Tool catalog
Choose a workflow
Structure Prediction
Boltz-2 (new)
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Protein, Antibody, Peptide Structure PredictionAlphaFold
Accurate and quick protein structure prediction for multimers and monomers
Peptide, Protein, Antibody Structure PredictionChai-1
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Protein, Antibody, Peptide Structure PredictionESMFold2
Predicts protein, DNA, RNA, and ligand complexes
Protein, Peptide, Enzyme Structure PredictionProtenix-v2
Predict protein/nucleic acid/small molecule complexes. Outperforms AlphaFold3 with major gains on antibody-antigen interfaces.
Protein, Antibody, Peptide Structure PredictionOpenFold3
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Protein, Antibody, Enzyme Structure PredictionIntelliFold 2
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3
Protein, Antibody, Peptide Structure PredictionImmuneBuilder
Antibody, Nanobody and TCR structure prediction
Protein, Antibody Structure PredictionRosettaFold-3
AlphaFold3 reproduction
Protein, Small Molecule, Small Molecule Binding Protein Structure PredictionAFSample2
Modified AlphaFold for higher accuracy multimer structure prediction
Protein Structure PredictionFlashABB
Fast antibody structure, developability, and embeddings
Protein, Antibody Structure PredictionABodyBuilder3
Antibody structure prediction
Protein, Antibody Structure PredictionABB4-STEROIDS
Antibody conformational ensemble prediction
Protein, Antibody Structure PredictionHighfold
Cyclic peptide structure prediction
Protein, Peptide Structure PredictionAlphaFlow
AlphaFold fine tuned with a flow matching objective
Protein Structure PredictionTCRModel2
Predict T Cell Receptor structures
Protein, Antibody Structure PredictionAF Cluster
Predicting multiple conformations via sequence clustering
Protein Structure PredictionPromera
Unified model for biomolecular cofolding (protein/RNA/DNA/ligand), binder filtering (iCS/ipSAE), and de novo binder design (minibinders + VHH nanobodies)
Protein, Antibody, Peptide Structure PredictionMHC-Fine
Glukhov E et. al
Protein, Peptide Structure PredictionAF Unmasked
Structure prediction with multimeric templates
Protein, Antibody, Peptide Structure PredictionGRASP
Protein complex structure prediction conditioned on experimental restraints (XL-MS, interface residues)
Protein, Antibody, Peptide Structure PredictionAlphaLink2
Protein complex structure prediction from crosslinking mass-spectrometry restraints (XL-MS)
Protein, Antibody, Peptide Structure PredictionESMFold
Predict protein structure given a sequence
Protein, Peptide, Enzyme Structure PredictionAF-Traj
Predict protein conformations with subsampled AlphaFold2
Protein Structure PredictionOmegaFold
Predict protein structure without MSA
Protein Structure PredictionRNA-FM
RNA foundation model for sequence embeddings and secondary structure prediction
Nucleic Acid Structure PredictionNbForge
Nanobody structure prediction with HCDR3 blueprint and disulphide priors
Protein, Antibody Structure PredictionCryoBoltz
Boltz-1 structure prediction guided by a cryo-EM density map
Protein, Antibody, Enzyme Structure PredictionCombFold
End-to-end structure prediction of large protein complexes: AlphaFold-Multimer on subunit pairs plus combinatorial assembly, from sequence
ProteinAntibody Design
RFantibody
De novo antibody design with RFdiffusion
Protein, Antibody Antibody DesignIgGM
De novo antibody design
Protein, Antibody Antibody DesignIgDesign
In vitro validated antibody design against antigens
Protein, Antibody Antibody DesignAntiFold
Design sequences for antibodies
Protein, Antibody Antibody DesignAbLang2
Antibody language model
Protein, Antibody Antibody DesignAbLang-MPNN
Hybrid antibody design using AbLang + ProteinMPNN ensemble
Protein, Antibody Antibody DesignAntiBERTy
Optimize antibody/nanobody sequence affinity
Protein, Antibody Antibody DesignAbMPNN
Antibody sequence design
Protein, Antibody Antibody DesignMAGE
De novo antibody generation from antigen sequence using language models
Protein, Antibody Antibody DesignLICHEN
Generate light chain sequences conditioned on heavy chain using machine learning
Protein, Antibody Antibody DesignCoSiNE
Evolve antibody sequences along realistic affinity-maturation trajectories
Antibody, Protein Antibody DesignODesign Antibody
Antibody CDR design with ODesign all-atom generative model
Protein, AntibodyUtilities
BLAST Search
Search proteins against public databases
Protein UtilitiesMolstar Viewer
A web macromolecule viewer embedded into Tamarind (Visualize your PDB files and more!)
