Best drug discovery and cheminformatics skills, page 2

Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.

learningmatter-mit/AtomisticSkills

A skill your agent uses whenever the user wants to add, register, edit, list, show, or validate a Proteina-Complexa design target for any pipeline — protein binder (default), ligand binder, or AME /…

NVIDIA-BioNeMo/bionemo-agent-toolkit

A standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings), model training (regression/classification), and property prediction with built-in…

jinzhezenggroup/computational-chemistry-agent-skills

Batch insert reagents into Uni-Lab platform — add chemicals with CAS, SMILES, supplier info.

deepmodeling/Uni-Lab-OS

Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained…

K-Dense-AI/scientific-agent-skills

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query…

K-Dense-AI/scientific-agent-skills

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and…

K-Dense-AI/scientific-agent-skills

Write code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity, ETKDG conformer embedding, MMFF/UFF…

NVIDIA-BioNeMo/bionemo-agent-toolkit

A skill your agent uses when a developer asks how to get started building healthcare or life sciences agents, wants to understand the HCLS Agents Toolkit, or asks what's available in this repository.

aws-samples/amazon-bedrock-agents-healthcare-lifesciences

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

JimLiu/science-skills

Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab).

JimLiu/science-skills

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML.

K-Dense-AI/scientific-agent-skills

Prepare and convert atomistic structures before calculations.

JCLiuGroup/AI-Computational-Chemist

Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

InternScience/scp

Predict protein-ligand binding affinity using Boltz-2 model to assess molecular interactions and binding probability for drug discovery.

InternScience/scp

Query public drug-discovery and translational-research databases including PubChem, ChEMBL, BindingDB, openFDA, ClinicalTrials.gov, and OpenAlex.

DrugClaw/DrugClaw

Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns

ClawBio/ClawBio

Look up chemicals in CAS Common Chemistry (name, CAS RN, SMILES, InChI; ~500k compounds)

lamm-mit/scienceclaw

Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50).

LeonChaoX/qinyan-academic-skills

Pharmaceutical machine-learning workflow guide for library profiling, molecular featurization, benchmark dataset fetch, medicinal-chemistry filtering, and optional pose-generation handoff.

DrugClaw/DrugClaw

Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets.

NVIDIA/skills

Generate novel drug-like molecules using the GenMol NIM microservice.

NVIDIA/skills

Continue KERMT pretraining on a custom SMILES corpus with a groverbase, cmim, or hybrid checkpoint.

NVIDIA/skills

Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint.

NVIDIA/skills

A skill your agent uses for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization.

NVIDIA/skills

A skill your agent uses when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.

NVIDIA/skills

Build molecules with RDKit — from SMILES or a scaffold, analogues and series (each with its parent), properties (MW, cLogP, TPSA, Lipinski, Veber, QED, alerts), similarity and substructure search…

autonomous-ai/openharness

Patsnap Chemical Molecular MCP for AI agents. An agent skill from patsnap/mcp.

patsnap/mcp

Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape)…

GPTomics/bioSkills

Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product…

GPTomics/bioSkills

Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape +…

GPTomics/bioSkills

Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches.

wu-yc/LabClaw

Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions.

wu-yc/LabClaw

Comprehensive computational validation of drug targets for early-stage drug discovery.

wu-yc/LabClaw

Analyze chemical structures from compound names to retrieve SMILES, molecular formulas, molecular weight, and LogP values.

InternScience/scp

NOTE: molecule and target inputs and your NGCAPIKEY are transmitted to external NVIDIA-hosted API endpoints on every call.

NVIDIA/skills

Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV.

NVIDIA/skills

End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels.

wu-yc/LabClaw

Search ChEMBL bioactive molecules database with natural language queries.

wu-yc/LabClaw

Use Boltz2 NIM for biomolecular structure prediction and binding affinity.

NVIDIA/skills

Extract per-molecule embeddings from any encoder-bearing KERMT checkpoint (groverbase / cmim / hybrid / finetuned).

NVIDIA-BioNeMo/bionemo-agent-toolkit

A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics simulations, by automating atom/bond…

jinzhezenggroup/computational-chemistry-agent-skills

Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware…

GPTomics/bioSkills

Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain…

GPTomics/bioSkills

Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking…

GPTomics/bioSkills

Patsnap Chemistry & Small Molecule MCP for AI agents. An agent skill from patsnap/mcp.

patsnap/mcp

Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.

InternScience/scp

Model, forecast, and interpret volatility using time-series models and options-implied measures.

JoelLewis/finance_skills