Software

Protein Networks

    D-SCRIPT

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

        $ pip install dscript
        

    MINT

    The Multimer Interaction Transformer (MINT) is a 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

    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.

        $ pip install dscript
        

    VirDTL

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