AspirinCode

Awesome-LLM-KG

Awesome papers about unifying LLMs and KGs

smiles-transformer

Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.

CHEM101.6

BEND

Benchmarking DNA Language Models on Biologically Meaningful Tasks

GeoDock

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

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]

ORDerly

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

2022-2023-DGM-MIPT-course

Deep Generative Models course, 2022-2023

Structural-Bioinformatics

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

DeepICL

Official Github for "3D Molecular Generative Framework for Interaction-guided Drug Design" (Nature Communications)

LLM4Mol

A comprehensive repository dedicated to the collection and exploration of studies utilizing Large Language Models for molecular design, protein research, and material science.

2022-2023-DGM-AIMasters-course

Deep Generative Models course, AIMasters, 2022

2023-DGM-MIPT-course

Deep Generative Models course, 2023

LS-MolGen

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

AI-for-Bio

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

KGDiff

Towards Explainable Target-Aware Molecule Generation with Knowledge Guidance

DeepRank-GNN-esm

Graph Network for protein-protein interface including language model features

Ligand_Generation

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

GraphRXN

GraphRXN

ShapeLinker

nucleic-acid-binding

icons-for-chemists

xyz2svg

A lightweight script to make vector images of molecules

bVAE-IM

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

MultiPPIMI

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

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.

mrl

Molecular Reinforcement Learning

Docking-Based-VS

Docking-Based VS

LLM4Mol

A comprehensive repository dedicated to the collection and exploration of studies utilizing Large Language Models for molecular design, protein research, and material science.

MultiPPIMI

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