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Model name Included proteins Protein name Uniprot entry name Uniprot ID PDB ID Species Ligand(s) Membrane composition Replicates Author Num. of atoms Software Force field
DESRES 100 µs MD of 3CLpro, no water or ions (100 µs) NSP5 Replicase polyprotein 1ab R1AB_SARS2 P0DTD1 6Y84 SARS-CoV-2 1 D. E. Shaw Research 9364 Anton supercomputer specific tools None DES-Amber
Main Protease (Mpro) in Complex with ML188 (no mutation) NSP5 Replicase polyprotein 1ab R1AB_SARS2 P0DTD1 7L0D SARS-CoV-2 ML188 3 Institut Hospital del Mar d'Investigacions Mèdiques 83351 AceMD 3.2.3 CHARMM36 2019
Main Protease (Mpro) in Complex with ML188 (A191V mutation) NSP5 Replicase polyprotein 1ab R1AB_SARS2 P0DTD1 7L0D SARS-CoV-2 ML188 3 Institut Hospital del Mar d'Investigacions Mèdiques 83402 AceMD 3.2.3 CHARMM36 2019
Main Protease (Mpro) in Complex with ML188 (T24A mutation) NSP5 Replicase polyprotein 1ab R1AB_SARS2 P0DTD1 7L0D SARS-CoV-2 ML188 3 Institut Hospital del Mar d'Investigacions Mèdiques 83338 AceMD 3.2.3 CHARMM36 2019
NSP5 Apo form NSP5 Replicase polyprotein 1ab R1AB_SARS2 P0DTD1 6LU7 SARS-CoV-2 2 Exscalate4CoV - CINECA 9364 GROMACS 2020.2 AMBER 99