Protein UtilitiesAllMetal3D
Add metal ions to protein
Protein UtilitiesSuperWater
Add waters to protein
Protein UtilitiesPULCHRA
All-atom reconstruction and refinement of reduced protein models
Protein UtilitiesDLKcat
Deep learning-based kcat prediction
Protein, Enzyme, Small Molecule UtilitiesParaSurf
Predict paratope residues
Protein, Antibody UtilitiesFoldMason
Multiple Protein Structure Alignment at Scale
Protein UtilitiesFoldseek
Ultra-fast protein structure search, multimer search, and clustering
Protein, Antibody UtilitiesFPocket
Detect pockets on a protein
Protein, Enzyme UtilitiespyKVFinder
Detect and characterize biomolecular cavities
Protein UtilitiesPSI-BLAST Search
Position-Specific Iterated BLAST for detecting distant protein homologs
Protein UtilitiesSPACE2
Cluster antibodies by structural similarity and accurately group those bind the same epitope
Protein, Antibody UtilitiesMultiple Sequence Alignment
Multiple sequence alignment (MSA)
Protein UtilitiesIgBLAST
Search immune proteins against public databases using nucleotides or AA sequences as input
Antibody UtilitiesMSA Clustering
Clustering by MSA
Protein UtilitiesMSA Analysis
Multiple sequence alignment
Protein UtilitiesAncestral Sequence Reconstruction
Reconstruct ancestral sequences from modern sequences
Protein UtilitiespySCA
Statistical coupling analysis of protein sequence alignments
Protein UtilitiesANARCI
Annotate immune proteins
Protein, Antibody UtilitiesAntibody Annotation
Annotate immune proteins
Protein, Antibody UtilitiesMolProbity
Check protein structure quality
Protein UtilitiesHMMalign
Align list of sequences
Protein UtilitiesPROPKA
Predict the pKa values of ionizable groups in proteins
Protein UtilitiesPLAbDab
Search antibody sequences from patents and literature
Antibody UtilitiesAlign PDBs
Align a list of PDB files
Protein UtilitiesAlphaCutter
Remove non-globular regions from predicted protein structures given a pdb file
Protein UtilitiesRMSD Calculator
Calculate RMSD between two protein structures
Protein UtilitiesMin Distance Between Selected Residues
Min distance between two sets of selected residues
Protein UtilitiesRadius of Gyration
Calculate radius of gyration of a protein structure
Protein UtilitiesUSalign
Structurally align proteins and nucleic acids
Protein, Nucleic Acid UtilitiesEmboss Backtranseq
Back-translation of a protein sequence
Nucleic Acid UtilitiesDNAWorks
Automatic oligonucleotide design for PCR-based gene synthesis
Nucleic Acid UtilitiesLegolas
Predict protein chemical shifts from PDB structures
Protein UtilitiesParagraph Paratope Prediction
Predict antibody paratopes from heavy chain structures
Antibody UtilitiesOAS Search
Search Observed Antibody Space (OAS) paired sequence database to find similar protein sequences
Protein, Antibody UtilitiesFile Converter
Convert between different file formats
Protein, Small Molecule UtilitiesChemBL Search
Search ChemBL database to find similar molecules
Small Molecule UtilitiesPubChem Search
Search PubChem database to find similar molecules
Small Molecule UtilitiesPDBsum
Generate overview and schematic diagrams of protein chains, DNA, ligands, and metal ions
Protein UtilitiesINTERCAAT
Identify interface residues between protein chains using Voronoi tessellation
Protein UtilitiesITsFlexible
Predict conformational flexibility of antibody and TCR CDR3 loops
Antibody, Protein UtilitiesCluster PDBs
Cluster a list of PDB files or a trajectory
ProteinDevelopability
Protein Scoring
Score protein sequences/structures
Protein DevelopabilityTNP (Therapeutic Nanobody Profiler)
Predict nanobody developability
Protein, Antibody DevelopabilityTAP2 (Therapeutic Antibody Profiler)
Developability profiler for antibodies
Protein, Antibody DevelopabilitySURFMAP
2D projection of protein surface features
Protein DevelopabilityDeepImmuno
Prediction of immunogenic epitopes for T cell immunity (Class 1)
Protein, Antibody DevelopabilityTLimmuno
Class II Immunogenicity Prediction
Protein, Antibody DevelopabilityPALM
Protein aggregation propensity prediction
Protein, Antibody, Peptide DevelopabilityCANYA
Amyloid nucleation propensity prediction
Protein, Peptide DevelopabilityPolyXpert
Antibody polyreactivity prediction
Protein, Antibody DevelopabilityNanobody Polyreactivity
Nanobody (VHH) polyreactivity prediction
Protein, Antibody DevelopabilityDeepSP
Viscosity, spatial charge map (SCM) and spatial aggregation propensity (SAP) predictions for antibodies
Protein, Antibody DevelopabilityPepFuNN Peptide Sequence Analysis
Predict properties for peptides
Protein, Peptide DevelopabilityIPC 2.0
Predict protein isoelectric point and pKa
Protein DevelopabilityN-Linked Glycosylation Prediction
Predict N-Linked Glycosylation sites
Protein DevelopabilityPeptiVerse
Unified platform for therapeutic peptide property prediction using sequence and SMILES
Peptide, Small MoleculeSmall Molecule Property Prediction
Ligand Scoring
Score ligand smiles or sdfs
Small Molecule Small Molecule Property PredictionBoltz ADME
Predict small-molecule ADME (lipophilicity, permeability, solubility)
Small Molecule Small Molecule Property PredictionQupKake
Predict pKa for organic molecules
Small Molecule Small Molecule Property PredictionADMET
Quickly predict drug properties
