Kaimei

Tools.

The scientific tools in Kaimei: structure prediction, docking, protein and molecule design, properties and public databases, set up and wired in. Run each one from a node on your canvas, or let the agent run it for you.

Tools available
19
Categories
6
Labs and publishers
15
Need no key of your own
10
Filter19 tools

Structure prediction4 tools

  • Boltz LabDocs

    Boltz-2

    Co-folds a protein, DNA, RNA or ligand complex and predicts binding affinity in one pass.

    Works on
    ProteinProtein ComplexDNARNASmall MoleculePeptide
    Tasks
    Structure PredictionDockingProperty Prediction
    Runs as
    Predict Structure

    Boltz.bio, NVIDIA NIM or your own server

  • Meta AIDocs

    ESMFold

    Single-sequence protein folding with no MSA step, so it answers in seconds. Lower accuracy than an MSA model on hard targets.

    Works on
    Protein
    Tasks
    Structure Prediction
    Runs as
    Predict Structure

    ESM Atlas

  • OpenFold ConsortiumDocs

    OpenFold2

    An open reimplementation of AlphaFold2 that folds a protein from its sequence and a multiple sequence alignment.

    Works on
    Protein
    Tasks
    Structure Prediction
    Runs as
    Predict Structure

    NVIDIA NIM

  • EMBL-EBI / DeepMindDocs

    AlphaFold DB

    200M+ precomputed structures with pLDDT and PAE, by UniProt accession. A lookup, not a fold, so the structure comes back at once.

    Works on
    Protein
    Tasks
    Structure PredictionSearch
    Runs as
    Structure Acquisition

    EMBL-EBI

Docking1 tool

  • MITDocs

    DiffDock

    Diffusion-based blind docking - ranked ligand poses against a protein structure.

    Works on
    ProteinSmall Molecule
    Tasks
    Docking
    Runs as
    Dock

    NVIDIA NIM

Design5 tools

  • Boltz LabDocs

    BoltzProt-1

    Boltz's protein design pipeline: de novo binders, scored by a protein-protein affinity model (Boltz-PPI).

    Works on
    ProteinAntibodyNanobody
    Tasks
    Design
    Runs as
    Binder Design

    Boltz.bio

  • Boltz LabDocs

    BoltzMol-1

    Boltz's small-molecule hit-discovery pipeline: candidate hits for a protein target, generated and scored in one run.

    Works on
    Small MoleculeProtein
    Tasks
    DesignDockingSearch
    Runs as
    Molecule Design

    Boltz.bio

  • Institute for Protein DesignDocs

    RFdiffusion

    Generates protein backbones for binder design, shaped by the regions you ask it to build.

    Works on
    Protein
    Tasks
    Design
    Runs as
    Backbone Design

    NVIDIA NIM

  • Institute for Protein DesignDocs

    ProteinMPNN

    Inverse folding: designs sequences that fold to a given backbone.

    Works on
    Protein
    Tasks
    Design
    Runs as
    Sequence Design

    NVIDIA NIM

  • NVIDIADocs

    MolMIM

    Guided small-molecule generation - optimises QED or logP around a seed SMILES with CMA-ES.

    Works on
    Small Molecule
    Tasks
    DesignOptimization
    Runs as
    Molecule Optimization

    NVIDIA NIM

Properties and ADMET4 tools

  • Boltz LabDocs

    Boltz ADME

    Three ADME properties from a SMILES - lipophilicity, permeability, and a solubility risk band.

    Works on
    Small Molecule
    Tasks
    Property Prediction
    Runs as
    ADMET Screening

    Boltz.bio

  • RDKitDocs

    RDKit descriptors

    MW, logP, TPSA, QED and the rest, straight from a SMILES.

    Works on
    Small Molecule
    Tasks
    Property Prediction
    Runs as
    Molecule Properties

    Kaimei

  • Bonvin LabDocs

    PRODIGY

    Binding free energy of a protein-protein interface, counted from the contacts in a structure you already have.

    Works on
    Protein Complex
    Tasks
    Property Prediction
    Runs as
    Interaction Score

    Kaimei

  • Swanson et al.Docs

    ADMET-AI

    41 ADMET properties from a SMILES - toxicity, absorption, metabolism - each with its percentile among approved drugs.

    Works on
    Small Molecule
    Tasks
    Property Prediction
    Runs as
    ADMET Screening

    Kaimei

Databases4 tools

  • RCSBDocs

    RCSB PDB

    Experimental structures, ligand chemistry and full-text search.

    Works on
    ProteinProtein ComplexSmall MoleculeDNARNA
    Tasks
    SearchAnnotation
    Runs as
    Structure Acquisition

    RCSB

  • UniProt ConsortiumDocs

    UniProt

    Protein sequences, names and annotations, by accession or search.

    Works on
    Protein
    Tasks
    SearchAnnotation
    Runs as
    Target Input - the accession importer

    UniProt

  • NCBIDocs

    PubChem PUG-REST

    Name to structure and back, for more than 100M compounds.

    Works on
    Small Molecule
    Tasks
    SearchProperty Prediction
    Runs as
    Candidate Library - the molecule name lookup

    NCBI

  • EMBL-EBIDocs

    ChEMBL

    Measured bioactivities (IC50, Ki, Kd) - the real-world comparator for a predicted affinity.

    Works on
    Small MoleculeProtein
    Tasks
    SearchProperty Prediction
    Runs as
    Bioactivity Lookup

    EMBL-EBI

Annotation1 tool

  • NaturalAntibodyDocs

    riot-na numbering

    Antibody and nanobody numbering: the CDRs and the frameworks of a sequence.

    Works on
    AntibodyNanobody
    Tasks
    Annotation
    Runs as
    Antibody Annotation

    Kaimei