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    AI-driven solutions for antibody, peptide, and protein design.

    .


    AI-driven solutions

    AI pipelines for biologics discovery

    From protein structure to binder design

    From protein structure to binder design

    From protein structure to binder design

    From protein structure to binder design

    From protein structure to binder design

    A scenic landscape featuring mountains, trees, and a clear blue sky.

    Predictive modeling

    From protein structure to binder design

    Predictive modeling

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    Our Free Tools

    Boltz2 (Small Molecule-Protein Binding Prediction）

    Boltz2 (Small Molecule-Protein Binding Prediction）

    Boltz2 (Small Molecule-Protein Binding Prediction）

    Input: Small molecule in SMILES format; Protein in single-letter amino acid sequence

    Output: Predicted binding affinity;3D structures of the protein–ligand complex

    Mode: Batch-processing of up to 200 jobs

    Software Link:

    batch_processing_of_the_small_molecule_protein_interaction_using_boltz2.ipynb

    AlphaFold/ColabFold (Protein Structure Prediction）

    Boltz2 (Small Molecule-Protein Binding Prediction）

    Boltz2 (Small Molecule-Protein Binding Prediction）

    Input: Protein in single-letter amino acid sequence

    Output: Predicted 3D structure of a single protein or a protein complex

    Mode: Single input

    Software Link:

    AlphaFold2_ColabFold.ipynb - Colab 

    BindCraft (Binder Design)

    Boltz2 (Small Molecule-Protein Binding Prediction）

    RFdiffusion (Binder Design)

    Input: A PDB file of your target protein

    Output: Amino acid sequences of binders (mini-proteins or peptides) and predicted 3D structures of the target-binder complex

    Mode:  Iterative cycles of design 

    Software Link:

    bindcraft.ipynb

    RFdiffusion (Binder Design)

    Autodock Vina (Small Molecule-Protein Binding Prediction)

    RFdiffusion (Binder Design)

    Input: the PDB file of your target protein Output: Amino acid sequences of binders (mini-proteins or

    Input: the PDB file of your target protein

    Output: Amino acid sequences of binders (mini-proteins or peptides) and predicted 3D structures of the target-binder complex

    Mode:  Iterative cycles of design 

    Software Link:

    RFdiffusion_design_binder.ipynb - Colab 

    Boltz2 (Protein-Protein Binding Prediction)

    Autodock Vina (Small Molecule-Protein Binding Prediction)

    Autodock Vina (Small Molecule-Protein Binding Prediction)

    Input: Protein A and B in single-letter amino acid sequence

    Output: Predicted interface quality (ipTM);3D structures of the protein–protein complex

    Mode: Batch-processing of up to 200 jobs

    Software Link: batch_processing_of_the_protein_protein_interaction_using_boltz2.ipynb


    Autodock Vina (Small Molecule-Protein Binding Prediction)

    Autodock Vina (Small Molecule-Protein Binding Prediction)

    Autodock Vina (Small Molecule-Protein Binding Prediction)

    Input: Small molecule in SMILES format; Protein in single-letter amino acid sequence Output: Predict

    Input: Small molecule in SMILES format; the PBD file of your target protein to be docked

    Output: Docking score and docked ligand PBD files

    Mode: Batch-processing of up to 10,000 jobs

    Software Link:

    autodock_vina.ipynb


    ProteinMPNN (Protein Variant Creation)

    Similarity Ensemble Approach (Similarity Based on Chemical 2D Structure)

    Small Molecule Drug Developability Prediction

    Input: the PDB file of your target protein

    Output: Amino acid sequences of protein variants and their score

    Mode:  batch-processing

    Software Link:

    proteinmpnn.ipynb



    Small Molecule Drug Developability Prediction

    Similarity Ensemble Approach (Similarity Based on Chemical 2D Structure)

    Small Molecule Drug Developability Prediction

    Input: Small molecule in SMILES format

    Output: Predicted physicochemical properties, drug-likeness, and ADMET-related features