Small Molecule Small Molecule Property PredictionLogP
Predict molecular lipophilicity (LogP)
Small Molecule Small Molecule Property PredictionCharge & Dipole
Atomic partial charges and molecular dipole moment
Small Molecule Small Molecule Property PredictionElectronic Properties
Frontier orbitals, Fukui indices, and reactivity descriptors
Small Molecule Small Molecule Property PredictionH-Bond Strength
Per-site hydrogen bond donor and acceptor strength prediction
Small Molecule Small Molecule Property PredictionMicroscopic pKa
Site-specific microscopic pKa values
Small Molecule Small Molecule Property PredictionElectrostatic Potential
Molecular electrostatic potential surface and Politzer analysis
Small Molecule Small Molecule Property PredictionTD-DFT UV-Vis
UV-Vis absorption spectrum prediction
Small Molecule Small Molecule Property PredictionReaction Energy
Reaction energy, enthalpy, and Gibbs free energy
Small Molecule Small Molecule Property PredictionProtonation State
Dominant protonation state at a given pH
Small Molecule Small Molecule Property PredictionMolecular Descriptors
200+ molecular descriptors, drug-likeness, and fingerprints
Small Molecule Small Molecule Property PredictionRedox Potential
Reduction and oxidation potential prediction
Small Molecule Small Molecule Property PredictionMacroscopic pKa
Macroscopic acid dissociation constants (pKa)
Small Molecule Small Molecule Property PredictionBond Dissociation Energy
Bond dissociation energies for metabolic stability analysis
Small Molecule Small Molecule Property PredictionSpin State Energies
Spin state energy comparison for open-shell systems
Small Molecule Small Molecule Property PredictionTautomer Enumeration
Enumerate and energy-rank tautomeric forms
Small Molecule Small Molecule Property PredictionAqueous Solubility
Predict aqueous solubility (logS)
Small MoleculeDe Novo Binder Design
ESMFold2 Binder Design
Design de novo protein binders against a target
Protein, Peptide De Novo Binder DesignBoltzGen
De novo binder design for nanobodies, antibodies, proteins, peptides, and cyclotides
Protein, Antibody, Peptide De Novo Binder DesignBoltzProt-1
De novo protein binder design against a target protein
Protein, Antibody, Peptide De Novo Binder DesignBoltz Protein Screen
Screen a protein library against a target protein
Protein, Antibody De Novo Binder DesignGenie 3
De novo binder design
Protein De Novo Binder DesignBindCraft
Design de novo binders for your target
Protein, Peptide De Novo Binder DesignProteina-Complexa
Fully atomistic protein and ligand binder design
Protein, Peptide, Enzyme De Novo Binder DesignPepMLM
Design linear peptide binders
Protein, Peptide De Novo Binder DesignPepMimic
Design peptide binders by mimicking a known binder's interface
Protein, Peptide De Novo Binder DesignPXDesign
De novo protein binder design using diffusion models
Protein De Novo Binder DesignBoltzDesign1
Invert Boltz-1 to design protein binders
Protein, Antibody, Peptide De Novo Binder DesignAfCycDesign
Design cyclic peptides
Protein, Peptide De Novo Binder DesignEvoPro
Genetic algorithm-based protein binder optimization pipeline
Protein, Peptide De Novo Binder DesignRSO Binder Design
Efficient binder design
Protein, Peptide De Novo Binder DesignMosaic Hallucination
Gradient-based binder design using Boltz-2
Protein, Peptide De Novo Binder DesignMosaic Hallucination (Protenix)
Gradient-based binder design using Protenix
Protein, PeptideInverse Folding
ProteinMPNN
Protein structure to sequence prediction
Peptide, Protein, Antibody Inverse FoldingFAMPNN
Protein structure to sequence design with full-atom packed outputs
Protein, Enzyme, Antibody Inverse FoldingAntiDIF
Antibody inverse folding
Protein, Antibody Inverse FoldingProteinMPNN-ddG Binder
Predict stability of point mutations
Protein, Enzyme, Antibody Inverse FoldingLigandMPNN
Inverse folding with modeling of small molecules and more
Protein, Enzyme, Small Molecule Binding Protein Inverse FoldingNA-MPNN
Sequence design for protein, RNA, DNA, and mixed-polymer structures; protein-DNA binding specificity prediction
Protein, Nucleic Acid Inverse FoldingCaliby
Potts model-based protein sequence design method that can condition on structural ensembles
Peptide, Protein, Antibody Inverse FoldingProteinMPNN Score
Protein structure to sequence prediction
Peptide, Protein, Antibody Inverse FoldingHyperMPNN
Design thermostable proteins
Protein, Antibody, Enzyme Inverse FoldingESM-IF1
Inverse folding with ESM-IF1 language model
Protein Inverse FoldingRhoDesign
Deep generative design of RNA sequences from 3D structure
Nucleic Acid Inverse FoldingRiboDiffusion
Tertiary-structure-conditioned RNA inverse folding with diffusion models
Nucleic Acid Inverse FoldingCyclicMPNN
Design stable cyclic peptide sequences for a given backbone
Protein, Peptide Inverse FoldingDynamicMPNN
Design sequences compatible with multiple conformational states
ProteinProtein Design
All Atom Protein Design
Design ligand-binding proteins with RFdiffusion All Atom
Protein, Small Molecule Binding Protein Protein DesignRFpeptides
Design macrocyclic proteins
Protein, Peptide Protein DesignRFdiffusion3
All atom protein design with atom-level and residue-level motif scaffolding
Protein, Antibody, Peptide Protein DesignRFdiffusion2
