MDBind 5nme 1 | MDRepo

Description

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

Molecular system

Starting structure: 5NMEPDB 5NME(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 chains12,814 atoms819 residues
OtherOther141 atoms
Total12,955 atoms820 residues
Box dimensions: a9.319nm
b15.168nm
c11.02nm

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 · 201 residues

KEVEQNSGPL SVPEGAIASL NCTYSDRGSQ SFFWYRQYSG KSPELIMFIY SNGDKEDGRF TAQLNKASQY ISLLIRDSKL SDSATYLCAV RTNSGYALNF GKGTSLLVTP HIQKPDPAVY QLRDSKSSDK SVCLFTDFDS QTNVSQSKDS DVYITDKCVL DMRSMDFKSN SAVAWSNKSD FACANAFNNS IIPEDTFFPS P

Sequence 4Protein · 242 residues

DAGVTQSPTH LIKTRGQQVT LRCSPKQGHD TVSWYQQALG QGPQFIFQYY EEEERQRGNF PDRFSGHQFP NYSSELNVNA LLLGDSALYL CASSDTVSYE QYFGPGTRLT VTEDLKNVFP PEVAVFEPSE AEISHTQKAT LVCLATGFYP DHVELSWWVN GKEVHSGVCT DPQPLKEQPA LNDSRYALSS RLRVSATFWQ DPRNHFRCQV QFYGLSENDE WTQDRAKPVT QIVSAEAWGR AD

Experiments

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

Files

29 files · 190 MB

All files190 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