AspirinCode

SRCPPIS

md-agent

Molecular dynamics simulations with an LLM agent

Molly.jl

Molecular simulation in Julia

ML-augmented-docking-CYP-inhibition

Code repository for Machine Learning-Augmented Docking. 1. CYP inhibition prediction. Authors: Benjamin Weiser, Jérôme Genzling , Mihai Burai Patrascu, and Nicolas Moitessier

ScaffoldGVAE

ScaffoldGVAE: A Variational Autoencoder Based on Multi-View Graph Neural Networks for Scaffold Generation and Scaffold Hopping of Drug Molecules

NYUTron

public code repository for paper "Health system scale language models are general purpose clinical prediction engines"

compchem

Computational Chemistry

outlines

Structured Text Generation

UNFRAMED

RDKit_to_graph

GraphRXN

GraphRXN

Ligand_Generation

Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning

2022-2023-DGM-AIMasters-course

Deep Generative Models course, AIMasters, 2022

2023-DGM-MIPT-course

Deep Generative Models course, 2023

2022-2023-DGM-MIPT-course

Deep Generative Models course, 2022-2023

xyz2svg

A lightweight script to make vector images of molecules

rxdock

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]

KGDiff

Towards Explainable Target-Aware Molecule Generation with Knowledge Guidance

nucleic-acid-binding

optimalpdb

This script gets 3D structures by taking UniProt ID(s) as input, figures out the currently available PDB structures that are experimentally validated, and chooses the best structure based on lowest resolution (A value). Then it extracts PDB ID(s) that should be retrieved and stores it in a CSV file.

MultiPPIMI

a deep learning framework for predicting interactions between protein-protein interaction targets and modulators

ORDerly

Chemical reaction data & benchmarks. Extraction and cleaning of data from Open Reaction Database (ORD)

mrl

Molecular Reinforcement Learning

GeoDock

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer.

DeepRank-GNN-esm

Graph Network for protein-protein interface including language model features

bVAE-IM

Implementation of "Chemical Design with GPU-based Ising Machine"

Docking-Based-VS

Docking-Based VS

LS-MolGen

A ligand-and-structure dual-driven deep reinforcement learning method for target-specific molecular generation

icons-for-chemists

AI-for-Bio

A free and collaborative space for Machine Learning 🤖 applied to Biology 🧬