Enzyme active site scaffolding with atom-level or residue-level motif specification
Enzyme, Small Molecule Binding Protein Protein DesignGerminal
De novo antibody design
Protein, Antibody Protein DesignmBER
VHH binder design
Protein, Antibody Protein DesignAntibody Diffusion Properties
Design property-aware CDR sequence/structure
Protein, Antibody Protein DesignRFdiffusion
Design or diversify proteins
Protein, Antibody, Peptide Protein DesignFrameFlow
Motif scaffolding protein design
Protein Protein DesignZymCTRL
Conditionally generate artificial enzymes
Enzyme, Small Molecule Binding Protein Protein DesignProtein Hunter
De novo protein design
Protein, Peptide, Small Molecule Binding Protein Protein DesignEvoProtGrad
Generate mutations with directed evolution
Protein, Antibody, Enzyme Protein DesignDayhoff
Generate sequences conditioned on existing sequence
Protein, Antibody Protein DesignPocketGen
(Re)Generate a binding pocket for a given small molecule
Protein, Enzyme, Small Molecule Protein DesignProtein Solubilization
Solubilize membrane proteins
Protein Protein DesignRFdiffusion with Chai verification
Protein design with Chai verification
Protein Protein DesignColabDesign Fixed Backbone
Generate sequences given structure via reversing AlphaFold
Protein Protein DesignAPM
All-Atom Protein Generative Model
Protein, Antibody Protein DesignRiffDiff-ProtFlow
Generate backbone fragments from a theozyme to build a motif library
Protein, Enzyme, Small Molecule Binding Protein Protein DesignEnzyGen2
Motif-conditioned functional enzyme sequence and structure co-design
Protein, Enzyme, Small Molecule Binding Protein Protein DesignMULTI-evolve
Model-guided directed evolution workflow for multi-mutant nomination and assembly design
Protein, Enzyme, Antibody Protein DesignADAPT
Structure-based TCR design for peptide-MHC targets
Protein, Antibody Protein DesignDISCO
Diffusion-based protein sequence-structure co-design conditioned on ligands, DNA, or RNA
Protein, Enzyme, Small Molecule Protein DesignNeuroBind (from NS)
Design antibodies, nanobodies, scFvs, and peptides with high affinity and low immunogenicity.
Protein, Antibody, Peptide Protein DesignBindFilter (from NS)
Fold and score many binder candidates with a unified, machine-readable output.
Protein Protein DesignNeuroFold2 (from NS)
Design next-generation enzymes by co-optimizing for catalytic activity, stability, and solubility.
Protein Protein DesignBAGEL Protein Design (from NS)
User-configured BAGEL workflows for mini-enzyme, mimic-enzyme, and binder design.
Protein Protein DesignESMC Mutation Scoring (from NS)
Zero-shot ESMC entropy and mutation scoring from sequence alone.
Protein Protein DesignPocketXMol | Protein Design (from NS)
Pocket-conditioned peptide generation and redesign.
Protein, Peptide Protein DesignEvoEF2 (from NS)
Protein stability and binding energy analysis using EvoEF2.
Protein Protein DesignEvoEF2 Mutant Stability Analysis (from NS)
Analyze the impact of mutations on protein stability using EvoEF2.
Protein Protein DesignMIF-ST (from NS)
Predict alternative sequences for an input protein structure with high accuracy.
Protein, Nucleic Acid Protein DesignSoDoPE Solubility Optimization (from NS)
A sequence based method for optimizing protein solubility.
Protein Protein DesignRealKcat (from NS)
Predict kcat and Km class ranges from one enzyme sequence and a substrate panel.
Protein Protein DesignProtein Fold Stability Prediction (from NS)
Predict protein stability from structure using ESM-IF.
Protein Protein DesignEpHod Optimal Enzyme pH Prediction (from NS)
EpHod is a semi-supervised language model that predicts optimal pH for enzymes from sequence alone.
Protein Protein DesignDiffAb Antibody Design (from NS)
Design Antibodies for a target Antigen using the Antigen structure. DiffAb leverages a probabalistic diffusion model.
Protein, Antibody Protein DesignPAMmla (from NS)
Machine learning models to predict SpCas9 PAM preference from amino acid sequence.
Protein Protein DesignPAMmla Evolve (from NS)
Evolve SpCas9 PAM preference using evolutionary algorithms.
Protein Protein DesignProGen2 (from NS)
Create protein variants using nothing but the amino acid sequence.
Protein Protein DesignImaPEp Antibody-Antigen Binding Prediction (from NS)
ImaPEp predicts binding probabilities for antibody–antigen pairs by representing their binding interfaces as 2D images and leveraging convolutional neural networks.
Protein, Antibody Protein DesignEfficient Evolution (from NS)
A protein language model-based tool for efficient, task-agnostic design of high-functionality protein variants.
Protein Protein DesignHumatch (from NS)
A CNN-based tool for rapid, gene-specific humanization and classification of antibody heavy and light chains.
Protein, Antibody Protein DesignBioPhi (from NS)
AI-driven antibody humanization + humanness scoring from natural repertoire data.
Protein, Antibody Protein DesignProSST Mutation Effect Prediction (from NS)
ProSST predicts protein mutation effects and functions by integrating sequence and structural data via quantized tokens and disentangled attention.
Protein Protein DesignABACUS-R Sequence Design (from NS)
Use ABACUS-R to design protein sequences for a given backbone structure using an encoder-decoder model.
