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MULTICOM_ligand 0.4.0

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MULTICOM_ligand 0.4.0

Contents:

Installation
DynamicBind checkpoint (~0.25 GB)
Tutorials
RoseTTAFold-All-Atom checkpoint (~1.5 GB)
How to prepare MULTICOM_ligand data
Available inference methods
How to run inference with individual methods
How to run inference with a method ensemble
NOTE: the suffixes for both output_dir and ensemble_benchmarking_repeat_index should be modified to e.g., 2, 3, …
benchmark using the PoseBusters Benchmark dataset e.g., after generating 40 complexes per target with each method
benchmark using the Astex Diverse dataset e.g., after generating 40 complexes per target with each method
benchmark using the DockGen dataset e.g., after generating 40 complexes per target with each method
benchmark using the CASP15 dataset e.g., after generating 40 complexes per target with each method
analyze benchmarking results for the PoseBusters Benchmark dataset
How to create comparative plots of inference results
analyze benchmarking results for the CASP15 dataset
For developers
Acknowledgements
Citing this work
Bonus

Default Configs

Analysis
Data
Model

API Reference

Binding site crop preparation
Complex alignment
Inference relaxation
Minimize energy
Ensemble generation
Data utilities
Model utilities
General utilities
OmegaConf resolvers

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Bonus¶

If you use the code or benchmark method predictions associated with this repository or otherwise find this work useful, please cite:

My brain after building MULTICOM_ligand

Citing this work

Copyright © 2025, Alex Morehead

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