A toolkit developed to predict and analyze PROTAC-mediated protein degradation complexes using AlphaFold3.

Predicting stoichiometry of protein complexes using AlphaFold3 and structural templates

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.

Clean, minimal, accessible reproduction of DeepSeek R1-Zero

This is the repository for PIPR. This repository contains the source code and links to some datasets used in the ISMB/ECCB-2019 paper "Multifaceted Protein-Protein Interaction Prediction Based on S…

Learning and Aligning Large Protein Families with support of protein language models.

Differentiable Pairing using Soft Scores

Bib'23: Improved the Heterodimer Protein Complex Prediction with Protein Language Models

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RBFE) calculations on protein-ligand systems, compatible with …

Prediction of ligand binding site

MaSIF-neosurf: surface-based protein design for ternary complexes.

Ligand Binding Site detection using Deep Learning

Fast deep learning methods for large-scale protein-protein interaction screening

📐 Symmetry-corrected RMSD in Python

Toolkit for alphafold3 input and output files

SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

Official repository for the Boltz-1 biomolecular interaction model

[ICLR 2024] ProFSA: Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment

[NeurIPS 2023] DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening