mdCATH 3vk5B00

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

Molecular system

Starting structure: 3VK5PDB 3VK5(opens in a new tab)
Force field: CHARMM22*TIP3P
Engine: ACEMD
Method: Classical MD
Ensemble: NVT
Temperature: 320 K
Timestep: 4 fs
Frames: 11,020
Composition: Molecules of interest
ProteinProtein · 1 chain3,908 atoms252 residues
Total3,908 atoms252 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 252 residues

PPLWRPGRVL ARLREHQPGP VHIIDPFKVP VTEAVEKAAE LTRLGFAAVL LASTDYESFE SHMEPYVAAV KAATPLPVVL HFPPRPGAGF PVVRGADALL LPALLGSGDD YFVWKSFLET LAAFPGRIPR EEWPELLLTV ALTFGEDPRT GDLLGTVPVS TASTEEIDRY LHVARAFGFH MVYLYSRNEH VPPEVVRHFR KGLGPDQVLF VSGNVRSGRQ VTEYLDSGAD YVGFAGALEQ PDWRSALAEI AG

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

44 files · 735 MB

All files735 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: 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 3vk5B00

Description

Molecular system

Sequences

Experiments

Files

Contributors