mdCATH 3topA03

Open

Antonio Mirarchi;Toni Giorgino;Gianni De Fabritiis;

MD-A00BV2

Created: 7 Jun 2026
License: This trajectory is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. (opens in a new tab)

Description

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

Starting structure: 3TOPPDB 3TOP(opens in a new tab)
Force field: CHARMM22*TIP3P
Engine: ACEMD
Method: Classical MD
Ensemble: NVT
Temperature: 320 K
Timestep: 4 fs
Frames: 11,760
Composition: Molecules of interest
ProteinProtein · 1 chain5,984 atoms379 residues
Total5,984 atoms379 residues
Box dimensions: Cubic

Sequences

Sequence 1Protein · 379 residues

PVMVPYWSLG FQLCRYGYQN DSEIASLYDE MVAAQIPYDV QYSDIDYMER QLDFTLSPKF AGFPALINRM KADGMRVILI LDPAISGNET QPYPAFTRGV EDDVFIKYPN DGDIVWGKVW PDFPDVVVNG SLDWDSQVEL YRAYVAFPDF FRNSTAKWWK REIEELYNNP QNPERSLKFD GMWIDMNEPS SFVNGAVSPG CRDASLNHPP YMPHLESRDR GLSSKTLCME SQQILPDGSL VQHYNVHNLY GWSQTRPTYE AVQEVTGQRG VVITRSTFPS SGRWAGHWLG DNTAAWDQLK KSIIGMMEFS LFGISYTGAD ICGFFQDAEY EMCVRWMQLG AFYPFSRNHN TIGTRRQDPV SWDVAFVNIS RTVLQTRYT

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

48 files · 1.1 GB

All files1.1 GB

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 3topA03

Description

Molecular system

Sequences

Experiments

Files

Contributors