Multiseq aligns two protein structures using a tool called Structural Alignment of Multiple Proteins (STAMP). By locating regions with low Qres, we can hopefully identify regions of structural differences between the two RBDs. In this tutorial, we will get started with VMD and then calculate Qres between the SARS-CoV-2 RBD (PDB entry: 6vw1) and SARS-CoV RBD (PDB entry: 2ajf) using the VMD plugin Multiseq. Aligning the RBD regions of two spike proteins.Software Tutorial: Finding Local Differences in the SARS-CoV and SARS-CoV-2 Spike Protein Structures Integrating molecular dynamics analyses with DynOmics.Adding directionality to spike protein GNM simulations using ANM.Analyzing coronavirus spike proteins using GNM.
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