Dynarepo 4LVN | MDRepo

Description

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

Molecular system

Starting structure: 4LVNPDB 4LVN(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 · 4 chains12,954 atoms849 residues
Total12,954 atoms849 residues
Box dimensions: Dodecahedron
a14.784nm
b14.784nm
c10.453nm

Sequences

Sequence 1Protein · 212 residues

DIVLTQSPAT MSASLGQRVS MSCSASSSVS TSYFHWYQQK PGSSPKLWIY STSNLASGVP GRFSGSGSGT SYSLSISSME AEDAATYYCH QFHRSPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV LNSWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NR

Sequence 2Protein · 336 residues

HFNDEFRNLQ WGLDLSRLDE TQELINEHQV MSTRICVIDS GIDYNHPDLK DNIELNLKEL HGRKGFDDDN NGIVDDIYGA NFVNNSGNPM DDNYHGTHVS GIISAIGNNN IGVVGVDVNS KLIICKALDE HKLGRLGDMF KCLDYCISRN AHMINGSFSF DEYSGIFNSS VEYLQRKGIL FFVSASNCSH PKSSTPDIRK CDLSINAKYP PILSTVYDNV ISVANLKKND NNNHYSLSIN SFYSNKYCQL AAPGTNIYST APHNSYRKLN GTSMAAPHVA AIASLIFSIN PDLSYKKVIQ ILKDSIVYLP SLKNMVAWAG YADINKAVNL AIKSKK

Sequence 3Protein · 220 residues

QVQLQESGPD LVKPSSSLKL TCTTTGYSIS SGYSWHWIRQ EPGKSLEWMG YIHYSGSTDY NDSLKARITI TRDTASNMFF LQLSSVTSDD TAVYYCVIYR YDGQWVFDDW GAGTTVTVSS AKTTPPSVFP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT WNSGSLSSGV HTFPGVLQSG LYTLSSSVTV PSSPWPSETV TCNVAHPASS TKVDKKIVPR

Sequence 4Protein · 81 residues

KLRLIVSENH ATTPSFFQES LLEPDVLSFL ESKGNLSNLK NINSMIIELK EDTTDDELIS YIKILEEKGA LIESDKLVSA D

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