Software

Expand All

Protein Networks

D-SCRIPT
Sequence-based prediction of protein-protein interactions using a protein language model.

    $ pip install dscript
    


MINT
Protein language model trained to learn the distribution over sets of interacting protein sequences.



PHILHARMONIC
An engine for biological hypothesis generation and de novo functional inference in non-model organisms.

    $ pip install philharmonic
    


TT3D
Updates Topsy-Turvy to use explicit protein structure information based on the Foldseek 3di sequence.
    $ pip install dscript
    


Topsy-Turvy
Improves upon D-SCRIPT by integrating top-down (graph-based) and bottom-up (sequence-based) prediction of protein-protein interactions.

Drug Discovery

ConPLex
High-throughput prediction of drug-target interactions using a protein language model and contrastive learning.

    $ pip install conplex-dti
    

Protein Structure

RocketSHP
Ultra-fast proteome-scale prediction of protein dynamics.



Seq2Symm
Accurate and high-throughput prediction of the quaternary symmetry class of homo-oligomers using a language model.

Phylogenetics

TreeFix-TP
Error correction for viral phylogenies based on parsimonious reconciliation with a species tree.



VirDTL
Inference of ancestral and extant strain recombination in viral genomes using phylogenetic reconciliation.