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Sharing, Learning, and Working in One Place!

As computational biology platforms continue to evolve, our goal is to make accessing open-source code and software even more straightforward for researchers. No coding skills are required, no usage limits, and no cost involved.

We run as a collaborative learning workshop, curating cutting-edge tools such as AlphaFold, RFdiffusion, BindCraft, and Boltz. Through carefully designed interactive Python notebooks, we guide you in using these tools independently on Google Colab—empowering you with full control over your research, including data security, scalability, and accessibility.

Our mission is to help you confidently apply these tools to real-world problems, create custom code for ad-hoc questions, and bridge the gap between your domain expertise and computational methods.

A growing list of tools:

Boltz2, AlphaFold, BindCraft, RFdiffusion, Autodock Vina, ProteinMPNN, RFantibody, ThermoMPNN, PepMLM, DeepViscosity, Antibody Evolution, BoltzDesign1, molecular dynamics simulation, ESMFold, AntiFold, PepFunn, LigandMPNN, ANARCI, AFDesign, ImmuneBuilder, TNP, PLAbDab, DiffSBDD, Prodigy, MM-GBSA/MM-PBSA

Our Free Tools

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）

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 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)

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)

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)

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

Input: Your antigen PDB and nanobody framework PDB

Output: Designed nanobody

Mode: Single input

Software Link:

RFantibody(Nanobody).ipynb - Colab

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)

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)

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)

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)

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)

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)

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)

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_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)

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)

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)

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)

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)

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)

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)

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)

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)

Input: Antibody sequence(s)

Output: Predicted paratopes

Mode: Single input

Software Link:

ParaSurf Online | Neurosnap

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)

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)

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)

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)

Input: Protein amino acid sequence

Output: Favorable mutations

Mode: Single input

Software Link:

ESM_Scan_wechatbio.ipynb - Colab

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)

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)

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)

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)

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)

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

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

Artificial Intelligence

Our AI-powered drug discovery and development platform uses machine learning and other advanced techniques to accelerate the discovery of new treatments.

Bioengineering

Artificial Intelligence

Our bioengineering expertise enables us to create novel biomaterials, implants, and other medical devices, improving patient outcomes and quality of life.

More Support

Personal Coach

Computation Support

Local Deployments

We offer personalized one-on-one coaching to help beginners make the most of Google Colab. This gives you full control over the free tools listed above. If you run into any issues, we're also here to assist with troubleshooting.

Local Deployments

Computation Support

Local Deployments

We assist with deploying the software package to your local computer, allowing you to seamlessly integrate the computational pipelines into your workflow.

Computation Support

The computations require significant processing power and time, but we handle all of that for you. Additionally, we develop custom code tailored to your specific questions and needs.

Easy and Free Computation for Biomedical Research

Sharing, Learning, and Working in One Place!

Our Free Tools

Boltz2 (Small Molecule-Protein Binding Prediction）

Boltz2 (Small Molecule-Protein Binding Prediction）

Boltz2 (Small Molecule-Protein Binding Prediction）

AlphaFold/ColabFold (Protein Structure Prediction）

Boltz2 (Small Molecule-Protein Binding Prediction）

Boltz2 (Small Molecule-Protein Binding Prediction）

BindCraft (Binder Design)

Boltz2 (Small Molecule-Protein Binding Prediction）

RFdiffusion (Binder Design)

RFdiffusion (Binder Design)

Autodock Vina (Small Molecule-Protein Binding Prediction)

RFdiffusion (Binder Design)

Boltz2 (Protein-Protein Binding Prediction)

Autodock Vina (Small Molecule-Protein Binding Prediction)

Autodock Vina (Small Molecule-Protein Binding Prediction)

Autodock Vina (Small Molecule-Protein Binding Prediction)

Autodock Vina (Small Molecule-Protein Binding Prediction)

Autodock Vina (Small Molecule-Protein Binding Prediction)

ProteinMPNN (Protein Variant Creation)

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

Small Molecule Drug Developability Prediction

Small Molecule Drug Developability Prediction

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

Small Molecule Drug Developability Prediction

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)

RFantibody

Molecular Dynamics Simulation

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

RFantibody(nanobody)

Molecular Dynamics Simulation

Molecular Dynamics Simulation

Molecular Dynamics Simulation

Molecular Dynamics Simulation

Molecular Dynamics Simulation

ThermoMPNN

DeepViscosity (Predict Antibody Viscosity)

PepMLM (Peptide Binder)

PepMLM (Peptide Binder)

DeepViscosity (Predict Antibody Viscosity)

PepMLM (Peptide Binder)

DeepViscosity (Predict Antibody Viscosity)

DeepViscosity (Predict Antibody Viscosity)

DeepViscosity (Predict Antibody Viscosity)

Efficient Evolution of Antibody

ESMfold (Protein Structure Prediction)

DeepViscosity (Predict Antibody Viscosity)

Boltzdesign1 (Ligand Binder Design)

ESMfold (Protein Structure Prediction)

ESMfold (Protein Structure Prediction)

ESMfold (Protein Structure Prediction)

ESMfold (Protein Structure Prediction)

ESMfold (Protein Structure Prediction)

AntiFold (Predict Antibody Structure)

AntiFold (Predict Antibody Structure)

AntiFold (Predict Antibody Structure)

PepFunn (All about Peptides)

AntiFold (Predict Antibody Structure)

AntiFold (Predict Antibody Structure)

LigandMPNN

AntiFold (Predict Antibody Structure)

ANARCI (Antibody Annotation)

ANARCI (Antibody Annotation)

AFDesign (Generation of Fold Variants)

ANARCI (Antibody Annotation)

AFDesign (Generation of Fold Variants)

AFDesign (Generation of Fold Variants)

AFDesign (Generation of Fold Variants)

AFDesign (Design of Binders)

AFDesign (Generation of Fold Variants)

AFDesign (Generation of Fold Variants)

ImmuneBuilder

PLAbDab (Search Antibodies from Patent and Literature)

TNP (Nanobody Developability)

TNP (Nanobody Developability)

PLAbDab (Search Antibodies from Patent and Literature)