mdCATH 3dgtA00

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

Molecular system

Starting structure: 3DGTPDB 3DGT(opens in a new tab)
Force field: CHARMM22*TIP3P
Engine: ACEMD
Method: Classical MD
Ensemble: NVT
Temperature: 320 K
Timestep: 4 fs
Frames: 12,500
Composition: Molecules of interest
ProteinProtein · 1 chain3,950 atoms278 residues
Total3,950 atoms278 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 278 residues

SAPAPPSGWS QVFLDDFDGA AGSSVNTANW QFDTGTSYPG GAGNWGTGEV ESMTSSTSNV SLDGNGDLLI TPRRDASGNW TSGRIETTRT DFQPPAGGKL RVEARLQMPN VTGDAAAGYW PAFWMLGAPF RGNYQNWPGV GELDIMENVQ GLNKTWATMX CGTSPGGPCN ETSGIGNSTA CPNTTCQSGF HTYTMEWDRS VSPEAIRFSV DGVTYQTVTA NQMDAATWTN ATNHGFFVIL NVAMGGGFPG AFGGGPTGAT EPGHPMVVDY VQVTSLSP

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 · 821 MB

All files821 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 3dgtA00

Description

Molecular system

Sequences

Experiments

Files

Contributors