[Setup] Setting up NSP15, NSP9, NSP5 (main protease), nucleoprotein (N-term), NSP3 (x domain), NSP12, NSP10, NSP13 #40
Description
Just as a heads up to try and prevent further duplication - we are looking to simulate many of the SARS1 versions of proteins, in addition to the SARS2 proteins, so we can compare how the viruses are fundamentally different, which might provide insight into their disease-level differences. Here's a list of proteins we've set up and are currently making FAH projects for :
NSP5 - Main protease, 3CL-PRO, DIMER (SARS2) [PDB: 6y2g]
NSP5 - Main protease, 3CL-PRO, DIMER (SARS1) [PDB: 3VB3]
NSP15, HEXAMER (SARS2) [PDB: 6VWW]
NSP15, HEXAMER (SARS1) [PDB: 2H85]
Nucleoprotein (N-term), MONOMER (SARS2) [PDB: 6VYO]
Nucleoprotein (N-term), MONOMER (SARS1) [PDB: 2OFZ]
NSP3 - Mac1-Mac2 (X) domain, MONOMER (SARS2) [PDB: 6W02]
NSP3 - Mac1-Mac2 (X) domain, MONOMER (SARS1) [PDB: 2FAV]
NSP12 (polymerase), MONOMER (SARS2) [https://swissmodel.expasy.org/interactive/JDUya4/models/]
--Homology model of 6NUR
NSP9, DIMER (SARS2) [https://swissmodel.expasy.org/interactive/GqQg8A/models/03]
--Homology model of 1qz8
NSP9, DIMER (SARS1) [PDB: 1qz8]
SARS-CoV-2 NSP10 ('6W4H')
SARS-CoV-2 NSP13 ('swiss model 01 - 6jyt homolog')
We have made some overlap on SARS2 proteins - this is mainly because we are having to set them up to run FAST on them and our protocol is a little bit different than the systems @choderalab has already setup. So, we figure we should throw those on FAH as well since we're setting them up anyway. In general we are using Amber03, so while the SARS2 proteins are duplicated, the force field is different.