ProteinProtein Language Models
ESM-C 6B
ESM-C 6B protein language model
Protein Protein Language ModelsProfluent E1
Protein language model
Protein Protein Language ModelsAntibody Evolution
Language models to recommend mutations for increased antibody binding affinity
Protein, Antibody Protein Language ModelsEvoNB
Mutate nanobody sequences
Protein, Antibody Protein Language ModelsAbGPT
Generate antibody sequences
Protein, Antibody Protein Language ModelsCatPred
ESM-2 based kcat, Km, and Ki prediction
Protein, Enzyme, Small Molecule Protein Language ModelsCOMPSS Protein Metrics
Score sequences using language model metrics
Protein Protein Language ModelsSynCodonLM
Codon language model
Nucleic Acid Protein Language ModelsStructural Evolution
Mutate protein complexes with structure-informed language model
Protein, Antibody, Enzyme Protein Language ModelsPLM Crystallization Prediction
Sequence-based crystallization predictor. Mean-ensemble of LightGBM classifiers trained on ESM2 T30-150M and ESM2 T36-3B embeddings.
Protein Protein Language ModelsDeepFRI
Predict protein function
Protein, Enzyme Protein Language ModelsAbMAP
Antibody language model
Protein, Antibody Protein Language ModelsESM2 Embeddings
Generate ESM2 Embeddings
Protein Protein Language ModelsProt T5 XL Embeddings
Generate Prot T5 Embeddings
Protein Protein Language ModelsProFam
Protein family language model
ProteinGenerate Small Molecules
BoltzMol-1
De novo small-molecule binder design against a target protein
Small Molecule, Protein Generate Small MoleculesThompson Sampling
Screen billions of ligands against target receptors
Small Molecule Generate Small MoleculesFree Wilson SAR
SAR Analysis
Small Molecule Generate Small MoleculesDrugFlow
Generate small molecules
Protein, Small Molecule Generate Small MoleculesFLOWR
Generate small molecules
Protein, Small Molecule Generate Small MoleculesDiffSBDD
Generate small molecules
Protein, Small Molecule Generate Small MoleculesREINVENT4
REINVENT4: de novo design, molecule optimization, scaffold decoration, linker design, peptide design, scoring, and finetuning with multi-stage RL
Small Molecule Generate Small MoleculesLibInvent
Given a scaffold, decorate it to generate molecules
Small Molecule Generate Small MoleculesMoFlow
Generate small molecules
Small Molecule Generate Small MoleculesR-Group Enumeration
Generate molecular libraries from scaffold + R-group fragments
Small MoleculeSmall Molecule Modeling
Boltz Small Molecule Screen
Screen a small-molecule library against a target protein
Small Molecule, Protein, Small Molecule Binding Protein Small Molecule ModelingROSHAMBO
Molecular shape comparison and similarity scoring
Small Molecule Small Molecule ModelingPharmit
Pharmacophore search of the ChEMBL public compound library or your own SDF
Small Molecule Small Molecule ModelingSingle Point Energy
Calculate the electronic energy of a molecule at a fixed geometry
Small Molecule Small Molecule ModelingGeometry Optimization
Find the lowest-energy 3D structure of a molecule
Small Molecule Small Molecule ModelingFrequency Analysis
Vibrational frequencies, IR spectrum, and thermodynamic properties
Small Molecule Small Molecule ModelingOpenConf
Generate diverse small-molecule conformer ensembles with use-case presets
Small Molecule Small Molecule ModelingLoQI
Low-energy molecular conformer generation with quantum-mechanical accuracy
Small Molecule Small Molecule ModelingConformer Generation
Generate, cluster, and energy-rank molecular conformers
Small MoleculeFinetuning and Active Learning
NOS
Generate antibodies optimized for a given property
Protein, Antibody Finetuning and Active LearningSaProt Finetuning
SaProt finetuning
Protein Finetuning and Active LearningFinetune Protein Language Model
Protein sequence property prediction finetuning
Protein Finetuning and Active LearningFinetune BALM
Protein-ligand binding affinity prediction finetuning
Protein, Small Molecule Binding Protein Finetuning and Active LearningProteusAI
ML-assisted Directed Evolution
Protein, Enzyme Finetuning and Active LearningProGen2 Finetuning
Finetune generative protein language model
Protein Finetuning and Active LearningMAVE Neural Network Training
Tools for training neural networks on MAVE datasets and running MCMC simulations
Protein Finetuning and Active LearningEnzyGen2 Finetuning
Finetune EnzyGen2 on a specific enzyme family
Protein, Enzyme, Small Molecule Binding Protein Finetuning and Active LearningDynamicsPLM Finetuning
Finetune a dynamics-aware protein language model on your data
Protein Finetuning and Active LearningBoltz-2 Affinity Finetuning
Finetune the Boltz-2 affinity head on your protein-ligand binding data
Protein, Small Molecule, Small Molecule Binding ProteinThermostability
ThermoMPNN
Protein mutation recommendation for increased thermostability
Protein, Antibody, Enzyme ThermostabilityProteinMPNN-ddG
Predict stability of point mutations
Protein, Enzyme, Antibody ThermostabilityTEMPRO
Nanobody melting temperature prediction
Antibody ThermostabilitySaProtΔG
Absolute protein stability (ΔG) prediction from structure
Protein, Antibody, Enzyme ThermostabilityTemStaPro
Protein thermostability prediction
Protein, Antibody, Enzyme ThermostabilityThermoMPNN-D
