zachary-mcdargh

zachary-mcdargh's Stars

• NVIDIA/DeepLearningExamples

  State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.

  Language:Jupyter Notebook13.7k2968493.3k

• huggingface/accelerate

  🚀 A simple way to launch, train, and use PyTorch models on almost any device and distributed configuration, automatic mixed precision (including fp8), and easy-to-configure FSDP and DeepSpeed support

  Language:Python8.1k981.7k1k

• facebookresearch/esm

  Evolutionary Scale Modeling (esm): Pretrained language models for proteins

  Language:Python3.4k65320658

• sokrypton/ColabFold

  Making Protein folding accessible to all!

  Language:Jupyter Notebook2k49564507

• lucidrains/performer-pytorch

  An implementation of Performer, a linear attention-based transformer, in Pytorch

  Language:Python1.1k1786145

• dauparas/ProteinMPNN

  Code for the ProteinMPNN paper

  Language:Jupyter Notebook1.1k2496319

• e3nn/e3nn

  A modular framework for neural networks with Euclidean symmetry

  Language:Python99718158149

• PatWalters/practical_cheminformatics_tutorials

  Practical Cheminformatics Tutorials

  Language:Jupyter Notebook8474710150

• deepmodeling/Uni-Mol

  Official Repository for the Uni-Mol Series Methods

  Language:Python75717178132

• LPDI-EPFL/masif

  MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

  Language:Python6072482157

• HeliXonProtein/OmegaFold

  OmegaFold Release Code

  Language:Python558136079

• nadavbra/protein_bert

  Language:Jupyter Notebook507490102

• markovmodel/PyEMMA

  🚂 Python API for Emma's Markov Model Algorithms 🚂

  Language:Python31231892121

• microsoft/constrained-graph-variational-autoencoder

  Sample code for Constrained Graph Variational Autoencoders

  Language:Python23311956

• PattanaikL/GeoMol

  Language:Python15471342

• keiserlab/e3fp

  3D molecular fingerprints

  Language:Python124215733

• undeadpixel/reinvent-randomized

  Recurrent Neural Network using randomized SMILES strings to generate molecules

  Language:Python872331

• playmolecule/ligdream

  Novel molecules from a reference shape!

  Language:Jupyter Notebook817024

• borchero/natural-posterior-network

  Official Implementation of "Natural Posterior Network: Deep Bayesian Predictive Uncertainty for Exponential Family Distributions" (ICLR, 2022)

  Language:Python794113

• biomed-AI/PROTAC-RL

  Language:Python581625

• ostrokach/proteinsolver

  Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

  Language:Jupyter Notebook55238

• GMPavanLab/Swarm-CG

  Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

  Language:Python4471212

• torchmd/torchmd-cg

  Example to fit parameters and run CG simulations using TorchMD and Schnet

  Language:Jupyter Notebook4272010

• bowman-lab/diffnets

  Self-supervised neural nets to understand protein mutations

  Language:Python384311

• learningmatter-mit/Coarse-Graining-Auto-encoders

  Language:Jupyter Notebook21607

• luigibonati/deep-learning-slow-modes

  Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"

  Language:Roff192310

• ramanathanlab/mdlearn

  Machine learning for molecular dynamics

  Language:Python132397

• xmwebb/GBCG

  Language:Python10103

• bio-phys/complexespp

  Coarse-grained simulations of biomolecular complexes

  Language:C++93274

• andrewlferguson/snrv

  State-free (non)-reversible VAMPnets

  Language:Jupyter Notebook7160