Software

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Protein Networks

D-SCRIPT
Sequence-based prediction of protein-protein interactions using a protein language model.
    $ pip install dscript
    


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.