MDBind 4jfd | MDRepo

Description

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

Molecular system

Starting structure: 4JFDPDB 4JFD(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 chains12,754 atoms817 residues
OtherOther151 atoms
Total12,905 atoms818 residues
Box dimensions: a12.918nm
b11.903nm
c10.65nm

Sequences

Sequence 1Protein · 276 residues

GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQRMEPRAP WIEQEGPEYW DGETRKVKAH SQTHRVDLGT LRGYYNQSEA GSHTVQRMYG CDVGSDWRFL RGYHQYAYDG KDYIALKEDL RSWTAADMAA QTTKHKWEAA HVAEQLRAYL EGTCVEWLRR YLENGKETLQ RTDAPKTHMT HHAVSDHEAT LRCWALSFYP AEITLTWQRD GEDQTQDTEL VETRPAGDGT FQKWAAVVVP SGQEQRYTCH VQHEGLPKPL TLRWEP

Sequence 2Protein · 100 residues

MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLSQ PKIVKWDRDM

Sequence 3Protein · 196 residues

KQEVEQNSGP LSVPEGAIAS LNCTYSFLGS QSFFWYRQYS GKSPELIMFT YREGDKEDGR FTAQLNKASQ HVSLLIRDSQ PSDSATYLCA VNDGGRLTFG DGTTLTVKPN IQNPDPAVYQ LRDSKSSDKS VCLFTDFDSQ TNVSQSKDSD VYITDKCVLD MRSMDFKSNS AVAWSNKSDF ACANAFNNSI IPEDTF

Sequence 4Protein · 245 residues

MSQTIHQWPA TLVQPVGSPL SLECTVEGTS NPNLYWYRQA AGRGPQLLFY WGPFGQISSE VPQNLSASRP QDRQFILSSK KLLLSDSGFY LCAWSETGLG MGGWQFGEGS RLTVLEDLKN VFPPEVAVFE PSEAEISHTQ KATLVCLATG FYPDHVELSW WVNGKEVHSG VCTDPQPLKE QPALNDSRYA LSSRLRVSAT FWQDPRNHFR CQVQFYGLSE NDEWTQDRAK PVTQIVSAEA WGRAD

Experiments

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

Files

30 files · 197 MB

All files197 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