    Mode:  batch-processing of millions of molecules

    Software Link: small_molecule_drug_developability_analysis.ipynb

    Similarity Ensemble Approach (Similarity Based on Chemical 2D Structure)

    Similarity Ensemble Approach (Similarity Based on Chemical 2D Structure)

    Similarity Ensemble Approach (Similarity Based on Chemical 2D Structure)

    Input: Small molecule in SMILES format

    Output: Predicted similarity to the target SMILES

    Mode:  batch-processing of millions of molecules

    Software Link: 

    sea_2d.ipynb



    RFantibody

    Molecular Dynamics Simulation

    Similarity Ensemble Approach (Similarity Based on Chemical 2D Structure)

    Input: Your antigen PDB

    Output: Designed antibody (CDRs)

    Mode: Single input

    Software Link: 

    RFantibody.ipynb - Colab 


    RFantibody(nanobody)

    Molecular Dynamics Simulation

    Molecular Dynamics Simulation

    Input: Your antigen PDB and nanobody framework PDB

    Output: Designed nanobody

    Mode: Single input

    Software Link: 

    RFantibody(Nanobody).ipynb - Colab 


    Molecular Dynamics Simulation

    Molecular Dynamics Simulation

    Molecular Dynamics Simulation

    Input: the PDB file

    Output: Trajectory files

    Mode: Single input

    Software Link:

    molecular_dynamics_simulation.ipynb 

    ThermoMPNN

    DeepViscosity (Predict Antibody Viscosity)

    PepMLM (Peptide Binder)

     Input: Your target PDB

    Output: Predicted  ΔΔG caused by mutations

    Mode: Single input

    Software Link: 

    thermompnn.ipynb

    PepMLM (Peptide Binder)

    DeepViscosity (Predict Antibody Viscosity)

    PepMLM (Peptide Binder)

    Input: Your target protein sequence

    Output: Predicted peptide binders

    Mode: Single input

    Software Link: 

    PepMLM.ipynb - Colab 

    DeepViscosity (Predict Antibody Viscosity)

    DeepViscosity (Predict Antibody Viscosity)

    DeepViscosity (Predict Antibody Viscosity)

    Input: Your antibody sequences

    Output: Predicted viscosity

    Mode: Single input

    Software Link: 

    deepviscosity_antibody.ipynb

    Efficient Evolution of Antibody

    ESMfold (Protein Structure Prediction)

    DeepViscosity (Predict Antibody Viscosity)

    Input: Your antibody VH/VL sequences

    Output: Predicted mutations to improve affinity or developability

    Mode: Single input

    Software Link: 

    efficient_evolution.ipynb

    Boltzdesign1 (Ligand Binder Design)

    ESMfold (Protein Structure Prediction)

    ESMfold (Protein Structure Prediction)

    Input: Your ligand in its SMILES format

    Output: Designed binder sequences

    Mode: Single input

    Software Link:

    Boltzdesign1(ligand_binder)_revised.ipynb - Colab 

    ESMfold (Protein Structure Prediction)

    ESMfold (Protein Structure Prediction)

    ESMfold (Protein Structure Prediction)

    Input: Protein in single-letter amino acid sequence

    Output: Predicted 3D structure of a single protein or a protein complex

    Mode: Single input

    Software Link:

    esmfold.ipynb

    AntiFold (Predict Antibody Structure)

    AntiFold (Predict Antibody Structure)

    AntiFold (Predict Antibody Structure)

    Input: Your antibody PDB file

    Output: Predicted structure and optimized residues

    Mode: Single input

    Software Link: 

    antifold_colab.ipynb

    PepFunn (All about Peptides)

    AntiFold (Predict Antibody Structure)

    AntiFold (Predict Antibody Structure)

    Input: not required

    Output: Generated peptide libraries and advanced analysis

    Mode: Single input

    Software Link (5 links): 

    1-generate_libraries.ipynb

    2-analyze_sequences.ipynb

    3-similarity_peptides.ipynb

    4-matched_pairs.ipynb

    5-clustering_molecules.ipynb

    LigandMPNN

    AntiFold (Predict Antibody Structure)

