Software

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.