mdCATH 3pdiA02

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

Molecular system

Starting structure: 3PDIPDB 3PDI(opens in a new tab)
Force field: CHARMM22*TIP3P
Engine: ACEMD
Method: Classical MD
Ensemble: NVT
Temperature: 320 K
Timestep: 4 fs
Frames: 12,130
Composition: Molecules of interest
ProteinProtein · 1 chain4,331 atoms273 residues
Total4,331 atoms273 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 273 residues

TREPDPLPVG SERPGIRVHD VNLIGEYNIA GEFWHVLPLL DELGLRVLCT LAGDARYREV QTMHRAEVNM MVCSKAMLNV ARKLQETYGT PWFEGSFYGI TDTSQALRDF ARLLDDPDLT ARTEALIARE EAKVRAALEP WRARLEGKRV LLYTGGVKSW SVVSALQDLG MKVVATGTKK STEEDKARIR ELMGDDVKML DEGNARVLLK TVDEYQADIL IAGGRNMYTA LKGRVPFLDI NQEREFGYAG YDGMLELVRQ LCITLECPVW EAV

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

36 files · 874 MB

All files874 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 3pdiA02

Description

Molecular system

Sequences

Experiments

Files

Contributors