mdcao
Head of Data Science @TandemAI, former ML Scientist at Gritstone Bio and QuantumSi. Interested in Deep Learning, Information Theory and Bioinformaics
Tandem AIBoston, MA, USA
Pinned Repositories
3DLinker
An E(3) Equivariant Variational Autoencoder for Molecular Linker Design
algorithms
Minimal examples of data structures and algorithms in Python
alphafold3-pytorch
Implementation of Alphafold 3 in Pytorch
capsim
japsa
Just Another JAva Package for Sequence Analysis
npAnalysis
Software for Nanopore Analysis
npReader
Read nanopore sequence reads in real-time
npScarf
PhageXpress
Realtime grouping of insert sequences
xm
Expert Model
mdcao's Repositories
mdcao/DRlinker
mdcao/dockstring
A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discovery.
mdcao/3DLinker
An E(3) Equivariant Variational Autoencoder for Molecular Linker Design
mdcao/ProteinMPNN
Code for the ProteinMPNN paper
mdcao/TamGent
Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design
mdcao/TDC
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
mdcao/deepHops
source code for deppHop
mdcao/dgl-lifesci
Python package for graph neural networks in chemistry and biology
mdcao/chemprop
Message Passing Neural Networks for Molecule Property Prediction
mdcao/EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
mdcao/guacamol
Benchmarks for generative chemistry
mdcao/crem
CReM: chemically reasonable mutations framework
mdcao/algorithms
Minimal examples of data structures and algorithms in Python
mdcao/deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
mdcao/dpgen
The deep potential generator
mdcao/Meeko
Interfacing RDKit and AutoDock
mdcao/D2
Speed virtual screening by 50X
mdcao/GraphINVENT
Graph neural networks for molecular design.
mdcao/practical_cheminformatics_tutorials
Practical Cheminformatics Tutorials
mdcao/pyscreener
pythonic interface to virtual screening software
mdcao/pytorch-lightning
The lightweight PyTorch wrapper for high-performance AI research. Scale your models, not the boilerplate.
mdcao/DD_protocol
Official repository for the Deep Docking protocol
mdcao/pytorch_geometric
Graph Neural Network Library for PyTorch
mdcao/ttic-31230
mdcao/fsdl-text-recognizer-2021-labs
Complete deep learning project developed in Full Stack Deep Learning, Spring 2021
mdcao/Lib-INVENT
mdcao/DeLinker
mdcao/d2l-en
Interactive deep learning book with code, math, and discussions. Available in multi-frameworks.
mdcao/molecule-generation
Molecular SMILE generation with recurrent neural networks
mdcao/spoa
SIMD partial order alignment tool/library