    ANARCI (Antibody Annotation)

    Input: Your PDB file

    Output: New protein sequences to meet your needs

    Mode: Single input

    Software Link: 

    ligandmpnn.ipynb

    ANARCI (Antibody Annotation)

    AFDesign (Generation of Fold Variants)

    ANARCI (Antibody Annotation)

    Input: Your antibody sequence(s)

    Output: Annotation and more

    Mode: Single input

    Software Link: 

    anarci.ipynb 

    AFDesign (Generation of Fold Variants)

    AFDesign (Generation of Fold Variants)

    AFDesign (Generation of Fold Variants)

     

    Input: Your PDB file as the template

    Output: New protein sequences that take the same fold

    Mode: Single input

    Software Link: 

    afdesign_fold_variants.ipynb



    AFDesign (Design of Binders)

    AFDesign (Generation of Fold Variants)

    AFDesign (Generation of Fold Variants)

     

    Input: Your PDB file as the target

    Output: New protein sequences that bind to the target

    Mode: Single input

    Software Link: 

    AFDesign_Binder_Design.ipynb - Colab 

    ImmuneBuilder

    PLAbDab (Search Antibodies from Patent and Literature)

    TNP (Nanobody Developability)

    Input: The protein sequence(s) of antibody, nanobody or TCR

    Output: Predicted structure

    Mode: Single input

    Software Link: 

    immunebuilder.ipynb


    TNP (Nanobody Developability)

    PLAbDab (Search Antibodies from Patent and Literature)

    TNP (Nanobody Developability)

    Input: Nanobody sequence(s)

    Output: Predicted developability metrics

    Mode: Single input

    Software Link: 

    TNP_wechatbio.ipynb - Colab 

    PLAbDab (Search Antibodies from Patent and Literature)

    PLAbDab (Search Antibodies from Patent and Literature)

    PLAbDab_nano (Search Nanobodies from Patent and Literature)

    Input: Antibody sequence

    Output: Retrieved antibody information based on similarity of structure and sequences, and key words

    Mode: Single input

    Software Link: 

    plabdab.ipynb 

    PLAbDab_nano (Search Nanobodies from Patent and Literature)

    DiffSBDD (Design Small Molecule Binding to Your Protein Target)

    PLAbDab_nano (Search Nanobodies from Patent and Literature)

     

    Input: Nanobody sequence

    Output: Retrieved Nanobody information based on similarity of structure and sequences, and key words

    Mode: Single input

    Software Link: 

    plabdab_nano.ipynb

    DiffSBDD (Design Small Molecule Binding to Your Protein Target)

    DiffSBDD (Design Small Molecule Binding to Your Protein Target)

    DiffSBDD (Design Small Molecule Binding to Your Protein Target)

     

    Input: Target protein PDB file

    Output: Designed small molecule binder

    Mode: Single input

    Software Link: 

    DiffSBDD_wechatbio.ipynb - Colab 

    Prodigy (Binding Affinity Prediction)

    DiffSBDD (Design Small Molecule Binding to Your Protein Target)

    DiffSBDD (Design Small Molecule Binding to Your Protein Target)

    Input: PDB files (protein complex)

    Output: Predicted binding affinity

    Mode: Single input

    Software Link: 

    Prodigy.ipynb - Colab 

    Ligand/Protein Binding Energy (Simulation and MM-GBSA/MM-PBSA)

    Ligand/Protein Binding Energy (Simulation and MM-GBSA/MM-PBSA)

    Ligand/Protein Binding Energy (Simulation and MM-GBSA/MM-PBSA)

    Input: Protein and ligand PDB files

    Output: Binding energy (MM-GBSA and MM-PBSA) plus trajectories

    Mode: Single input

    Software Link: 

    Protein_ligand_MD_and_Binding_Energy.ipynb - Colab 

    SEPPA (Predict Antigen Epitopes)

    Ligand/Protein Binding Energy (Simulation and MM-GBSA/MM-PBSA)

