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NeuroBind
Design antibodies, nanobodies, scFvs, and peptides with high affinity and low immunogenicity.
BindFilter
Fold and score many binder candidates with a unified, machine-readable output.
NeuroFold2
Design next-generation enzymes by co-optimizing for catalytic activity, stability, and solubility.
Chai-1 (AlphaFold3)
Commercial friendly alternative to AlphaFold3 with competitive MSA-less option.
Boltz-2 (AlphaFold3)
Open-source AlphaFold3-class model (Boltz-2) with built-in affinity prediction.
OpenDDE
Open-source all-atom co-folding model for proteins, nucleic acids, ligands, and ions.
Protenix (AlphaFold3)
Another AlphaFold3 implementation developed by the ByteDance team.
IntelliFold (AlphaFold3)
Open-source AlphaFold3-class model (IntelliFold) with fast, accurate structure prediction across biomolecules.
AlphaFold2
Accurately predict protein and complex structures at the atomic level using their amino acid sequence.
BoltzGen
Generate high-affinity binders for proteins, nucleic acids, and small molecules using an all-atom diffusion model.
Prot2Prop Protein Property Prediction
Predict multiple protein developability properties from sequence in one batch workflow.
BAGEL Protein Design
User-configured BAGEL workflows for mini-enzyme, mimic-enzyme, and binder design.
Proteina-Complexa
Fully atomistic binder and motif design with generative search and structure-prediction validation.
ProteinEBM Scoring
Score, rank, and compare protein structures with ProteinEBM energy.
ProteinEBM Dynamics
Sample ProteinEBM folding dynamics and export trajectories.
BindCraft2
Campaign-based protein binder design across multiple binder modalities.
BindCraft
One-shot design of functional protein binders.
FreeBindCraft
PyRosetta-free one-shot design of functional protein binders.
OpenFold3 (AlphaFold3)
Open-source AlphaFold3 reproduction achieving near-parity accuracy across biomolecular modalities.
ESMFold2
Biohub all-atom ESMFold2 for proteins, nucleic acids, ligands, and complexes.
ESMC Feature Interpretation
Interpret residue-level biological patterns learned by ESMC using sparse autoencoder features.
ESMFold2 Binder Design
Design minibinders and antibody CDRs with ESMFold2 structural gradients and ESMC sequence regularization.
ESMC Mutation Scoring
Zero-shot ESMC entropy and mutation scoring from sequence alone.
GNINA
Enhanced molecular docking with deep learning.
DynamicBind
Predict protein-ligand complexes using protein structure files and ligands in SMILES format.
DiffDock-L
Dock a ligand onto any protein receptor with high accuracy.
RFantibody
Generative antibody/nanobody design with fine-tuned RFdiffusion
RFdiffusion3
All-atom generative diffusion model for designing proteins, nucleic acid binders, and enzymes with precise non-protein interaction conditioning.
RFdiffusion2
Design functional enzymes from their reaction mechanisms using an atom-resolution generative model.
RFdiffusion
Design proteins, binders, and more with this protein diffusion model.
OpenMM Molecular Dynamics
Run all-atom OpenMM molecular dynamics simulations with staged minimization, NVT, NPT, and production MD.
Martini OpenMM Molecular Dynamics
Run Martini coarse-grained OpenMM molecular dynamics simulations with staged minimization, NVT, NPT, and production MD.
GROMACS Molecular Dynamics
Perform Molecular Dynamics using GROMACS framework, simulating many different solvent solute systems.
gmx_MMPBSA
Calculate binding energetics for GROMACS trajectories using MMPBSA/MMGBSA calculations
Single-Point Energy Calculation
Evaluate a fixed molecular geometry across a broad, provenance-rich catalog of electronic-structure methods and molecular potentials.
Grid Inhomogeneous Solvation Theory (GIST)
Simulate and map local binding-site hydration thermodynamics with a reproducible OpenMM and cpptraj GIST workflow.
BETA
OpenFE Relative Binding Free Energy
Rank a positioned ligand series with OpenFE relative binding free energy calculations.
BETA
OpenFE Absolute Binding Free Energy
Compute an OpenFE absolute binding free energy from a positioned SDF ligand.
BETA
OpenFE Hydration Free Energy
Compute OpenFE hydration free energies for small molecules.
MDAnalysis Trajectory Analysis
Post-process molecular-dynamics trajectories into stability, flexibility, exposure, contact, and secondary-structure CSV outputs.
CatPred
A deep learning framework for predicting enzyme kinetic parameters (kcat, Km, Ki).
EvoEF2
Protein stability and binding energy analysis using EvoEF2.
AutoDock Vina (smina)
An enhanced fork of AutoDock Vina offering customizable scoring functions, improved sampling, and better performance for molecular docking simulations.
Protein Fold Stability Prediction
Predict protein stability from structure using ESM-IF.
Prodigy Binding Affinity Prediction
PRODIGY predicts binding affinity and dissociation constants for protein–protein complexes based on their 3D structures.
PDB-mmCIF Converter
Converts PDB files to CIF / mmCIF files and vice versa
ProteinMPNN
Predict alternative sequences for an input protein structure with high accuracy. Also supports SolubleMPNN.
Boltz-1 (AlphaFold3)
An open-source version of AlphaFold3 developed by an MIT lab.
ADMET-AI
Predict ADMET properties swiftly and accurately using machine learning.
SaProt
SaProt integrates sequence and structure information through a structure-aware vocabulary to predict protein properties accurately.
mmseqs2 MSA Generation
Rapidly generate diverse and quality MSAs with support for various pairing modes.
LigandMPNN
Predict alternative sequences for an input protein structure with high accuracy. