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MoDEL 1D8U

MoDEL 1D8U

Tim Meyer,Marco D'Abramo,Adam Hospital,Manuel Rueda,Carles Ferrer-Costa,Alberto Pérez,Oliver Carrillo,Jordi Camps,Carles Fenollosa,Dmitry Repchevsky,

Created 28 Dec 2022Updated 26 Jun 2026This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License

MD-A000CE

Overview
Experiments 1
Analyses
People 12

Publishing

License

This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public LicenseView the license text (opens in a new tab)

Related work

PDB

1D8U (opens in a new tab)

UniProt

O04986 (opens in a new tab)

3D structure

Description

10 ns simulation of 1D8U pdb structure from MoDEL dataset

Molecular system

Starting structure: 1D8UPDB 1D8U(opens in a new tab)
Program: Amber 8
Force field: Amber Parm99
Water model: TIP3P
Method: Classical MD
Ensemble: NPT
Temperature: 300 K
Timestep: 2 fs
Length: 10 ns
Frames: 10,000
Size: 5,200 atoms

Sequences

1

Sequence 1Protein · 165 residues

ALVEDNNAVA VSFSEEQEAL VLKSWAILKK DSANIALRFF LKIFEVAPSA SQMFSFLRNS DVPLEKNPKL KTHAMSVFVM TCEAAAQLRK AGKVTVRDTT LKRLGATHLK YGVGDAHFEV VKFALLDTIK EEVPADMWSP AMKSAWSEAY DHLVAAIKQE MKPAE

Experiments

1

Run	Outputs
replica 1	Trajectory Analyses

Files

27

27 files · 790 MB

All files790 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: IRB Barcelona, Orozco lab
Contact: For any questions please send a mail to adam.hospital@irbbarcelona.org or daniel.beltran@irbbarcelona.org