MDBind 4mji | MDRepo

Description

10 ns simulation of 4mji pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 4MJIPDB 4MJI(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 · 4 chains12,606 atoms807 residues
OtherOther124 atoms
Total12,730 atoms808 residues
Box dimensions: a8.601nm
b8.211nm
c15.031nm

Sequences

Sequence 1Protein · 276 residues

GSHSMRYFYT AMSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASPRTEPRAP WIEQEGPEYW DRNTQIFKTN TQTYRENLRI ALRYYNQSEA GSHTWQTMYG CDVGPDGRLL RGHNQYAYDG KDYIALNEDL SSWTAADTAA QITQRKWEAA REAEQLRAYL EGLCVEWLRR HLENGKETLQ RADPPKTHVT HHPVSDHEAT LRCWALGFYP AEITLTWQRD GEDQTQDTEL VETRPAGDRT FQKWAAVVVP SGEEQRYTCH VQHEGLPKPL TLRWEP

Sequence 2Protein · 99 residues

IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQP KIVKWDRDM

Sequence 3Protein · 192 residues

DPQALSIQEG ENATMNCSYK TSINNLQWYR QNSGRGLVHL ILIRSNEREK HSGRLRVTLD TSKKSSSLLI TASRAADTAS YFCATDDDSA RQLTFGSGTQ LTVLPDIQNP DPAVYQLRDS KSSDKSVCLF TDFDSQTNVS QSKDSDVYIT DKCVLDMRSM DFKSNSAVAW SNKSDFACAN AFNNSIIPED TF

Sequence 4Protein · 240 residues

AGVSQTPSNK VTEKGKYVEL RCDPISGHTA LYWYRQSLGQ GPEFLIYFQG TGAADDSGLP NDRFFAVRPE GSVSTLKIQR TERGDSAVYL CASSLTGGGE LFFGEGSRLT VLEDLKNVFP PEVAVFEPSE AEISHTQKAT LVCLATGFYP DHVELSWWVN GKEVHSGVCT DPQPLKEQPA LNDSRYALSS RLRVSATFWQ DPRNHFRCQV QFYGLSENDE WTQDRAKPVT QIVSAEAWGR

Experiments

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

Files

29 files · 192 MB

All files192 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