drug-discovery-agent-skills

In the author's own words, from each skill's SKILL.md — showing the first 30 of 37 files.

• adaptyv

  How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adapt…

  skills/adaptyv/SKILL.md on GitHub (opens in a new tab)

• admet-prediction

  Turn a set of structures into absorption, distribution, metabolism, excretion, and toxicity estimates with ADMET-AI, and read them as a developability verdict rather than a table of numbers. Use this skill to run batch prediction over a library, interpret each endpoint against its DrugBank-approved percentile, and flag the liabilities that stop a series — hERG blockade, CYP inhibition, poor Caco-…

  skills/admet-prediction/SKILL.md on GitHub (opens in a new tab)

• antibody-engineering

  Number antibody variable domains, annotate CDRs, and assess developability from sequence. Use this skill to apply IMGT, Kabat, Chothia, Martin, or AHo numbering with ANARCI, delimit CDRs and framework regions, scan for chemical liabilities (N-glycosylation sequons, deamidation NG, isomerisation DG, oxidation, unpaired cysteine, fragmentation), compute pI, net charge, extinction coefficient and hy…

  skills/antibody-engineering/SKILL.md on GitHub (opens in a new tab)

• autodock-vina

  Structure-based docking with AutoDock Vina, Vinardo, and AutoDock4 through the Meeko toolchain. Use this skill to define a docking box, prepare receptors and ligands as PDBQT, run single or batch docking, rescore, and interpret affinities, poses, and ligand efficiency. Covers box definition from a reference ligand or pocket residues, protonation and tautomer decisions, flexible side chains, exhau…

  skills/autodock-vina/SKILL.md on GitHub (opens in a new tab)

• binding-site-analysis

  Decide whether a protein has a pocket worth targeting, and where it is, before committing to a docking or design campaign. Use this skill to run fpocket cavity detection, rank cavities by druggability and volume, compare apo and holo conformations to spot induced fit, identify allosteric and cryptic cavities that only open in simulation, and convert a chosen cavity into the search box coordinates…

  skills/binding-site-analysis/SKILL.md on GitHub (opens in a new tab)

• boltz

  Cofold protein-ligand, protein-protein, and nucleic-acid complexes with Boltz-2, and predict binding affinity with its trained affinity head. Use this skill to build Boltz input YAML, run structure prediction with MSAs, pocket constraints, templates, and modified residues, screen compound libraries by cofolding, and interpret confidence scores (pLDDT, pTM, ipTM, PDE) and affinity output (binder p…

  skills/boltz/SKILL.md on GitHub (opens in a new tab)

• chembl

  Query the ChEMBL database web services for measured bioactivity data, compound records and calculated properties, targets, assays, mechanisms of action, drug indications and warnings. Use this skill to build curated SAR or QSAR datasets for a target, look compounds up by SMILES, InChIKey, name, or ChEMBL id, run similarity and substructure searches, and check what chemistry is already known again…

  skills/chembl/SKILL.md on GitHub (opens in a new tab)

• chemical-space

  Navigate make-on-demand catalogues — ZINC-22 through CartBlanche and Enamine REAL Space — to find compounds that can actually be ordered. Use this skill to look substances up by ZINC identifier or structure, understand tranche partitioning by heavy-atom count and logP, and choose between screening an enumerated subset and searching a combinatorial synthon space with a fragment-growing method such…

  skills/chemical-space/SKILL.md on GitHub (opens in a new tab)

• clinicaltrials

  Search the ClinicalTrials.gov registry through its version 2 REST API for interventional and observational studies, their phases, enrolment, endpoints, sponsors, and posted results. Use this skill to survey who is developing what against an indication, date a competitor's programme, read primary and secondary outcome measures, find eligibility criteria, and distinguish a study that completed from…

  skills/clinicaltrials/SKILL.md on GitHub (opens in a new tab)

• datamol

  Pythonic wrapper around RDKit with a simplified interface and sensible defaults. Preferred for standard drug discovery work — SMILES/SELFIES/InChI conversion, molecule standardization and sanitization, descriptors, ECFP and other fingerprints, Tanimoto distance matrices, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds and scaffold splits, BRICS/RECAP fragmentation, 3D conform…

  skills/datamol/SKILL.md on GitHub (opens in a new tab)

