Inference of couplings in proteins and RNAs from sequence variation

Visually explore covariation in protein families

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

Evolution of protein interactomes across the tree of life

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.

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

Compiling human protein–protein interactions

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

Efficient search of complex motifs in kmer space

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

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

R package (Multi-Omics Database Browser)

GraphCompression is a Python script for simplifying protein interaction networks. It retrieves interaction data from the STRING API using protein information or a user-provided dataset, constructs an interaction graph, and applies Spectral Clustering. The output is a condensed network saved as a graph image and CSV file.

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

Candidate OPC–endothelial cell interactors

Protein-protein interaction identifier