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ASMC is a precision tool for deciphering the amino acid diversity that composes the active site of a given homologous protein family.

Selection of reference structure(s)

This step is critical since the structure-based ASMC relies on the homology modeling step to obtain relevant 3D models, i.e. the structural constraints imposed by the selected reference structure(s) may generate irrelevant models that could ultimately be misclassified. The subsequent goal is to identify interesting 3D conformations of your queried protein within the Protein Data Bank (PDB). Reference structure(s) should be carefully chosen under the biological context (open/close state, monomer, ligands, enzymatic results...) and priority should be given to high-resolution holo structures, namely protein-ligand complexes, since active sites are often better characterized.

Active site pocket

ASMC analyses amino acid diversity of protein active sites either given by the user or directly predicted through the ASMC workflow. We advise users to carefully define their queried active site by selecting its amino acid composition based on their own experience (enzymatic assays, mutation, docking...) or literature.