mdCATH 3vbaA00

mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics

Molecular system

Starting structure: 3VBAPDB 3VBA(opens in a new tab)
Force field: CHARMM22*TIP3P
Engine: ACEMD
Method: Classical MD
Ensemble: NVT
Temperature: 320 K
Timestep: 4 fs
Frames: 10,650
Composition: Molecules of interest
ProteinProtein · 1 chain2,640 atoms169 residues
Total2,640 atoms169 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 169 residues

MRSIIKGRVW KFGNNVDTDA ILPARYLVYT KPEELAQFVM TGADPDFPKK VKPGDIIVGG KNFGCGSSRE HAPLGLKGAG ISCVIAESFA RIFYRNAINV GLPLIECKGI SEKVNEGDEL EVNLETGEIK NLTTGEVLKG QKLPEFMMEI LEAGGLMPYL KKKMAESQL

Run	Outputs
320_rep1	Trajectory Analyses
320_rep2	Trajectory Analyses
320_rep3	Trajectory Analyses
320_rep4	Trajectory Analyses
320_rep5	Trajectory Analyses
348_rep1	Trajectory Analyses
348_rep2	Trajectory Analyses
348_rep3	Trajectory Analyses
348_rep4	Trajectory Analyses
348_rep5	Trajectory Analyses
379_rep1	Trajectory Analyses
379_rep2	Trajectory Analyses
379_rep3	Trajectory Analyses
379_rep4	Trajectory Analyses
379_rep5	Trajectory Analyses
413_rep1	Trajectory Analyses
413_rep2	Trajectory Analyses
413_rep3	Trajectory Analyses
413_rep4	Trajectory Analyses
413_rep5	Trajectory Analyses
450_rep1	Trajectory Analyses
450_rep2	Trajectory Analyses
450_rep3	Trajectory Analyses
450_rep4	Trajectory Analyses
450_rep5	Trajectory Analyses

Files

31 files · 463 MB

All files463 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
structure.pdbPDB
trajectory.xtcXTC

Contributors

Research groups: Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB)Institució Catalana de Recerca i Estudis Avançats (ICREA)Acellera LabsBiophysics Institute, National Research Council (CNR-IBF)
Contact: g.defabritiis@gmail.com

mdCATH 3vbaA00

Description

Molecular system

Sequences

Experiments

Files

Contributors