inductive-bio / strong-docking-baseline
Code accompanying our blog post on a stronger docking baseline for Alpha Fold 3 docking
☆20Updated 11 months ago
Alternatives and similar repositories for strong-docking-baseline:
Users that are interested in strong-docking-baseline are comparing it to the libraries listed below
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆46Updated 2 weeks ago
- Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3…☆53Updated 3 months ago
- Convert coarse-grained protein structure to all-atom model☆37Updated 10 months ago
- It's a package for evaluation of predicted poses, right?☆52Updated this week
- an ultra-fast and accurate program for deterministic protein sidechain packing☆30Updated 2 months ago
- A benchmark for 3D biomolecular structure prediction models☆57Updated 4 months ago
- ☆68Updated 10 months ago
- Python package for the analysis of natural and modified peptides using a set of modules to study their sequences☆33Updated 3 months ago
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆41Updated last month
- Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file☆32Updated last year
- BitBIRCH clustering algorithm☆70Updated last month
- Quick mapping of Uniprot sequences to PDB structures☆31Updated last month
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆47Updated last week
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆23Updated this week
- Training and inference code for ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design [ICLR 2025 ora…☆63Updated 3 weeks ago
- ☆25Updated 8 months ago
- ☆59Updated last year
- A benchmark dataset for protein-ligand co-folding prediction☆20Updated 3 months ago
- ☆37Updated last year
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆18Updated last year
- PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking☆34Updated 7 months ago
- ☆59Updated this week
- Calculation of interatomic interactions in molecular structures☆92Updated 8 months ago
- Composing Unbalanced Flows for Flexible Docking and Relaxation (ICLR 2025)☆36Updated 2 weeks ago
- ☆89Updated 2 months ago
- Data sharing for High-throughput Prediction of Changes in Protein Conformational Distributions with Subsampled AlphaFold2☆39Updated 11 months ago
- Novana is a cheminformatics tool that extends the decomposition of molecules into Bemis-Murcko frameworks.☆52Updated 2 months ago
- Fully automated high-throughput MD pipeline☆60Updated last week
- Kinase-focused fragment library☆65Updated 3 months ago
- Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, …☆57Updated 6 months ago