    Ligand/Protein Binding Energy (Simulation and MM-GBSA/MM-PBSA)

    Input: Antigen PDB file

    Output: Predicted epitopes

    Mode: Single input

    Software Link: 

    seppa.ipynb

    IgGM (Antibody and Nanobody Design)

    Ligand/Protein Binding Energy (Simulation and MM-GBSA/MM-PBSA)

    IgGM (Antibody and Nanobody Design)

    Input: Antigen and antibody/nanobody PDB files

    Output: Predicted epitope-specific binders

    Mode: Single input

    Software Link (2 links): 

    IgGM_Part1.ipynb - Colab 

    IgGM_Part2.ipynb - Colab 

    Antibody/Nanobody CDR Masking

    NetSolP-1.0 (Protein Solubility)

    IgGM (Antibody and Nanobody Design)

    Input: Antibody/Nanobody sequence(s)

    Output: CDR masked sequence(s)

    Mode: Single input

    Software Link: 

    cdr_masking.ipynb 

    MBER (Nanobody Design)

    NetSolP-1.0 (Protein Solubility)

    NetSolP-1.0 (Protein Solubility)

    Input: Antigen Uniprot ID and CDR masked nanobody sequence

    Output: Predicted epitope-specific binders

    Mode: Single input

    Software Link: 

    MBER_wechatbio.ipynb - Colab 

    NetSolP-1.0 (Protein Solubility)

    NetSolP-1.0 (Protein Solubility)

    NetSolP-1.0 (Protein Solubility)

    Input: Protein sequence(s)

    Output: Predicted solubility and/or usability

    Mode: Single input

    Software Link: 

    NetSolP 1.0 - DTU Health Tech - Bioinformatic Services 

     

    NetMHC (Binding of peptides to MHC class I molecules)

    NetMHCII (Binding of peptides to MHC class II molecules)

    NetMHCII (Binding of peptides to MHC class II molecules)

    Input: Peptide sequence(s)

    Output: Predicted binding affinity to MHCI

    Mode: Single input

    Software Link: 

    NetMHC 4.0 - DTU Health Tech - Bioinformatic Services 

    NetMHCII (Binding of peptides to MHC class II molecules)

    NetMHCII (Binding of peptides to MHC class II molecules)

    NetMHCII (Binding of peptides to MHC class II molecules)

    Input: Peptide sequence(s)

    Output: Predicted binding affinity to MHCII

    Mode: Single input

    Software Link: 

    NetMHCII 2.3 - DTU Health Tech - Bioinformatic Services 

    EvoNB (Nanobody Mutation Prediction and Optimization)

    NetMHCII (Binding of peptides to MHC class II molecules)

    EvoNB (Nanobody Mutation Prediction and Optimization)

    Input: Nanobody sequence(s)

    Output: Predicted mutations to optimize nanobodies

    Mode: Single input

    Software Link: 

    EvoNB_wechatbio.ipynb - Colab 

     

    TEMPRO (Predict Nanobody Tm)

    Humatch (Antibody Classification and Humanisation)

    EvoNB (Nanobody Mutation Prediction and Optimization)

    Input: Nanobody sequence(s) in the Fasta format

    Output: Predicted Tm

    Mode: Single input

    Software Link: 

    TEMPRO_wechatbio.ipynb - Colab 

    ParaSurf (Predict Antibody Paratope)

    Humatch (Antibody Classification and Humanisation)

    Humatch (Antibody Classification and Humanisation)

    Input: Antibody sequence(s)

    Output: Predicted paratopes

    Mode: Single input

    Software Link: 

    ParaSurf Online | Neurosnap 

    Humatch (Antibody Classification and Humanisation)

    Humatch (Antibody Classification and Humanisation)

    Humatch (Antibody Classification and Humanisation)

    Input: Antibody sequence(s)

    Output: Similarity assessment and predicted mutations for humanisation

    Mode: Single input

    Software Link (2 links): 

    humatch_part_1_prealign.ipynb

    humatch_part_2_humanisation.ipynb  


    TemStaPro (Predict Protein Thermostability)

