PARCE: Protocol for Amino acid Refinement through Computational Evolution

The in silico design of peptides and proteins as binders is useful for diagnosis therapeutics due to their low adverse effects major specificity. To select the most promising candidates, a key matter understand interactions with protein targets. In this work, we present PARCE, an open source Protocol Amino acid Refinement through Computational Evolution that implements advanced method proteins. protocol performs random mutation binder sequence, then samples bound conformations using molecular dynamics simulations, evaluates protein-protein from multiple scoring. Finally, it accepts or rejects by applying consensus criterion based on binding scores. procedure iterated aim explore efficiently novel sequences potential better affinities toward We also provide tutorial running reproducing methodology.