Double protein point mutation recommendation for increased thermostability
Protein, Antibody, Enzyme ThermostabilitydeepSTABp
Predict protein melting temperature
Protein, Antibody, Enzyme ThermostabilitySPURS
Protein stability (ddG) prediction from structure for single and multi-mutations
Protein, Antibody, EnzymeProtein Ligand Docking
PLACER
Protein-ligand docking
Enzyme, Small Molecule, Small Molecule Binding Protein Protein Ligand DockingAutodock Vina
Protein-ligand docking
Enzyme, Small Molecule, Small Molecule Binding Protein Protein Ligand DockingDiffDock
Protein-ligand docking with diffusion models
Protein, Enzyme, Small Molecule Protein Ligand DockingSurfDock
Surface-informed diffusion model for protein-ligand docking
Protein, Enzyme, Small Molecule Protein Ligand DockingSmina
Modified AutoDock, (unconventional) small molecule docking
Protein, Small Molecule, Enzyme Protein Ligand DockingGNINA
Molecular docking with deep learning
Protein, Small Molecule, Enzyme Protein Ligand DockingUnimol DockingV2
State of the art protein-ligand docking
Small Molecule, Protein, Small Molecule Binding Protein Protein Ligand DockingVirtual Screening
High-throughput ligand screening powered by QuickVina2 and AFVS
Small Molecule, Protein Protein Ligand DockingFlowDock
Protein ligand docking and affinity prediction
Protein, Enzyme, Small Molecule Protein Ligand DockingAF2BIND
Predict ligand binding sites
Protein, Small Molecule, Small Molecule Binding Protein Protein Ligand DockingVirtuDockDL
Deep learning virtual screening pipeline combining GNN ligand prioritization, OpenMM protein refinement, and AutoDock Vina docking
Protein, Enzyme, Small MoleculeMolecular Dynamics
GROMACS
Simulate protein only or protein-ligand interactions using GROMACS force field
Protein, Antibody, Peptide Molecular DynamicsMembrane Protein MD (GROMACS)
Simulate membrane proteins embedded in lipid bilayers using GROMACS with CHARMM36 force field
Protein, Antibody, Peptide Molecular DynamicsOpenMM MD
Simulate protein only or protein-ligand interactions using AMBER force field
Protein, Antibody, Peptide Molecular DynamicsBioEmu
Approximate equilibrium distribution
Protein, Peptide Molecular DynamicsMM/GB(PB)SA
Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area
Protein, Enzyme, Small Molecule Molecular DynamicsRelative Binding Free Energy
Relative energy of protein-ligand complexes
Enzyme, Small Molecule, Small Molecule Binding Protein Molecular DynamicsOrb Models 3
Protein ligand interaction energy
Small Molecule, Small Molecule Binding Protein Molecular DynamicsMDGen
Generative modeling of molecular dynamics trajectories
Peptide Molecular DynamicsOpenFE
Run different free energy protocols
Small Molecule, Small Molecule Binding Protein Molecular DynamicsTMD
Differentiable molecular dynamics engine for RBFE calculations with GPU-accelerated HREX sampling
Small Molecule, Small Molecule Binding Protein Molecular DynamicsAF2Rave
Generates diverse protein structures using reduced MSA AlphaFold2
Protein Molecular DynamicsOpenMM Protein Relaxation
Relax a protein structure using OpenMM
Protein Molecular Dynamicsg_mmpbsa
Estimate binding free energy (ΔGbind) from protein-ligand or protein-protein trajectories.
Protein, Enzyme, Small Molecule Molecular DynamicsOpenMM Metadynamics
Efficiently explore free energy landscapes for conformational changes, protein-ligand binding, and other biophysical processes using well-tempered metadynamics.
Protein, Antibody, Peptide Molecular DynamicsOpenMM Temperature Replica Exchange
Perform temperature replica exchange molecular dynamics for enhanced conformational sampling
Protein, Antibody, PeptideNucleic Acid
Model Angelo
Given a density map and a protein sequence automatically build a model for it
Antibody Nucleic AcidCryFold
Given a density map and a protein sequence automatically build a model for it
Antibody Nucleic AcidRFDpoly
Diffusion-based de novo design of RNA, DNA, and nucleoprotein complex structures
ProteinProtein Protein Docking
ColabDock
Protein-protein docking using inverted AlphaFold
Protein, Antibody, Peptide Protein Protein DockingEquiDock
Rigid body protein-protein docking
Protein Protein Protein DockingGeoDock
Deep learning protein-protein docking with SE(3) equivariance
Protein Protein Protein DockingAF2Dock
AlphaFold2-derived diffusion model for protein-protein docking. Upload receptor and ligand structures; outputs docked PDBs and ipTM scores per sample.
Protein Protein Protein DockingBinding ddG
Binding ddG prediction of protein complexes
Protein, Antibody Protein Protein DockingPRODIGY
Protein-protein binding affinity prediction
Protein Protein Protein DockingPPAP
Protein-protein binding affinity prediction for multiple complexes
Protein, Antibody Protein Protein DockingDockQ
Evaluate your docking interface
Protein, Peptide, Antibody Protein Protein DockingDeepRank-Ab
Score and rank antibody-antigen complex models by predicted DockQ
Antibody, Protein, Peptide Protein Protein DockingSpatial PPI v2
Predict PPI of structures or sequences
Protein Protein Protein DockingDSMBind
Predict antibody-antigen binding affinity
Protein, Antibody Protein Protein DockingMaSIF
Molecular surface interaction fingerprints.
