Protein Binder Design
K-Dense-AI/drug-discovery-agent-skillsDesign 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 predicted TM-score, predicted aligned error at the interface, buried surface area, and shape complementarity. Also trigger on BindCraft, RFdiffusion, ProteinMPNN, minibinder, hallucination, inverse fol...
At a glance
This skill is for Marketing and helps you design protein binders for target epitopes, generate protein sequences with alphafold2, and optimize protein-surface interfaces.
git clone --depth 1 https://github.com/K-Dense-AI/drug-discovery-agent-skills
cp -r drug-discovery-agent-skills/skills/protein-binder-design ~/.claude/skills/protein-binder-design
Alphafold2RfdiffusionProteinmpnnprotein-engineeringcomputational-biologydrug-discovery
Also in K-Dense-AI/drug-discovery-agent-skills
View the repoHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whene...
Turn a set of structures into absorption, distribution, metabolism, excretion, and toxicity estimates with ADMET-AI, and read them as a deve...
Number antibody variable domains, annotate CDRs, and assess developability from sequence. Use this skill to apply IMGT, Kabat, Chothia, Mart...
Structure-based docking with AutoDock Vina, Vinardo, and AutoDock4 through the Meeko toolchain. Use this skill to define a docking box, prep...
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...
Cofold protein-ligand, protein-protein, and nucleic-acid complexes with Boltz-2, and predict binding affinity with its trained affinity head...
Query the ChEMBL database web services for measured bioactivity data, compound records and calculated properties, targets, assays, mechanism...
Navigate make-on-demand catalogues — ZINC-22 through CartBlanche and Enamine REAL Space — to find compounds that can actually be ordered. Us...
Search the ClinicalTrials.gov registry through its version 2 REST API for interventional and observational studies, their phases, enrolment,...
Pythonic wrapper around RDKit with a simplified interface and sensible defaults. Preferred for standard drug discovery work — SMILES/SELFIES...
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when...
Work on bifunctional degraders and molecular glues, where potency comes from a ternary complex rather than occupancy. Use this skill to appl...
Other Marketing skills
A set of resources to help me write all kinds of internal communications, using the formats that my company likes to use. Claude should use...
Single-page SaaS landing with hero, features, social proof, pricing, and CTA. Respects the active DESIGN.md color/typography/layout tokens....
Generate creative domain name ideas and check availability across multiple TLDs including .com, .io, .dev, and .ai.
For marketing and gtm work: bind launches, campaigns, events, and brand plans to growth and pipeline outcomes. Built around the core query "...
A brand product-launch email — masthead with wordmark, hero image block, headline lockup with skewed-italic accent, body copy, primary CTA,...
Generate and iterate ad creative including headlines, descriptions, and primary text. Useful for paid social and search ad iteration.