aipoch/open-science

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alphafold2 Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, g…

aipoch/open-science

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boltz Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. …

aipoch/open-science

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borzoi Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when…

aipoch/open-science

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chai1 Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai D…

aipoch/open-science

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diffdock Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind dif…

aipoch/open-science

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esmfold2 Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and…

aipoch/open-science

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evo2 Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1…

aipoch/open-science

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fair-esm2 Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequ…

aipoch/open-science

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indication-dossier Generate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of …

aipoch/open-science

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ligandmpnn Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.c…

aipoch/open-science

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literature-review Find, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source …

aipoch/open-science

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openfold3 Structure prediction using OpenFold3, an open-weights PyTorch reproduction of AlphaFold3 from the AlQuraishi Lab. Use…

aipoch/open-science

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proteinmpnn Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, gith…

aipoch/open-science

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scgpt Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill…

aipoch/open-science

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scvi-tools Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervis…

aipoch/open-science

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solublempnn Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for…

aipoch/open-science

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