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MoDEL 1MK3

MoDEL 1MK3

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

Created 29 Dec 2022Updated 26 Jun 2026This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License

MD-A000PL

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

1MK3 (opens in a new tab)

UniProt

Q92843 (opens in a new tab)

3D structure

Description

10 ns simulation of 1MK3 pdb structure from MoDEL dataset

Molecular system

Starting structure: 1MK3PDB 1MK3(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: 2,698 atoms

Sequences

1

Sequence 1Protein · 178 residues

ATPASAPDTR ALVADFVGYK LRQKGYVCGA GPGEGPAADP LHQAMRAAGD EFETRFRRTF SDLAAQLHVT PGSAQQRFTQ VSDELFQGGP NWGRLVAFFV FGAALCAESV NKEMEVLVGQ VQEWMVAYLE TRLADWIHSS GGWAEFTALY GDGALEEARR LREGNWASVR LEHHHHHH

Experiments

1

Run	Outputs
replica 1	Trajectory Analyses

Files

25

25 files · 410 MB

All files410 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