNDEY IVSYGNDNNF AECYIFFNNE NSILIKPEKY GNTAAGCYGG TFVKIDENRA LFIYSSSQGI YNIHTIYYAN YE

Sequence 3Protein · 215 residues

QVQLQQSGPQ LVRPGASVKI SCKTSGYSFT SFWMHWVKQW PGQGLEWIGM IDPSENKIRL NQNFKDRATL TVDTSSATAY IQFSRPTSED SGVYYCAMVR RGYWGQGTTL TVSAAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK IVPRD

Experiments

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

Files

All files

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: Delta team, Inria center at the University of Lorraine
Contact: yasaman.karami@inria.fr

Acknowledgements

DynaRepo Acknowledgements