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alfatclust

Biological sequence clustering tool with dynamic threshold

alphafold_finetune

Python code for fine-tuning AlphaFold to perform protein-peptide binding predictions

attract

ATTRACT program suite for macromolecular docking (protein-protein, protein-nucleic acid, protein-peptide)

bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

blind_docking

Experiment script of ICLR MLDD 2023 paper

blindpypr

Perform probe-guided blind docking with FTMap and DOCK6

camp

predicting peptide-protein interactions

d4-rescore

Re-scoring a set of docked ligands with off-the-shelf algorithms to assess utility in virtual screening

datascienceprojects

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deepdockinggui

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

deeprank-gnn

Graph Network for protein-protein interface

diffdock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

dockingml

A package for MD, Docking and Machine learning drug discovery pipeline

dockingpie

A Consensus Docking Plugin for PyMOL

dsdp

Deep Site and Docking Pose (DSDP) is a blind docking strategy accelerated by GPUs, developed by Gao Group. For the site prediction part, several modifications are introduced to PUResNet program. The pose sampling part is similar as AutoDock Vina combined with a number of modifications.

equibind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

fabind

FABind: Fast and Accurate Protein-Ligand Binding (NeurIPS 2023)

flipbookapp

getbox-pymol-plugin

A PyMOL Plugin for calculating docking box for LeDock, AutoDock and AutoDock Vina.

gnina

A deep learning framework for molecular docking

hsm

Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."

idock

idock is a multithreaded virtual screening tool for flexible ligand docking for computational drug discovery.

iidl-peppi

Interpretable Progressive Transfer Learning for Peptide-Protein-Specific Interaction Profiling based on Biological Sequence Pragmatic Analysis

info

karmadock

labodock

LABODOCK: A Colab-Based Molecular Docking Tools

labox

LaBOX: A Grid Box Calculation Tool for Molecular Docking

libmolgrid

Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows