locuaz optimization protocol

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locuaz is a high-performance software platform designed specifically for in-silico optimization of antibodies, antibody fragments like nanobodies, or any peptide binder towards other proteins and small ligands.

Rather than being a single protocol, locuaz provides a platform upon which multiple optimization protocols can be implemented, thus offering versatility and adaptability to diverse scientific needs.

locuaz initiates the optimization process by generating a variety of target-binder complexes through random mutations in the binder sequence. Following this, the complexes undergo parallel minimization and equilibration before a NPT Molecular Dynamics (MD) simulation is run. Target-binder interactions on each frame are then simultaneously assessed by a set of scorers, utilizing available processors to then estimate if the mutations improved affinity. If so, the procedure is repeated with the new complexes, continuing the exploration of new binders. This workflow is outlined in Figure 1.

With its tailored design for HPC environments and a flexible approach to various protocols, locuaz delivers efficient in-silico optimization.


Figure 1: The protocol’s workflow.

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