• deepchem

  Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For ready-made ADMET numbers without training a model use admet-prediction; for benchmark datasets and…

  skills/deepchem/SKILL.md on GitHub (opens in a new tab)

• degraders

  Work on bifunctional degraders and molecular glues, where potency comes from a ternary complex rather than occupancy. Use this skill to apply the property rules that govern this beyond-rule-of-five space, reason about linker length, attachment vector and E3 ligase choice, prepare inputs for ternary complex structure prediction, and interpret degradation readouts — DC50, Dmax, cooperativity, and t…

  skills/degraders/SKILL.md on GitHub (opens in a new tab)

• depmap

  Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), RNAi DEMETER2 scores, PRISM compound sensitivity, and gene effect profiles across the cell-line panel. Use for identifying cancer-selective vulnerabilities, separating pan-essential genes from selective ones, finding synthetic lethal interactions, correlating dependency with mutation, expression…

  skills/depmap/SKILL.md on GitHub (opens in a new tab)

• diffdock

  DiffDock and DiffDock-L diffusion-based molecular docking. Use for blind protein-small-molecule pose prediction from a PDB file or sequence plus SMILES/SDF/MOL2, batch docking over a CSV of complexes, virtual screening triage, sampling multiple poses per complex, and reading the confidence score correctly. Also trigger on DiffDock, DiffDock-L, inference.py, confidence_model, samples_per_complex,…

  skills/diffdock/SKILL.md on GitHub (opens in a new tab)

• esm

  Protein language models through the EvolutionaryScale `esm` Python SDK. Generate and embed sequences with ESM3 (multimodal sequence, structure and function prompting), extract per-residue and mean-pooled embeddings with ESM C, fold sequences with ESMFold2, and run inference locally or against the Forge and Biohub hosted clients. Use this skill for protein representation learning, variant effect a…

  skills/esm/SKILL.md on GitHub (opens in a new tab)

• free-energy-perturbation

  Compute relative and absolute binding free energies with the Open Free Energy toolkit — the rigorous alchemical alternative to docking scores when a congeneric series needs reliable potency ranking. Use this skill to plan a perturbation network over a ligand set, choose atom mappings, run hybrid-topology or separated-topology protocols, and analyse the result — per-edge ΔΔG with uncertainty, cycl…

  skills/free-energy-perturbation/SKILL.md on GitHub (opens in a new tab)

• generative-design

  Generate and optimise novel small molecules with REINVENT 4 — de novo sampling from a chemical language model, scaffold decoration with LibInvent, fragment linking with LinkInvent, and similarity-constrained analogue generation with Mol2Mol. Use this skill to set up reinforcement-learning or curriculum runs, compose a multi-parameter scoring function from docking scores, predictive models, and ph…

  skills/generative-design/SKILL.md on GitHub (opens in a new tab)

• glycoengineering

  Analyze and engineer protein glycosylation. Scan sequences for canonical N-glycosylation sequons (N-X-S/T with X not proline, including overlapping sites), predict O-GalNAc hotspots, read glycan notation, and reach the curated external tooling (NetNGlyc, NetOGlyc, GlycoShield, GlycoWorkbench, GlyTouCan, GlyConnect). Use this skill for therapeutic antibody glycoengineering and afucosylation for AD…

  skills/glycoengineering/SKILL.md on GitHub (opens in a new tab)

• immunogenicity

  Estimate how likely a protein therapeutic is to provoke an anti-drug antibody response, and locate the sequence regions responsible. Use this skill to tile a sequence into peptides, predict class II MHC presentation across a population-representative allele panel, aggregate predicted binders into a per-region and whole-molecule risk score, compare a candidate against its closest human germline, a…

  skills/immunogenicity/SKILL.md on GitHub (opens in a new tab)

