BioinfoMachineLearning/cryoppp

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Language
Python
License
MIT License
Created almost 2 years ago
Updated about 1 year ago

BioinfoMachineLearning/cryoppp

BioinfoMachineLearning

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The programs of creating cryo-EM particle picking datasets

bio-diffusion

A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization (Nature CommsChem)

PoseBench

Comprehensive benchmarking of protein-ligand structure generation methods (ICML 2024 AI4Science)

Jupyter Notebook

DeepInteract

A geometric deep learning pipeline for predicting protein interface contacts. (ICLR 2022)

DIPS-Plus

The Enhanced Database of Interacting Protein Structures for Interface Prediction

GCPNet

A PyTorch implementation of Geometry-Complete SE(3)-Equivariant Perceptron Networks (GCPNets)

CryoVirusDB

A dataset of labeled virus particles in cryo-EM micrographs (images) for training and testing machine learning methods of virus particle picking

MULTICOM3

The software system of improving AlphaFold2- and AlphaFold-Multimer-based protein tertiary & quaternary structure prediction. It was developed by the Bioinformatics and Machine Learning Lab at the University of Missouri. It was blindly tested in CASP15 and ranked among the best server predictors in 2022. It improves AlphaFold's accuracy by 5-10%.

ATOMRefine

3D equivariant graph transformer for all-atom refinement of protein tertiary structures

DeepRefine

A geometric deep learning method for refining and assessing protein complex structures.

CDPred

Deep transformer for predicting interchain residue-residue distances of protein complexes

cryo2struct

The programs for preprocessing cryo-EM density maps for machine learning

EnQA

A 3D-equivariant neural network for protein structure accuracy estimation

GCDM-SBDD

A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)

GCPNet-EMA

Protein Structure Accuracy Estimation using Geometry-Complete Perceptron Networks (Protein Science 2024)

DProQ

Deep learning prediction of protein complex structure quality

TransFew

Transformer for protein function prediction (version 2)

Jupyter Notebook

deep-learning-hpc-project-template

A PyTorch Lightning project template adapted for high-performance computing clusters such as Summit and Fugaku

MULTICOM_qa

Evaluate the quality of protein multimer structure models

FunBench

The programs and data for benchmarking protein function site prediction methods

Jupyter Notebook

BML_HiC_Data_Analysis

A set of tools for Hi-C data analysis developed by Bioinformatics and Machine Learning Lab