empyriumz

alphafold

Open source code for AlphaFold.

Ca-Backbone-Prediction

Deep Learning for Ca Backbone Prediction from High Resolution CryoEM Data

CoverMyMeds_TimeSeries

The Erdős Institute 2020 Bootcamp Team Project

CryoEM

Deep learning based cryoEM density map enhancement

Entanglement-Dynamics

Random unitary time evolution plus projective measurement in the one-dimensional quantum circuit model

GeoLDM

Geometric Latent Diffusion Models for 3D Molecule Generation

Numerical-Berry-curvature

Numerical implementation of Berry curvature calculation for tight binding Hamiltonians

Supervised-learning-of-Many-Body-Localization

A simple neural network structure to classify many-body localized (MBL) and thermalized phases

CryoFEM

Deep learning based cryoEM density map feature enhancement

ESMBind

Deep learning + physical modeling for 3D protein metal ion binding prediction

empyriumz/CryoEM

Deep learning based cryoEM density map enhancement

empyriumz/GeoLDM

Geometric Latent Diffusion Models for 3D Molecule Generation

empyriumz/alphafold

Open source code for AlphaFold.

empyriumz/Ca-Backbone-Prediction

Deep Learning for Ca Backbone Prediction from High Resolution CryoEM Data

empyriumz/deepEMhancer

Deep learning for cryo-EM maps post-processing

empyriumz/DPIR

Plug-and-Play Image Restoration with Deep Denoiser Prior (IEEE TPAMI 2021) (PyTorch)

empyriumz/DiffPack

Implementation of DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

empyriumz/DiffSBDD

A Euclidean diffusion model for structure-based drug design.

empyriumz/EM-GAN

EM-GAN is a computational tool, which enables capturing protein structure information from cryo-EM maps more effectively than raw maps. It is based on 3D deep learning. It is aimed to help protein structure modeling from cryo-EM maps.

empyriumz/esm

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

empyriumz/esm-3

empyriumz/GeoDiff

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

empyriumz/gradient-boosting-survival-embeddings

Improving gradient boosting survival analysis with embeddings and debiased estimators

empyriumz/LMetalSite

MetalSite: alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning

empyriumz/m-ionic

Protein-metal ion interaction modeling

empyriumz/metal-site-prediction

empyriumz/NAFNet

The state-of-the-art image restoration model without nonlinear activation functions.

empyriumz/NeuralPLexer

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

empyriumz/ngboost

Natural Gradient Boosting for Probabilistic Prediction

empyriumz/npc_gzip

empyriumz/OmegaFold

OmegaFold Release Code

empyriumz/openfold

Trainable PyTorch reproduction of AlphaFold 2

empyriumz/PocketGen

empyriumz/protein-sequence-models

empyriumz/ProteinMPNN

Code for the ProteinMPNN paper

empyriumz/reference-learning

empyriumz/RepLKNet-pytorch

Scaling Up Your Kernels to 31x31: Revisiting Large Kernel Design in CNNs (CVPR 2022)

empyriumz/SiamDiff

Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)

empyriumz/targetdiff

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

empyriumz/Uni-Mol

Official Repository for the Uni-Mol Series Methods