mdCATH 3pvtA00

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

Molecular system

Starting structure: 3PVTPDB 3PVT(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 chain4,851 atoms304 residues
Total4,851 atoms304 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 304 residues

MRSTQEERFE QRIAQETAIE PQDWMPDAYR KTLIRQIGQH AHSEIVGMLP EGNWITRAPT LRRKAILLAK VQDEAGXGLY LYSAAETLGC AREDIYQKML DGRMKYSSIF NYPTLSWADI GVIGWLVDGA AIVNQVALCR TSYGPYARAM VKICKEESFH QRQGFEACMA LAQGSEAQKQ MLQDAINRFW WPALMMFGPN DDNSPNSARS LTWKIKRFTN DELRQRFVDN TVPQVEMLGM TVPDPDLXFD TESGXYRFGE IDWQEFNEVI NGRGICNQER LDAKRKAWEE GTWVREAALA HAQK

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

33 files · 977 MB

All files977 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
structure.pdbPDB
trajectory.xtcXTC
clusters_00_screenshot_00.jpgJPG

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 3pvtA00

Description

Molecular system

Sequences

Experiments

Files

Contributors