locuaz optimization protocol

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.

Installation

• Installation
  • Prerequisites
  • Stable release
  • From sources (Option 3, developers only)
  • Post-installation

Learning

• Platform flow
  • Introduction
  • Platform DAGs
  • Summary
• Blocks
  • Introduction
  • Mutation Generator (deprecated)
  • Mutation Creator
  • Mutator
  • Sampler
  • Scorer
  • Pruner
  • Summary
• Tutorial: running a simple optimization with GROMACS topologies
  • Setting up the system
  • Necessary files
  • The configuration file
  • Running the protocol
• Tutorial: using Tleap topologies
  • Setting up the system
  • Necessary files
  • The configuration file
  • Running the protocol
• Tutorial: optimizing an antibody against a ligand
  • Necessary files
  • The configuration file
  • Running the protocol
• Job submission
  • Running from SLURM
  • Running from PBS
  • Running from within an apptainer container
• Frequently Asked Questions
  • 1_ I used tleap to build my initial system but now my starting PDB has no chainID information and locuaz won’t take it. What can I do about it?
  • 2_ My complex is spreading apart. Can I use GROMACS pulling to keep them together?
  • 3_ What is NUMA? How can I know the number of NUMA regions my machine has?
  • 4_ Why use both memory_positions and failed_memory_positions at the same time?
  • 5_ What are the empty brackets in the memory_positions list?
  • 6_ AssertionError: No valid branches in input.
  • 7_ AssertionError: Too few segments in the input PDB. There should be at least 3 (target+binder+solvent).

Reference

• Mutation
• Mutation Generators (deprecated)
• Mutation Creator
• Scorers
• Mutators
• Stats
• Pruners
• Miscellaneous
• YAML configuration file
• Citing
• History
• Developing

Indices and tables

• Index

• Module Index

• Search Page