Reproduce bioinformatics analysis for the paper Meyer, K. et al., Cell, 2018.

Protein-protein interaction identifier

Candidate OPC–endothelial cell interactors

Using the interface residues as input (interface chain known), finding the interacting partners, node & edge types

Investigating Protein Interaction Networks with Python Visualizations

defines the interface region of a protein complex making possible to calculate the i_rmsd between native and predicted structures following the CAPRI criteria

An efficient implementation of the Seriation problem which 'finds a suitable linear order for a set of objects'. It has been used to order a network of proteins such that 'related' nodes are closer in the other.

Protein-protein interaction network (with orthology) querying library

Another needleplot for mutation data, used by ActiveDriverDB

Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation

BEstimate, a Python module that systematically analyses guide RNA (gRNA) targetable sites across given sequences for given Base Editors, and functional and clinical effects of the potential edits on the resulting proteins.

Compiling human protein–protein interactions

A deep learning library to rank protein complexes using graph neural networks

Evolution of protein interactomes across the tree of life

Visually explore covariation in protein families

Inference of couplings in proteins and RNAs from sequence variation