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admetlab

A platform for systematic ADME evaluation of drug molecules, thereby accelerating the drug discovery process.

af2_conformations

A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2

algorithms_datastructure_specialization

this is repo about my solutions of problems in Data Structures and Algorithms Specialization in coursera site from algorithmic toolbox to Genome Assembly Programming Challenge

annotated_deep_learning_paper_implementations

🧑‍🏫 59 Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠

avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

binding-ddg-predictor

open source repository

binding-pocket-streamlit

the app is in the protein folder with the name app.py. To run the app, you need to clone DeepPocket , download the model checkpoints, and create an empty directory in the path something along the lines of DeepPocket/protein(check in code in app.py)

blog

colabdesign-cyclic-binder

colabfold

Making Protein folding accessible to all!

computational_aging_course

Free online course on computational biology of aging driven by Jupyter book and supported by Skoltech.

data-set-summarization

Image dataset summarization using submodular functions and CLIP embeddings. Diverse image subset selection(div.py) using diversipy library.

datasets

Dataset of Inorganic Compounds converted to smiles from cif & organic photovoltaics dataset with homo/lumo/gap data

deep-learning-with-python-notebooks

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

deep_learning_coronavirus_cure

Using deep learning to generate novel molecules as candidates for binding with coronavirus protease

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

deepscm

A convolutional neural network model to predict spatial charge map (SCM) score, a molecular dynamics simulation-based model to predict antibody viscosity.

delinker

dgpred

Script to calculate detalG values

differential-gene-expression

dlpacker

DLPacker

effmass

Calculates various definitions of effective mass from the electronic bandstructure of a semiconductor.

etoxpred

A simple tool to predict the general toxicity and calculate the synthesize accessibility (SA) score for small molecules.

giotto-tda

A high-performance topological machine learning toolbox in Python

gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

gxvaes

A PyTorch implementation of GxVAEs.

i-am-a-nerd

icsg3d

3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning (JCIM 2020)

iglm

Generative Language Modeling for Antibody Design