• medchem

  Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski rule of five, Veber, Oprea, CNS, lead-like, rule of three), structural alert catalogs (PAINS a/b/c, NIBR screening-deck severity, Brenk, BMS, Glaxo, Dundee, ChEMBL common alerts), ZINC-15 percentile complexity metrics (Bertz, SAscore, QED, Whitlock, Barone), chemical-group detection, Lilly demerits, and the medch…

  skills/medchem/SKILL.md on GitHub (opens in a new tab)

• molecular-dynamics

  Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contac…

  skills/molecular-dynamics/SKILL.md on GitHub (opens in a new tab)

• molfeat

  Molecular featurization hub with one consistent interface over 100+ featurizers. Fingerprints (ECFP/Morgan, MACCS, atom pair, topological torsion, Avalon, RDKit, ERG), RDKit and Mordred descriptor sets, pharmacophore and 3D shape descriptors, scaffold keys, and pretrained embeddings (ChemBERTa, ChemGPT, MolT5, GIN, Graphormer) through a common transformer API with caching and parallelism. Use thi…

  skills/molfeat/SKILL.md on GitHub (opens in a new tab)

• ncats-arax

  Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance…

  skills/ncats-arax/SKILL.md on GitHub (opens in a new tab)

• oligonucleotides

  Design small interfering RNA and antisense oligonucleotide sequences against a transcript, and screen them for the failure modes specific to nucleic-acid drugs. Use this skill to tile a target transcript, apply positional and thermodynamic selection rules including duplex asymmetry and nearest-neighbour melting temperature, scan candidates for seed-region complementarity to off-target transcripts…

  skills/oligonucleotides/SKILL.md on GitHub (opens in a new tab)

• open-targets

  Query the Open Targets Platform GraphQL API for target-disease associations, genetic and clinical evidence, tractability and safety liabilities, target prioritisation metrics, known drugs and mechanisms of action, and disease ontology. Use this skill for target identification and validation, target-disease evidence review, druggability assessment, drug repurposing, and resolving gene, disease, an…

  skills/open-targets/SKILL.md on GitHub (opens in a new tab)

• openfda

  Query the FDA's public openFDA APIs for post-market drug data — FAERS adverse-event reports, Drugs@FDA approval and submission history, Structured Product Labels including boxed warnings, the National Drug Code directory, recall enforcement reports, and drug shortages. Use this skill to check what a regulator has already concluded about a molecule or its class, to date an approval and count its e…

  skills/openfda/SKILL.md on GitHub (opens in a new tab)

• patent-landscape

  Find out whether a chemical series is already claimed, using SureChEMBL's patent-extracted compound corpus and, where a key is available, PatentsView for legal status and assignee history. Use this skill to trace a structure to the patent documents that disclose it, survey an assignee's filings around a target, and understand what the freedom-to-operate question requires that a structure search c…

  skills/patent-landscape/SKILL.md on GitHub (opens in a new tab)

• pkpd-translation

  Turn in vitro potency and animal pharmacokinetics into a defensible human dose projection — the arithmetic that decides whether a compound can reach its target concentration safely. Use this skill for non-compartmental analysis of a concentration-time profile (AUC, Cmax, terminal half-life, clearance, volume of distribution), one- and two-compartment simulation of a dosing regimen, interspecies a…

  skills/pkpd-translation/SKILL.md on GitHub (opens in a new tab)

• primekg

  Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological relationships across genes and proteins, drugs, diseases, phenotypes, pathways, biological processes, exposures and anatomy. Use this skill to search entities by name, pull direct neighbours and their evidence types, summarise the local network around a disease, and find direct or two-hop drug-disease connections for…

  skills/primekg/SKILL.md on GitHub (opens in a new tab)

• protein-binder-design

  Design new proteins that bind a chosen surface, using BindCraft's AlphaFold2-guided hallucination or the RFdiffusion backbone plus ProteinMPNN sequence pipeline. Use this skill to specify a target epitope by hotspot residue, trim a receptor to the region worth designing against, set up a design campaign, and filter the output on the in-silico metrics that predict experimental success — interface…

  skills/protein-binder-design/SKILL.md on GitHub (opens in a new tab)

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