Tools

Open-source software, web servers, deep learning suites, and interactive Google Colab notebooks developed by the Ovchinnikov Lab.

Lab GitHub ↗

Featured Tools

Evolution Python • PyTorch

MSA_Pairformer

Scaling down protein language modeling to protein-protein interactions with MSA Pairformer architecture.

GitHub Paper

Folding & Stability ESM3 • SaProt

absolute-stability-predictor

Fine-tuned models (ESM3ΔG, SaProtΔG) predicting per-residue protein stability (ΔG) and mutational effects from structure.

GitHub

Structure & EBM PyTorch • EBM

ProteinEBM

Energy-based models of protein structure learned from sequence via denoising score matching.

GitHub

Protein Design Diffusion • PyTorch

Protein-Hunter

Exploiting structure hallucination within diffusion for target-aware protein design.

GitHub

Sequence & Homology Embeddings

CIRPIN

Learning circular permutation-invariant representations to uncover putative protein homologs.

GitHub

Binder Design One-Shot Design

BindCraft

Automated one-shot computational design of functional, high-affinity protein binders.

GitHub

Visualization Colab • Jupyter

py2Dmol

Visualizing protein, DNA, and RNA structures in 2D directly inside Google Colab and Jupyter Notebooks.

GitHub Colab Notebook

Complete Tool Suite

Folding & Structure AlphaFold2 • MMseqs2

ColabFold

Accelerated, accessible protein folding via fast MSA generation (MMseqs2) and AlphaFold2 / RoseTTAFold.

GitHub Colab Notebook Paper

Protein Design Hallucination • Jax

ColabDesign

Flexible suite for back-propagation based protein design using TrRosetta, RoseTTAFold, and AlphaFold.

GitHub Colab Notebook

Binder Design All-Atom

BoltzDesign

Inverting all-atom structure prediction models for generalized biomolecular binder design.

GitHub Paper

Sequence & Alignment Differentiable SW

SMURF

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman optimization.

GitHub Paper

Structure Alignment Neural Alignment

SWAMPNN / SoftAlign

End-to-end neural protein structure alignment and fold-switching landscape evaluation.

GitHub Paper

Model Accuracy AlphaFold2 Scoring

AF2Rank

State-of-the-art estimation of protein model accuracy and decoy ranking using un-modified AlphaFold.

GitHub Paper

Binding Prediction AlphaFold Pair-Rep

AF2BIND

Lightweight and fast prediction of small-molecule binding sites using AlphaFold2 pair representations.

GitHub Colab Notebook Paper

Coevolution & Contacts C++ • Jax • TF

GREMLIN

Generative Regularized Estimation of Mutational Landscapes for predicting contact maps and couplings.

Web Server C++ GitHub Jax Notebook

Interpretability ESM2 • ESM3 • MPNN

CatJac (Categorical Jacobian)

Extracting pairwise relationships and coevolutionary matrices directly from generative protein language models.

ESM2 Colab ESM3 Colab MPNN Colab

Sequence Models Fitness Landscapes

seqsal

Investigating structure-fitness landscapes and pairwise relations in generative sequence models.

GitHub

Sequence Models Multivariate Modeling

seqmodels

Unified framework for modeling multivariate probability distributions in biological sequence data.

GitHub

Map Alignment C++ • Alignment

map_align

Fast contact map alignment algorithm for identifying structural similarities without coordinates.

GitHub Paper