Alex Morehead's repositories
awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
alphafold_non_docker
Open source code for AlphaFold.
lightning-hydra-template
PyTorch Lightning + Hydra. A very user-friendly template for rapid and reproducible ML experimentation with best practices. ⚡🔥⚡
SSL-With-DR-And-GNNs
[IEEE ICMLA '23] Semi-supervised learning with dimensionality reduction and graph neural networks.
awesome-docking
An awesome & curated list of docking papers
geometric-rna-design
Multi-State RNA Design with Geometric Multi-Graph Neural Networks
amorehead.github.io
A beautiful, simple, clean, and responsive Jekyll theme for academics
cense-ionic
Helping facilitate sensical personal finance practices.
chroma
A generative model for programmable protein design
conditional-flow-matching
TorchCFM: a Conditional Flow Matching library
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.
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.
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
torchdyn
A PyTorch library entirely dedicated to neural differential equations, implicit models and related numerical methods