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
Learning
- Platform flow
- Blocks
- Tutorial: running a simple optimization
- Tutorial: using Tleap topologies
- Tutorial: optimizing an antibody against a ligand
- Job submission
- 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_positionsandfailed_memory_positionsat the same time? - 5_ What are the empty brackets in the
memory_positionslist?