Protein structure and design

Goal-oriented binder design campaign planning and health assessment.

adaptyvbio/protein-design-skills

First-time setup for protein design tools. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Access UniProt for protein sequence and annotation retrieval.

adaptyvbio/protein-design-skills

Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone.

NVIDIA/skills

First-time setup, environment configuration, and model-weight installation for Proteina-Complexa.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis.

LeonChaoX/qinyan-academic-skills

Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.

wu-yc/LabClaw

Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design.

wu-yc/LabClaw

A skill your agent uses for OpenFold2, NVIDIA's BioNeMo NIM microservice for monomer protein structure prediction.

NVIDIA/skills

Run RFDiffusion protein backbone design via NVIDIA NIM. An agent skill from NVIDIA/skills.

NVIDIA/skills

Multi-objective, gradient-based protein binder design with Mosaic.

adaptyvbio/protein-design-skills

Structure prediction with Protenix, an open AlphaFold3 reproduction.

adaptyvbio/protein-design-skills

Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).

GPTomics/bioSkills

NOTE: your protein sequence and the retrieved MSA alignment are transmitted to external NVIDIA-hosted APIs (health.api.nvidia.com) on every call.

NVIDIA/skills

Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design.

FreedomIntelligence/OpenClaw-Medical-Skills

Perform geometric calculations on protein structures using Biopython Bio.PDB.

FreedomIntelligence/OpenClaw-Medical-Skills

Parse and write protein structure files using Biopython Bio.PDB.

FreedomIntelligence/OpenClaw-Medical-Skills

Modify protein structures using Biopython Bio.PDB. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model.

FreedomIntelligence/OpenClaw-Medical-Skills

Access and analyze AlphaFold protein structure predictions. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1.

FreedomIntelligence/OpenClaw-Medical-Skills

Use Boltz2 NIM for biomolecular structure prediction and binding affinity.

NVIDIA/skills

Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA.

GPTomics/bioSkills

Protein structure prediction with Boltz-2 (default) or OpenFold3.

ClawBio/ClawBio

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

aipoch/medical-research-skills

Unified CLI/Python interface for querying genomic, proteomic, structure, and expression data across 20+ bioinformatics databases; use when you need fast, scriptable retrieval by gene/protein IDs or…

aipoch/medical-research-skills

Predict B-cell and T-cell epitopes for vaccine antigen design and epitope mapping with BepiPred-3.0, DiscoTope-3.0, the IEDB tools, and EL-mode MHC presentation.

GPTomics/bioSkills

Retrieves and interprets AlphaFold Protein Structure Database (AFDB) models by UniProt accession, reading pLDDT and PAE confidence correctly.

GPTomics/bioSkills

Detects putative ligand-binding pockets and druggable cavities de novo on an apo protein structure with fpocket, P2Rank, CASTp, and DoGSiteScorer, ranking them by druggability/ligandability score.

GPTomics/bioSkills

Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran), superposition and RMSD…

GPTomics/bioSkills

Maps protein-protein and protein-ligand interfaces with Bio.PDB, computing contact residues and buried surface area (BSA).

GPTomics/bioSkills

Predicts protein and complex structures with deep-learning models (ESMFold, AlphaFold2/ColabFold, AlphaFold3, Chai-1, Boltz-1/2) and reconciles them with confidence metrics.

GPTomics/bioSkills

Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB.

GPTomics/bioSkills

Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities.

GPTomics/bioSkills

Navigate the Bio.PDB SMCRA hierarchy (Structure-Model-Chain-Residue-Atom) safely, surfacing the heterogeneity it hides by default.

GPTomics/bioSkills

Prepares a deposited or predicted structure for docking, molecular dynamics, or electrostatics by adding hydrogens, assigning protonation and tautomer states, and filling missing atoms and short…

GPTomics/bioSkills

ESM protein language models for embeddings, sequence scoring, structure prediction, and binder design.

adaptyvbio/protein-design-skills

Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS.

jaechang-hits/SciAgent-Skills

Unified biological database evidence owner. An agent skill from foryourhealth111-pixel/Vibe-Skills.

foryourhealth111-pixel/Vibe-Skills

Judges whether a macromolecular model (or a region of it) is reliable enough to build on, using resolution, R-free, B-factors, MolProbity geometry, and predicted-model confidence with Bio.PDB.

GPTomics/bioSkills

Analyze and engineer protein glycosylation. An agent skill from LeonChaoX/qinyan-academic-skills.

LeonChaoX/qinyan-academic-skills

Access AlphaFold DB's 200M+ predicted structures by UniProt ID.

jaechang-hits/SciAgent-Skills

Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.

aipoch/medical-research-skills

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D…

aipoch/medical-research-skills

Toolkit for protein language models (ESM3 for multimodal generative protein design; ESM C for efficient embeddings).

aipoch/medical-research-skills

AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring.

BioTender-max/awesome-bio-agent-skills

Python API for RCSB PDB 3D structures (search, fetch coordinates, metadata).

lamm-mit/scienceclaw

API + Python SDK for ordering cell-free protein expression and binding assays.

jaechang-hits/SciAgent-Skills