# Locuaz: an in silico platform for protein binders optimization

## TL;DR

Locuaz is a computational platform that optimizes protein binders by efficiently exploring mutations and simulating interactions to improve binding affinity.

## Contribution

The novel contribution is a modular and customizable platform for in silico optimization of protein binders with parallel mutation exploration.

## Key findings

- The platform supports parallel mutation stream exploration for high-throughput screening on HPC systems.
- It integrates molecular dynamics simulations and scoring functions to prioritize effective mutations.
- The platform is open-source with available documentation and supplementary data.

## Abstract

Engineering high-affinity binders targeting specific antigenic determinants remains a challenging and often daunting task, requiring extensive experimental screening. Computational methods have the potential to accelerate this process, reducing costs and time, but only if they demonstrate broad applicability and efficiency in exploring mutations, evaluating affinity, and pruning unproductive mutation paths.

In response to these challenges, we introduce a new computational platform for optimizing protein binders towards their targets. The platform is organized as a series of modules, performing mutation selection and application, molecular dynamics simulations to sample conformations around interaction poses, and mutation prioritization using suitable scoring functions. Notably, the platform supports parallel exploration of different mutation streams, enabling in silico high-throughput screening on High Performance Computing (HPC) systems. Furthermore, the platform is highly customizable, allowing users to implement their own protocols.

The source code is available at https://github.com/pgbarletta/locuaz and documentation is at https://locuaz.readthedocs.io/. The data underlying this article are available at https://github.com/pgbarletta/suppl_info_locuaz