mdCATH 1wd3A01

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

Molecular system

Starting structure: 1WD3PDB 1WD3(opens in a new tab)
Force field: CHARMM22*TIP3P
Engine: ACEMD
Method: Classical MD
Ensemble: NVT
Temperature: 320 K
Timestep: 4 fs
Frames: 10,612
Composition: Molecules of interest
ProteinProtein · 1 chain4,423 atoms320 residues
Total4,423 atoms320 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 320 residues

MGPCDIYEAG DTPCVAAHST TRALYSSFSG ALYQLQRGSD DTTTTISPLT AGGIADASAQ DTFCANTTCL ITIIYDQSGN GNHLTQAPPG GFDGPDTDGY DNLASAIGAP VTLNGQKAYG VFMSPGTGYR NNEATGTATG DEAEGMYAVL DGTHYNDACC FDYGNAETSS TDTGAGHMEA IYLGNSTTWG YGAGDGPWIM VDMENNLFSG ADEGYNSGDP SISYRFVTAA VKGGADKWAI RGANAASGSL STYYSGARPD YSGYNPMSKE GAIILGIGGD NSNGAQGTFY EGVMTSGYPS DDTENSVQEN IVAAKYVVGS

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

39 files · 808 MB

All files808 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 1wd3A01

Description

Molecular system

Sequences

Experiments

Files

Contributors