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SARS-CoV-2 spike receptor binding domain | MDRepo

SARS-CoV-2 spike receptor binding domain

Open

Vito Genna;

MD-A001MA

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 chain2,985 atoms193 residues
Total2,985 atoms193 residues
Box dimensions: Triclinic
a8.074nm
b7.612nm
c6.592nm

Sequences

1

Sequence 1Protein · 193 residues

NLCPFGEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG QTGVIADYNY KLPDDFMGCV LAWNTRNIDA TSTGNYNYKY RLFRKSNLKP FERDISTEIY QAGSTPCNGV EGFNCYFPLQ SYGFQPTNGV GYQPYRVVVL SFELLNAPTV CGP

Experiments

1

Run	Outputs
replica 1	Trajectory Analyses

Files

30 files · 905 MB

All files905 MB

average.pdbPDB
firstFrame.pdbPDB
structure.pdbPDB
trajectory.xtcXTC
noelem.pdbPDB
pocket_10.pdbPDB
pocket_06.pdbPDB
pocket_07.pdbPDB
pocket_08.pdbPDB
pocket_09.pdbPDB

Contributors

Research groups: IRB Barcelona, Orozco lab