Protein Protein Protein DockingPDockQ
Predict DockQ score of a predicted protein structure
Protein Protein Protein DockingIPSAE
Scoring function for interprotein interactions in AlphaFold
Protein Protein Protein DockingDFMDock
Protein-protein docking using diffusion and flow matching
Protein Protein Protein DockingContact MS
Contact molecular surface area for protein-protein interfaces
Protein, AntibodySolubility
SaProt
Language models for protein property prediction
Protein SolubilityNetSolP
Solubility and usability based on protein language models
Protein, Antibody, Enzyme SolubilityFastSolv
Solubility prediction for solute/solvent
Small Molecule SolubilityProtein-Sol
Sequence-based protein solubility prediction using compositional features
Protein, EnzymeAggregation
PEP-Patch
Quantify surface electrostatic potentials
Protein AggregationAggrescan3D
Predict aggregation propensity in protein structures and rationally design protein solubility
Protein, Antibody AggregationDeep Viscosity
Viscosity prediction for antibodies
Protein, Antibody AggregationProtein Properties
Calculate properties on input sequence/structure
ProteinRNA Language Models
Orthrus
Generate mRNA embeddings
Nucleic Acid RNA Language ModelsEvo 2
Genome modeling and design across all domains of life
Nucleic Acid RNA Language ModelsmRNABERT
Pretrained mRNA language model for sequence scoring, codon optimization, and embeddings.
Nucleic AcidAffinity Prediction
P2PXML
Predict antibody-antigen binding affinity (IC50) from structures
Antibody, Protein Affinity PredictionGEMS
GNN-based protein-ligand binding affinity prediction with language model embeddings
Protein, Enzyme, Small Molecule Affinity PredictionAEV-PLIG
Protein-ligand binding affinity prediction from 3D structure
Protein, Enzyme, Small Molecule Affinity PredictionStaB-ddG
Predict mutational effects on protein-protein binding from folding energy
Protein, AntibodyEmbeddings
Rosetta
Point Mutations
ESM2
Score point mutations or mask residues using ESM-2 language model
Protein Point MutationsAMPLIFY
Score using AMPLIFY language model
Protein Point MutationsBALM Paired
Score point mutations using BALM-paired language model
Protein, Antibody Point MutationsESM-Scan
Score point mutations using ESM1b language model
Protein, Enzyme Point MutationsDERNA
Pareto-optimal RNA sequence design from a target protein — jointly optimize structural stability (MFE) and codon adaptation (CAI).
Nucleic Acid Point MutationsVaxPress
Genetic-algorithm codon optimizer for mRNA vaccine design (ViennaRNA folding engine).
Nucleic Acid Point MutationsEVcouplings
Predict protein function and mutations using evolutionary sequence covariation
Protein, EnzymeStructure Prediction & Folding
LMI4Boltz (from NS)
Boltz-2-compatible low-memory fork with extra chunking and bfloat16 controls.
Not specified Structure Prediction & FoldingRoseTTAFold2 (from NS)
Protein structure prediction that's faster than AlphaFold2 and just as accurate.
Protein Structure Prediction & FoldingRoseTTAFold All-Atom (from NS)
Protein folding model that supports proteins, nucleotides, ligands, metal ions, and other small molecules.
Protein, Small Molecule Structure Prediction & FoldingCryoAtom Cryo-EM Model Builder (from NS)
CryoAtom builds atomic models from cryo-EM maps using local attention and 3D rotary position embedding, improving model completeness and speed while lowering resolution requirements.
Not specified Structure Prediction & FoldingDeepEMhancer (from NS)
DeepEMhancer is a deep learning approach for automatic post-processing of cryo-EM maps, performing masking and sharpening in a single step to improve interpretability.
Not specified Structure Prediction & FoldingCryoSAMU (from NS)
CryoSAMU enhances intermediate-resolution cryo-EM maps using a structure-aware multimodal U-Net, integrating map features with protein language model embeddings for faster, high-quality results.
Protein Structure Prediction & FoldingBoltz-1 (AlphaFold3) (from NS)
An open-source version of AlphaFold3 developed by an MIT lab.
Not specifiedLigand/Drug Design & Screening
DynamicBind (from NS)
Predict protein-ligand complexes using protein structure files and ligands in SMILES format.
Protein, Small Molecule Ligand/Drug Design & ScreeningDiffDock-L (from NS)
Dock a ligand onto any protein receptor with high accuracy.
Protein, Small Molecule Ligand/Drug Design & ScreeningGenMol (from NS)
Generative AI for small molecule design and optimization.
Small Molecule Ligand/Drug Design & ScreeningPocketFlow (from NS)
PocketFlow is a Deep Generative Model that generates ligands for target protein binding pockets.
Protein, Small Molecule Ligand/Drug Design & ScreeningPocketXMol | Dock (from NS)
Pocket-conditioned docking for small molecules or peptides.
Peptide, Small Molecule Ligand/Drug Design & ScreeningPocketXMol | Small Molecule Design (from NS)
Pocket-conditioned small-molecule generation and fragment expansion.
Small Molecule Ligand/Drug Design & ScreeningQEPPI (from NS)
Screen and evaluate early-stage PPI-targeting compounds with a tailored drug-likeness index.
Small Molecule Ligand/Drug Design & ScreeningChemBounce (from NS)
Fragment-based molecular generation and optimization tool.
Small Molecule Ligand/Drug Design & ScreeningSPRINT (from NS)
SPRINT is a fast, accurate, and scalable deep learning framework for virtual screening of thousands of molecules.
Small Molecule Ligand/Drug Design & ScreeningeTox Drug Toxicity Prediction (from NS)
Predict Toxicity and Synthetic Accessibility from SMILES text or file inputs.
Small Molecule Ligand/Drug Design & ScreeningToxinPred Peptide Toxicity Prediction (from NS)
Predict peptide toxicity from single protein sequences or in batch using an accelerated algorithm.