    TemStaPro (Predict Protein Thermostability)

    TemStaPro (Predict Protein Thermostability)

    Input: Protein seqeunce(s) in the fasta format

    Output: Predicted Tm

    Mode: Single input

    Software Link: 

     TemStaPro_wechatbio.ipynb - Colab 

    Fpocket (Find Ligand Binding Pockets)

    TemStaPro (Predict Protein Thermostability)

    TemStaPro (Predict Protein Thermostability)

    Input: Protein PDB file

    Output: Predicted ligand binding pockets

    Mode: Single input

    Software Link: 

    Fpocket_wechatbio.ipynb - Colab 

    EvoProtGrad

    TemStaPro (Predict Protein Thermostability)

    ADMET (Evaluate Small Molecule Developability)

    Input: Your protein sequence

    Output: Suggested mutations and score

    Mode: Single input

    Software Link: 

    EvoProtGrad_wechatbio.ipynb - Colab 

    ADMET (Evaluate Small Molecule Developability)

    Aggrescan (Predict Aggregation-prone Hotspot and Fix it)

    ADMET (Evaluate Small Molecule Developability)

    Input: Smiles of small molecules

    Output: Predict up to 50 different properties related to drug developability

    Mode: Single input

    Software Link: 

    admet_wechatbio.ipynb - Colab 

    Aggrescan (Predict Aggregation-prone Hotspot and Fix it)

    Aggrescan (Predict Aggregation-prone Hotspot and Fix it)

    Aggrescan (Predict Aggregation-prone Hotspot and Fix it)

    Input: PDB file

    Output: Identify aggregation-prone hot spots 

    Mode: Single input

    Software Link: 

    Aggrescan_wechatbio.ipynb - Colab  


    ESM-Scan (Predict Favorable Mutations of Protein)

    Aggrescan (Predict Aggregation-prone Hotspot and Fix it)

    Aggrescan (Predict Aggregation-prone Hotspot and Fix it)

    Input: Protein amino acid sequence

    Output: Favorable mutations

    Mode: Single input

    Software Link: 

    ESM_Scan_wechatbio.ipynb - Colab 

    AF2BIND (Predict Ligand Binding Residues/Pockets)

    AF2BIND (Predict Ligand Binding Residues/Pockets)

    AF2BIND (Predict Ligand Binding Residues/Pockets)

    Input: PDB file

    Output: Predict ligand binding residues/pockets

    Mode: Single input

    Software Link: 

    AF2BIND_wechatbio.ipynb - Colab 


    SpatialPPIv2 (Predict PPI)

    AF2BIND (Predict Ligand Binding Residues/Pockets)

    AF2BIND (Predict Ligand Binding Residues/Pockets)

    Input: PDB or FASTA files of target proteins

    Output: Possibility of interaction

    Mode: Single input

    Software Link: 

    SpatialPPIv2_wechatbio.ipynb - Colab 

    FPSim2 (Fast Compound Similarity Search)

    AF2BIND (Predict Ligand Binding Residues/Pockets)

    DeepSP (Predict Antibody Surface Charge and Aggregation Propensity)

    Input: Compound SMILES

    Output: Similar compound(s) from ChEMBL

    Mode: Single input

    Software Link: 

    fpsim2_wechatbio.ipynb - Colab 

    DeepSP (Predict Antibody Surface Charge and Aggregation Propensity)

    DeepSP (Predict Antibody Surface Charge and Aggregation Propensity)

    DeepSP (Predict Antibody Surface Charge and Aggregation Propensity)

    Input: Antibody amino acid sequences

    Output: CDR/Lv/Hv/Fv surface charge and aggregation propensity

    Mode: Single input

    Software Link: 

    DeepSP_wechatbio.ipynb - Colab 

    Paragraph (Predict Antibody Paratope)

    DeepSP (Predict Antibody Surface Charge and Aggregation Propensity)

    Paragraph (Predict Antibody Paratope)

    Input: Antibody PDB file

    Output:  Predicted paratope residues 

    Mode: Single input

    Software Link: 

