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de novo design of high affinity biological binders

Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)

Predict multiple protein conformations using sequence clustering and AlphaFold2.

BoltzGen: Toward Universal Binder Design

Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3

Enables using Boltz-1/1x to predict the structure of arbitrary covalent modifications / Non-Canonical Amino Acids. Covalent bonds are enforced. Also walks you through injecting a new residue into t…

composite-objective protein design

A deep learning framework (CreoPep) for target-specific design and optimization of conotoxin peptides

Benchmarking HelixFold3-Predicted Holo Structures for Relative Free Energy Perturbation Calculations

Fragment binding prediction with ColabFold

Tool to design cyclic peptides that mimic proteins and target their binding partners.

A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation

Chai-1, SOTA model for biomolecular structure prediction

Proteina is a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture.

Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package

RINGER: Rapid Conformer Generation for Macrocycles with Sequence-Conditioned Internal Coordinate Diffusion

CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning

Official repository for the Boltz biomolecular interaction models

Heuristic energy-based cyclic peptide design

Algorithm to predict new amidated peptides from mouse and human secretomes.