Software

Our lab develops open-source software for molecular and systems biology. These methods are released and maintained on the Sledzieski Lab GitHub organization.

Protein Networks

D-SCRIPT

Sequence-based prediction of protein-protein interactions using a protein language model. Also ships the Topsy-Turvy and TT3D models.

GitHub PyPI Paper

PHILHARMONIC

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

GitHub Database PyPI Paper

MINT

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

GitHub Paper

Phylogenetics

TreeFix-TP

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

GitHub Paper

VirDTL

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

GitHub Paper

Protein Structure

Seq2Symm

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

GitHub Paper

PLANET-MD

Ultra-fast proteome-scale prediction of protein dynamics. Formerly released as RocketSHP.

GitHub Paper

Drug Discovery

ConPLex

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

GitHub PyPI Paper

Foundation Models

MIMIC

A generative multimodal foundation model for biomolecules.

GitHub Paper