     Paragraph_wechatbio.ipynb - Colab 

    SynCodonLM (Codon Optimization)

    DeepSP (Predict Antibody Surface Charge and Aggregation Propensity)

    Paragraph (Predict Antibody Paratope)

    Input: Protein amino acid sequence

    Output:  Codon optimized nucleotide sequence

    Mode: Single input

    Software Link: 

    syncodonlm_codon_optimization.ipynb - Colab 

    Easy-MD (Easy Protein Ligand Simulation)

    eToxPred (Predict Toxicity and Synthetic Accessibility of Small Molecules)

    eToxPred (Predict Toxicity and Synthetic Accessibility of Small Molecules)

    Input: PDB file of the protein-ligand complex

    Output:  MD trajectory summary and animation 

    Mode: Single input

    Software Link: 

    easymd_wechatbio.ipynb - Colab 


    eToxPred (Predict Toxicity and Synthetic Accessibility of Small Molecules)

    eToxPred (Predict Toxicity and Synthetic Accessibility of Small Molecules)

    eToxPred (Predict Toxicity and Synthetic Accessibility of Small Molecules)

    Input: a SMI file containing SMILES strings of small molecules

    Output:  Tox-score and SA score

    Mode: Single input

    Software Link: 

    etoxpred_wechatbio.ipynb - Colab 

    QEPPI (Predict PPI Drug Likeness of Small Molecules)

    eToxPred (Predict Toxicity and Synthetic Accessibility of Small Molecules)

    WoLF PSORT (Predict Protein Subcellular Localization)

    Input: a SMILES string or a csv file containing many strings

    Output:  QEPPI score

    Mode: Single input

    Software Link: 

    qeppi_wechatbio.ipynb - Colab 

    WoLF PSORT (Predict Protein Subcellular Localization)

    WoLF PSORT (Predict Protein Subcellular Localization)

    WoLF PSORT (Predict Protein Subcellular Localization)

    Input: Protein sequence(s) in the FASTA format

    Output:  Predicted subcellular location

    Mode: Single input

    Software Link: 

    WoLF PSORT: Protein Subcellular Localization Prediction 

    CatPred (Predict Enzyme Kcat, Km, or Ki)

    WoLF PSORT (Predict Protein Subcellular Localization)

    CatPred (Predict Enzyme Kcat, Km, or Ki)

    Input: Enzyme protein sequence and small molecule SMILES string

    Output:  Predicted Kcat, Km, or Ki

    Mode: Single input

    Software Link:

    CatPred_wechatbio.ipynb - Colab 


    ToxinPred3 (Predict Peptide Toxicity)

    WoLF PSORT (Predict Protein Subcellular Localization)

    CatPred (Predict Enzyme Kcat, Km, or Ki)

    Input: Peptide sequence(s)

    Output:  Predicted toxicity

    Mode: Single input

    Software Link:

    toxinpred3_wechatbio.ipynb - Colab  

    EpHod (Predict Enzyme Optimal pH)

    Cyclic Peptide Design by AlphaFold

    Input: Enzyme sequence(s) in the FASTA format

    Output:  Predicted optimal pH for enzymatic activity

    Mode: Single input

    Software Link: 

    ephod.ipynb - Colab 

    Cyclic Peptide Design by AlphaFold

    Cyclic Peptide Design by AlphaFold

    Input: Template peptide PDB

    Output:  New sequence that folds into the same conformation

    Mode: Single input

    Software Link: 

    af_cyc_design_wechatbio.ipynb - Colab 

    ZymCTRL (Enzyme Design）

    Input: Enzyme EC number

    Output: Designed enzyme sequences

    Mode: Single input

    Software Link: 

    ZymCTRL_wechatbio.ipynb - Colab 

     

    RFpeptide (Cyclic Peptide Design)

    Input: Target protein PDB file

    Output: Designed macrocyclic peptides binding to specific sites on the target protein

    Mode: Single input

    Software Link: 

    RFdiffusion_working_cyclic.ipynb - Colab 


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