MDBind 3ifp | MDRepo

Description

10 ns simulation of 3ifp pdb structure from MDBind dataset, a dynamic view of the PDBBind database

Molecular system

Starting structure: 3IFPPDB 3IFP(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 chains6,703 atoms440 residues
OtherOther101 atoms
Total6,804 atoms441 residues
Box dimensions: a6.991nm
b9.823nm
c7.358nm

Sequences

Sequence 1Protein · 222 residues

VTLKESGPGI LQPSQTLSLT CSFSGFSLST NGMGVSWIRQ PSGKGLEWLA HIYWDEDKRY NPSLKSRLTI SKDTSNNQVF LKITNVDTAD TATYYCARRR IIYDVEDYFD YWGQGTTLTV SSAKTTPPSV YPLAPGSAAQ TNSMVTLGCL VKGYFPEPVT VTWNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKIV PR

Sequence 2Protein · 218 residues

DVLMTQTPLS LPVSLGDQAS ISCRSSQNIV HSNGNTYLEW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLGV YYCFQGSHVP LTFGAGTKLE LKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER QNGVLNSWTD QDSKDSTYSM SSTLTLTKDE YERHNSYTCE ATHKTSTSPI VKSFNRNE

Experiments

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

Files

28 files · 95.6 MB

All files95.6 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