amorehead
Machine learning & computational biology PhD @ University of Missouri. Prev: Research intern @ Profluent & Absci. Geometric deep learning & generative models.
University of MissouriColumbia, Missouri
Pinned Repositories
ProteinWorkshop
Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
alphafold_non_docker
Open source code for AlphaFold.
awesome-equivariant-network
Paper list for equivariant neural network
awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
EGNN-DGL
An implementation of the Equivariant Graph Neural Network (EGNN) layer type for DGL-PyTorch.
bio-diffusion
A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization
DeepInteract
A geometric deep learning pipeline for predicting protein interface contacts. (ICLR 2022)
GCPNet
A PyTorch implementation of Geometry-Complete SE(3)-Equivariant Perceptron Networks (GCPNets)
PoseBench
Comprehensive benchmarking of protein-ligand structure generation methods
MMDiff
Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
amorehead's Repositories
amorehead/awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
amorehead/alphafold_non_docker
Open source code for AlphaFold.
amorehead/SSL-With-DR-And-GNNs
[IEEE ICMLA '23] Semi-supervised learning with dimensionality reduction and graph neural networks.
amorehead/amorehead
My GitHub profile header.
amorehead/dots
A collection of dot configuration files for personal use.
amorehead/FoldFlow
Code release for our recent paper "SE(3)-Stochastic Flow Matching for Protein Backbone Generation" https://arxiv.org/abs/2310.02391
amorehead/gdown
Google Drive Public File Downloader when Curl/Wget Fails
amorehead/RoseTTAFold-All-Atom
amorehead/awesome-docking
An awesome & curated list of docking papers
amorehead/lightning
Deep learning framework to train, deploy, and ship AI products Lightning fast.
amorehead/MMDiff
Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
amorehead/alphafold3-pytorch-lightning-hydra
Implementation of AlphaFold 3 with the PyTorch Lightning + Hydra
amorehead/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
amorehead/cense-ionic
Helping facilitate sensical personal finance practices.
amorehead/chroma
A generative model for programmable protein design
amorehead/DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
amorehead/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.
amorehead/graphein
Protein Graph Library
amorehead/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.
amorehead/InterstellarOceans
A round-robin tournament scheduler written in Angular 6+.
amorehead/Meeko
Interfacing RDKit and AutoDock
amorehead/NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
amorehead/openfold
Trainable, memory-efficient, and GPU-friendly PyTorch 2.0 reproduction of AlphaFold 2
amorehead/posebusters
Plausibility checks for generated molecule poses.
amorehead/posecheck
Pose checks for 3D Structure-based Drug Design methods
amorehead/ProLIF
Interaction Fingerprints for protein-ligand complexes and more
amorehead/pytorch
Tensors and Dynamic neural networks in Python with strong GPU acceleration
amorehead/pytorch_geometric
Graph Neural Network Library for PyTorch
amorehead/RoseTTAFold2NA
RoseTTAFold2 protein/nucleic acid complex prediction
amorehead/torchdyn
A PyTorch library entirely dedicated to neural differential equations, implicit models and related numerical methods