Protein Data Bank PDB büyük biyolojik moleküllerin özellikle proteinler ve nükleik asitlerin üç boyutlu yapısal verileri

https://upload.wikimedia.org/wikipedia/commons/7/79/VEGFR2_bound_to_axitinib.gif" alt="image">

Introduction

This dataset is a replication of the dataset described in the paper Generative Modeling for Protein Structures by Namrata Anand and Po-Ssu Huang. The data is used to train a Generative Adversarial Network with the capability of creating protein structures.

Content

The data is stored in a hdf5 file and is structured in the following manner:

{
 "test_16": "16x16 numpy arrays",
 "train_16": "16x16 numpy arrays",
 "test_64": "64x64 numpy arrays",
 "train_64": "64x64 numpy arrays",
 "test_128": "128x128 numpy arrays"
 "train_128": "128x128 numpy arrays"
}

and contains the following number of numpy arrays:

test_16: 69,713

train_16: 1,820,586

test_64: 11,835

train_64: 331,006

test_128: 3,276

train_128: 98,748

Quickstart

Running the following will yeild ```python3 import h5py import matplotlib.pyplot as plt

dataset = h5py.File('dataset.hdf5', 'r') test_64 = dataset['test_64']

plt.imshow(test_64[1], cmap='viridis') plt.colorbar() plt.show() ``` https://i.imgur.com/lb2bOzo.png" alt="image">

Acknowledgements

@incollection{NIPS2018_7978,
title = {Generative modeling for protein structures},
author = {Anand, Namrata and Huang, Possu},
booktitle = {Advances in Neural Information Processing Systems 31},
editor = {S. Bengio and H. Wallach and H. Larochelle and K. Grauman and N. Cesa-Bianchi and R. Garnett},
pages = {7494--7505},
year = {2018},
publisher = {Curran Associates, Inc.},
url = {http://papers.nips.cc/paper/7978-generative-modeling-for-protein-structures.pdf}

https://cdn.rcsb.org/rcsb-pdb/v2/common/images/rcsb_logo.png" alt="image"> H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne. (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.

Protein Data Bank PDB büyük biyolojik moleküllerin özellikle proteinler ve nükleik asitlerin üç boyutlu yapısal verileri