Protein, Peptide, Small Molecule Ligand/Drug Design & ScreeningMordred Molecular Descriptor Calculator (from NS)
High-throughput descriptor engine for ML-ready molecular fingerprints.
Small Molecule Ligand/Drug Design & ScreeningADMET-AI (from NS)
Predict ADMET properties swiftly and accurately using machine learning.
Small MoleculeMulti-omics
Transcript Assembly (from NS)
Easily perform transcript quantification using an input fastq file.
Not specified Multi-omicsInterleaved FASTQ Splitter (from NS)
Split interleaved FASTQ into left/right FASTQ with validation.
Not specified Multi-omicsDEAnalysis (from NS)
Differential Expression Analysis pipeline configured for two-condition experiments.
Not specified Multi-omicsPangolin RNA Splicing Prediction (from NS)
Pangolin is a deep learning model to predict splice site strength and the impact of genetic variants on RNA splicing in multiple tissues.
Nucleic AcidMolecular Docking & Interactions
LightDock (from NS)
Powerful molecular docking algorithm for proteins and nucleotides.
Protein Molecular Docking & InteractionsScanNet Protein Binding Site Prediction (from NS)
A geometric deep learning model for predicting binding site probability from a structure.
Not specified Molecular Docking & InteractionsInteraction Fingerprint (from NS)
Compare protein-ligand interaction fingerprints across compounds with ProLIF.
Protein, Small MoleculeSequence Analysis & Annotation
DNA Chisel Sequence Optimizer (from NS)
DnaChisel edits DNA sequences to satisfy biological constraints and optimize properties like codon usage, motif distribution, and GC content.
Nucleic Acid Sequence Analysis & AnnotationCodonTransformer (from NS)
A deep learning-based tool for multispecies codon optimization.
Not specified Sequence Analysis & AnnotationTIsigner Expression Optimization (from NS)
A nucleotide sequence based method for optimizing protein expression.
Protein Sequence Analysis & AnnotationRazor Signal Peptide Detection (from NS)
A sequence based method for detecting signal peptides.
Peptide Sequence Analysis & AnnotationWoLF PSORT Protein Localization (from NS)
Predicts subcellular localization sites from protein sequence.
Protein Sequence Analysis & AnnotationProtNLM (from NS)
Predict protein annotations from sequence using ProtNLM.
Protein Sequence Analysis & AnnotationEnzBert E.C. Prediction (from NS)
Enzbert predicts enzymatic classes of protein sequences in batch or individually.
Protein Sequence Analysis & AnnotationANARCII (from NS)
ANARCII is a language model–based tool for scalable, accurate numbering and classification of antibody and TCR repertoires.
Antibody Sequence Analysis & AnnotationCAR-Toner (from NS)
CAR-Toner is an AI tool for rapid prediction of CAR-T tonic signaling by calculating Positively Charged Patch (PCP) scores.
Not specified Sequence Analysis & AnnotationStrucTFactor (from NS)
StrucTFactor leverages 3D protein structures for precise transcription factor prediction, outperforming existing methods.
Protein Sequence Analysis & AnnotationDR-BERT (from NS)
Efficiently annotate disordered protein regions with a compact language model.
ProteinUtilities & Conversions
ClusterProt (from NS)
Cluster same length proteins using only their structures.
Protein Utilities & ConversionsPDB Animator (from NS)
Render animated GIF and MP4 files from multi-model PDB structures.
Not specified Utilities & ConversionsPDBFixer (from NS)
Fix common issues with PDB files such as missing atoms.
Not specified Utilities & ConversionsPDB-mmCIF Converter (from NS)
Converts PDB files to CIF / mmCIF files and vice versa
Not specified Utilities & ConversionsChain Exporter (from NS)
Split one structure into separate chain-level PDB or mmCIF files.
Not specified Utilities & ConversionsPDB-SDF Converter (from NS)
Converts PDB files to SDF files and vice versa
Not specified Utilities & ConversionsPDB2PQR (from NS)
PDB2PQR converts PDB files to PQR format, adding missing atoms and assigning charges for electrostatics calculations.
Not specified Utilities & ConversionsPDB2Fasta (from NS)
Convert a PDB structure into FASTA sequences for each valid protein chain.
Protein Utilities & ConversionsLDDT Structural Comparison (from NS)
Evaluate protein structure quality with a superposition-free local distance difference score
Protein Utilities & ConversionsKluster (from NS)
Protein structure clustering and visualization tool using TM-align/US-align structural alignment and dimensionality reduction techniques (UMAP, t-SNE, PCA).
ProteinMolecular Dynamics & Simulation
Evolution & Phylogenetics
Foldtree (from NS)
Construct phylogenetic trees from protein structures using Foldseek.
Protein Evolution & Phylogeneticsmmseqs2 MSA Generation (from NS)
Rapidly generate diverse and quality MSAs with support for various pairing modes.
Not specified Evolution & PhylogeneticsMUSCLE v5 MSA Generation (from NS)
Rapidly generate high-quality multiple sequence alignments for protein sequences.
Protein Evolution & PhylogeneticsMAFFT MSA Generation (from NS)
Rapidly generate multiple sequence alignments for protein sequences.
Protein Evolution & PhylogeneticsFastTree (from NS)
Rapidly infer maximum-likelihood phylogenetic trees for large sequence datasets.
Not specified Evolution & PhylogeneticsAlphaFind (from NS)
Fast structure similarity search across AlphaFold DB.
Not specified