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deeplearning-500-questions

深度学习500问，以问答形式对常用的概率知识、线性代数、机器学习、深度学习、计算机视觉等热点问题进行阐述，以帮助自己及有需要的读者。 全书分为18个章节，50余万字。由于水平有限，书中不妥之处恳请广大读者批评指正。 未完待续............ 如有意合作，联系[email protected] 版权所有，违权必究 Tan 2018.06

deeplearning-biology

A list of deep learning implementations in biology

deeplearning-models

A collection of various deep learning architectures, models, and tips

deepmutsol

deepsolue

DeepSoluE

deep_learning_examples

Examples of using deep learning in Bioinformatics

diffdock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

diffusion-models-pytorch

Pytorch implementation of Diffusion Models (https://arxiv.org/pdf/2006.11239.pdf)

dlkcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

ecnet

An evolutionary context-integrated deep learning framework for protein engineering

embeddings_reproduction

enzyhtp

EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling

enzynet

EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation

esmtherm

esm_finetuning

This repository contains some scripts and Jupyter notebooks exploring how we can fine tune ESM2 protein language model for our custom requirements.

esp_prediction_function

evoprotgrad

Directed evolution of proteins in sequence space with gradients

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.

frame2seq

Structure-conditioned masked language modeling for protein sequence design

gmxanalysis

For the purpose of post progressing of MD carried by gromacs

gpd

Graphormer Based Protein Sequence Design--ProteinMPNN

gpro

gpt_protein_design

Efficient protein de novo design pipeline with GPT-based generator and transfer learning-based discrminator

graphkm

KM prediction model

gromacs

gromacs(Protein-Ligand Complex)

gvp-pytorch

Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

heme_binder_diffusion

instructplm

The first large protein language model trained follows structure instructions.

kcat_prediction_function