There are 9 repositories under protein-ligand-interactions topic.
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
RxDock is a fork of rDock. Note: the latest code is under development. Please do git checkout patched-rdock after clone if you want patched rDock. [IMPORTANT NOTE: pull requests should be posted on GitLab, this is a read-only source code mirror]
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
Structural Bioinformatics Training Workshop & Hackathon 2018
Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets
PSICHIC (pronounced Psychic) - PhySIcoCHemICal graph neural network for learning protein-ligand interaction fingerprints from sequence data
Implementation of ICLR23 paper "Molecule Generation for Target Protein Binding with Structural Motifs"
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
Implementation of Nvidia's NeuralPlexer, for end-to-end differentiable design of functional small-molecules and ligand-binding proteins, in Pytorch
DeltaVina scoring function
Protein target prediction using random forests and reliability-density neighbourhood analysis
Contact map analysis for biomolecules; based on MDTraj
Comparison of active site and full kinase sequences for drug-target affinity prediction and molecular generation. Full paper: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00889
This repository contains the code for the work on protein-ligand interaction with GNNs and XAI
Methods for mapping genomic data onto 3D protein structure.
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
Open source code for DyScore
A program analyzing 3D protein structures from PDB to generate 2D binding motifs
Some notes (cookbook) for pyMol. Protein Crystallography course.
Web application for protein-ligand binding sites analysis and visualization
[Bioinformatics 2022] Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction
All in one Structure-Based Vitual Screening workflow based on the concept of consensus docking.
Multi-Atom Structure/Selection Toolkit with Interaction Capabilities
[AAAI 2024] Binding-Adaptive Diffusion Models for Structure-Based Drug Design
Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes
Repository for the Taba tool
MLT-LE: predicting drug–target binding affinity with multi-task residual neural networks : https://arxiv.org/abs/2209.06274
PepFoot: a user friendly GUI for protein footprinting analysis
PrimaryOdors.org molecular docker.
[ICML 2024] Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation
This is a simple script to use [plip](https://github.com/pharmai/plip) to batch analysis of interactions between proteins and ligands that are results of smina (vina) docking.