/

Communities My depositions

MDRepoNeed help? e-INFRA CZ helpdesk

SARS spike receptor binding domain | MDRepo

SARS spike receptor binding domain

Open

Vito Genna;

MD-A001M9

Created: 20 Apr 2020
License: This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License (opens in a new tab)

Overview
Experiments 1
People & affiliations 1

Publishing

License

This trajectory dataset is released under a Creative Commons Attribution 4.0 International Public License (opens in a new tab)

Related work

PDB

6VW1 (opens in a new tab)

UniProt

P0DTC2 (opens in a new tab)

Last updated 26 Jun 2026

Description

Theoretical model generated using Modeller from the PDB 6vw1

Molecular system

Starting structure: 6VW1PDB 6VW1(opens in a new tab)
Engine: GROMACS 2019.1
Method: Classical MD
Ensemble: NPT
Temperature: 310 K
Timestep: 2 fs
Length: 200 ns
Frames: 20,001
Composition: Molecules of interest
RBDProtein · 1 chain3,000 atoms193 residues
Total3,000 atoms193 residues
Box dimensions: Triclinic
a8.258nm
b7.786nm
c6.743nm

Sequences

1

Sequence 1Protein · 193 residues

NLCPFGEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG QTGVIADYNY KLPDDFMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP FERDISNVPF SPDGKPCTPP ALNCYWPLND YGFYTTTGIG YQPYRVVVLS FELLNAPATV CGP

Experiments

1

Run	Outputs
replica 1	Trajectory Analyses

Files

31 files · 909 MB

All files909 MB

average.pdbPDB
firstFrame.pdbPDB
structure.pdbPDB
trajectory.xtcXTC
noelem.pdbPDB
pocket_10.pdbPDB
pocket_03.pdbPDB
pocket_04.pdbPDB
pocket_05.pdbPDB
pocket_06.pdbPDB

Contributors

Research groups: IRB Barcelona, Orozco lab