Resources

Code

  • Colab-AllAtom-ProteinFolding

    Google Colab notebooks for batch all-atom biomolecular structure prediction across Protenix, IntelliFold, Chai-1, OpenFold3, and Boltz-2. Unified CSV input format, calibration-based parallel GPU scheduling, automatic Google Drive upload. AlphaFold3-class quality without the commercial restrictions.

    structure predictionColabProtenixIntelliFoldChai-1OpenFold3Boltz-2

  • ipSAE_batch

    Batch processing of protein structure predictions for interaction scoring and visualisation. Combines ipSAE interaction metrics with AlphaBridge-inspired visualisation; supports AlphaFold 3, Protenix, IntelliFold, Chai-1, OpenFold3, and Boltz-2 output.

    protein interactionsipSAEvisualisation

  • Colab_TMbed

    Google Colab wrapper for TMbed (Bernhofer et al. 2022), a transmembrane protein predictor that uses ProtT5-XL-U50 language-model embeddings to call transmembrane alpha-helical and beta-barrel proteins, segment positions and orientations, and signal peptides.

    Colabtransmembrane predictionTMbed

  • BUSCO-Colab

    Google Colab wrapper for BUSCO v6.0.0 (Benchmarking Universal Single-Copy Orthologs; Manni et al. 2021), for assessing genome assembly and annotation completeness using OrthoDB v12 expectations. Optimised for proteome analysis.

    Colabgenome QCBUSCO

  • shift-circular-origin

    Python package for rotating circular DNA sequences to start at a specified origin. Useful for standardising plasmids and other circular genetic elements to a known origin of replication.

    sequence toolsplasmidPython

  • af3_json_processor

    Lightweight Python tool that converts CSV files containing AlphaFold 3 job specifications into JSON suitable for upload to the AlphaFold 3 Server.

    AlphaFold 3Pythonjob spec

  • Colab_Helixer

    Google Colab wrapper for Helixer (Weber et al.), a deep-learning ab initio gene structure prediction tool. Step-by-step notebook interface with intelligent parameter optimisation and result handling.

    Colabgene predictionHelixer

Data & code on Zenodo

Datasets and code that have broad utility beyond a single paper. Deposits tied to a specific publication appear instead inside that paper's entry on the Publications page, alongside the bioRxiv preprint and code links.

  • NLRome dataset from 124 genomes of plants in the Solanaceae family

    An open-access NLRome dataset of 66,665 NLR immune receptor protein sequences with domain annotations, extracted with NLRtracker from 124 Solanaceae genomes spanning Solanum (108), Capsicum (7), Nicotiana (8) and Physalis (1).

    Zenodo, 2023 · 10.5281/zenodo.10354350

    NLRdatabaseSolanaceae

Lab equipment

Hardware that powers the day-to-day science.

  • Bambu Lab H2C

    Bambu Lab Used for: Custom lab fixtures, plant-handling tools, protein structure prints.

    Dual-extruder, multi-colour 3D printer used in the lab to design and produce custom equipment, and to print physical models of NLR receptors and other protein structures for teaching and visualisation.

    Manufacturer page →

Protocols

Protocols coming soon; in the meantime see our protocols.io page.