Background

In order to identify new, unknown proteins associated with viruses, such as COVID-19, it is easiest to start by identifying structurally related proteins. LLNL scientists have created tools that identify structurally related proteins and their relevant residues, called cSpan.

Technology Overview

The cSpan (sequence conservation in structurally conserved “span” regions) calculation is a quantitative measure of residue conservation in local structure context. It is used to identify residues on a protein that are conserved with respect to a set of structurally related proteins. A set of protein structures (consisting of a reference protein, and any number of related proteins) is aligned using the LGA (local-global alignment) software (see Local-Global Alignment: A Method for Finding 3D Similarities in Protein Structures).