Instructions file
Instructions for PharMolix/OpenBioMed, covering claude.md, project overview, key commands, environment setup and training.
1.1k 1mo ago A 1,523 tokens
original MIT
Skill Claude CodeCodex
Predict comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) properties for drug candidate molecules using GraphMVP ensemble models. Use this skill when: (1) Predicting blood-brain barrier penetration, (2) Assessing side effect profiles, (3) Estimating Caco-2 permeability, half-life, or LD50…
1.1k 1mo ago A 96 tokens
original MIT
Skill Claude CodeCodex
Antibody design using IgGM model. Use this skill when: (1) Epitope-conditioned de novo antibody design, (2) Antibody affinity maturation, (3) Using antigen PDB structure and epitope information. For binding affinity evaluation, use prodigy.
1.1k 1mo ago A 63 tokens
original MIT
Skill Claude CodeCodex
Antibody-related structure prediction using tfold model. Use this skill when: (1) Predict antibody and nanobody structure of a given sequence, (2) Predict antigen-antibody complex structure of given sequences, (3) Using local GPU resources. For binding affinity evaluation, use prodigy.
1.1k 1mo ago A 69 tokens
original MIT
Skill Claude CodeCodex
Protein complex binding affinity prediction. Use this skill when: (1) Predict the binding affinity score, (2) Using protein complex structure.
1.1k 1mo ago A 38 tokens
original MIT
Skill Claude CodeCodex
Create new biomedical skills or improve existing ones for the OpenBioMed toolkit. Use this skill when: (1) Creating a new skill from scratch, (2) Capturing a workflow as a reusable skill, (3) Automating a biomedical task, (4) Improving an existing skill. This skill guides through an interactive process: define intent…
1.1k 1mo ago A 89 tokens
original MIT
Skill Claude CodeCodex
Find the most suitable skill for a given biomedical task. Use this skill when: (1) You are unsure which skill to use for a specific biomedical task, (2) You want to discover available skills for a particular domain, (3) You need to compare multiple skills for a given use case.
1.1k 1mo ago A 67 tokens
original MIT
Skill Claude CodeCodex
Search biomedical literature from PubMed and bioRxiv for research papers. Use this skill when: (1) Finding research papers on a specific topic or disease, (2) Retrieving recent preprints from bioRxiv, (3) Getting paper titles, abstracts, and metadata, (4) Literature review for drug discovery or biomedical research.
1.1k 1mo ago A 75 tokens
original MIT
Skill Claude CodeCodex
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, and integrate with scanpy/PyTorch for population-scale single-cell analysis. Use this skill when: (1) Querying single-cell expression data by cell type, tissue, or disease, (2) Exploring available single-cell datasets…
1.1k 1mo ago A 105 tokens
original MIT
chembl-query
10Skill Claude CodeCodex
Query ChEMBL database for bioactivity data on drug-like compounds. Use this skill when: (1) Finding compounds active against a protein target (target-based search), (2) Getting bioactivity profile for a molecule (molecule-based search), (3) Finding drugs for a disease indication (indication-based search).
1.1k 1mo ago A 69 tokens
original MIT
Skill Claude CodeCodex
A research workflow for combining information about diseases and experimental or approved drugs from several biomedical databases.
1.1k 1mo ago A 120 tokens
original MIT
Skill Claude CodeCodex
Generate diverse druggable molecules for a given target or disease using OpenBioMed's AI-powered drug discovery tools. Use this skill when: (1) Generating drug candidates, molecules, or compounds for a target/disease, (2) Performing structure-based drug design or de novo drug design, (3) Finding or creating molecules…
1.1k 1mo ago B 128 tokens
original MIT
Skill Claude CodeCodex
Analyze potential drug-drug interactions (DDI) for up to 5 drugs using KEGG DDI database. Use this skill when: (1) Checking interactions between multiple medications, (2) Assessing DDI risk for drug combinations, (3) Understanding interaction mechanisms and severity, (4) Analyzing CYP enzyme involvement in DDIs.
1.1k 1mo ago A 78 tokens
original MIT
Skill Claude CodeCodex
Analyze drug candidate molecules for drug-likeness, ADMET properties, and safety profiles. Use this skill when: (1) Evaluating a molecule's potential as a drug candidate, (2) Checking drug-likeness scores (QED, Lipinski), (3) Predicting blood-brain barrier penetration, (4) Assessing side effects and ADMET properties…
1.1k 1mo ago A 91 tokens
original MIT
Skill Claude CodeCodex
Directory Structure Organize your downloaded checkpoints and mapping files as follows.
1.1k 1mo ago A 6 tokens
original MIT
Skill Claude CodeCodex
Identify the IUPAC name of a molecule using BioT5 question answering model. Use this skill when: (1) User wants to find the IUPAC name of a molecule, (2) User asks "What is the IUPAC name?" or "What's the systematic name?", (3) User provides a SMILES string and wants the IUPAC nomenclature.
1.1k 1mo ago A 86 tokens
original MIT
kegg-query
17Skill Claude CodeCodex
Query KEGG database for drug information, pathway analysis, and disease-drug-target discovery. Use this skill when: (1) Looking up drug information including efficacy, targets, metabolism, and interactions, (2) Analyzing metabolic or signaling pathways to retrieve genes, compounds, and modules, (3) Discovering…
1.1k 1mo ago A 82 tokens
original MIT
Skill Claude CodeCodex
Query a molecule's biochemical significance and roles in biology and chemistry using BioT5 multi-modal model. Use this skill when: (1) Understanding a molecule's biological roles and functions, (2) Describing a molecule's chemical significance and applications, (3) Getting natural language explanations of molecular…
1.1k 1mo ago A 89 tokens
original MIT
Skill Claude CodeCodex
Propose high-fitness and high-diversity mutants of the VP1 capsid protein of Adeno-Associated Virus (AAV) through multi-round iterative optimization.
1.1k 1mo ago A 39 tokens
original MIT
Skill Claude CodeCodex
Propose high-fluorescence and high-diversity mutants of Green Fluorescent Protein (GFP) through multi-round iterative optimization.
1.1k 1mo ago A 34 tokens
original MIT
Skill Claude CodeCodex
Query STRING database for protein-protein interactions with confidence scores. Use this skill when: (1) Finding interaction partners for a protein of interest, (2) Retrieving confidence scores for protein-protein interactions, (3) Building protein interaction networks for pathway analysis.
1.1k 1mo ago A 57 tokens
original MIT
Skill Claude CodeCodex
Predict protein function and properties from amino acid sequence using BioT5. Use this skill when: (1) You have a protein sequence and want to understand its biological function, (2) You need to identify enzyme activity, pathway involvement, or molecular interactions, (3) You want a concise description of protein…
1.1k 1mo ago A 73 tokens
original MIT
Skill Claude CodeCodex
Analyze protein-ligand interactions in PDB structures using PLIP (Protein-Ligand Interaction Profiler). Use this skill when: (1) Analyzing binding interactions from a PDB structure file, (2) Identifying hydrogen bonds, hydrophobic contacts, π-stacking, salt bridges, and water bridges, (3) Generating 3D visualizations…
1.1k 1mo ago A 102 tokens
original MIT
Skill Claude CodeCodex
Analyze protein mutations by retrieving protein data, explaining mutation effects, predicting protein structure, and visualizing results. Use this skill when the user asks about protein mutations, wants to understand mutation effects, or needs to analyze genetic variants. Triggers on phrases like "analyze mutation"…
1.1k 1mo ago A 81 tokens
original MIT