amorehead

awesome-molecular-generation

Awesome papers related to generative molecular modeling and design.

alphafold_non_docker

Open source code for AlphaFold.

alphafold3-pytorch-lightning-hydra

Implementation of AlphaFold 3 with the PyTorch Lightning + Hydra

dots

A collection of dot configuration files for personal use.

SSL-With-DR-And-GNNs

[IEEE ICMLA '23] Semi-supervised learning with dimensionality reduction and graph neural networks.

gdown

Google Drive Public File Downloader when Curl/Wget Fails

RoseTTAFold-All-Atom

awesome-docking

An awesome & curated list of docking papers

MMDiff

Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion

amorehead.github.io

Personal website (based on al-folio)

amorehead.github.io.new

ccdutils

A set of python tools to deal with PDB chemical components definitions for small molecules, taken from the wwPDB Chemical Component Dictionary, uses RDKit

cense-ionic

Helping facilitate sensical personal finance practices.

DiffDock

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

dimorphite_dl

Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.

graphein

Protein Graph Library

gypsum_dl

Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.

InterstellarOceans

A round-robin tournament scheduler written in Angular 6+.

Meeko

Interfacing RDKit and AutoDock

NeMo

NeMo: a toolkit for conversational AI

NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch 2.0 reproduction of AlphaFold 2

posebusters

Plausibility checks for generated molecule poses.

posecheck

Pose checks for 3D Structure-based Drug Design methods

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

pytorch_geometric

Graph Neural Network Library for PyTorch

RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction

theme-academic-cv

torchdyn

A PyTorch library entirely dedicated to neural differential equations, implicit models and related numerical methods