(under development...)

Datasets

Protein Data Bank (RCSB-PDB):

• file format content v-3.3 [doc]
• Programmatic access [doc]

Basic Local Alignment Search Tool (BLAST):

• Using the Common URL API [doc]

UniProt

• Access programmatically [doc]

Papers

Review

A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli [paper]

Methods

Protein Solubility Prediction

DeepSol: A Deep Learning Framework for Sequence-Based Protein Solubility Prediction [paper] [source]

Structural Learning of Proteins Using Graph ConvolutionalNeural Networks [paper]

SolXplain: An Explainable Sequence-Based Protein Solubility Predictor [paper]

Solart: A Structure-Based Method To Predict Protein Solubility And Aggregation [paper] [Webserver]

Protein Function Prediction

deepNF: deep network fusion for protein function prediction (Bioinformatics 2018) [paper]

ps model

• graph construction: k-nearest neighbours according to relative distance

Tools

Biopython - freely available tools for biological computation [doc] [doc_cn]

ssbio - python package for structural systems biology [doc]

PyMOL - a user-sponsored molecular visualization system [web]

Pyecharts - open source visualization tools for Jupyter [Github]