medsci-agent

Shared operational contract for all MedSci agents: sequential execution, planning phase, retry limits, evidence standards.

Isolated exploratory code execution with medsci-sandbox tools. Use when analysis requires custom code beyond existing domain MCP tools.

AlphaFold DB for predicted protein structures and pLDDT confidence scores

Molecular biology toolkit. Use for FASTA parsing, sequence analysis, and translation.

ChEMBL database access for bioactivity data and target search

Datamol for molecular manipulation, SMILES processing, and cheminformatics

Molecular ML with DeepChem - featurizers, models, and molecular property prediction

ESM protein language models for sequence embeddings and structure prediction

Structured hypothesis formulation for scientific research. Use when generating testable hypotheses from observations.

Systematic literature review methodology, search strategy, and PRISMA reporting

Open Targets Platform for target-disease associations and genetic evidence

RCSB PDB for 3D protein structures, resolution, and experimental methods

PubMed biomedical literature search. Use for finding papers, clinical evidence, and research.

PyDESeq2 for differential gene expression analysis of RNA-seq count data

Cheminformatics with RDKit. Use for molecular analysis, drug-likeness, fingerprints, and similarity.

Single-cell RNA-seq analysis with Scanpy. Use when working with H5AD files, cell clustering, or differential expression.

UniProt protein database - accessions, annotations, and programmatic access