mdCATH 3pdiB01

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: 11,750
Composition: Molecules of interest
ProteinProtein · 1 chain2,204 atoms145 residues
Total2,204 atoms145 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 145 residues

SQTMGAALAI LGLARSMPLF HGSQGCTAFA KVFFVRHFRE PVPLQTTAMD QVSSVMGADE NVVEALKTIC ERQNPSVIGL LTTGLSETQG CDLHTALHEF RTQYEEYKDV PIVPVNTPDF SGCFESGFAA AVKAIVETLV PERRD

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

35 files · 439 MB

All files439 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 3pdiB01

Description

Molecular system

Sequences

Experiments

Files

Contributors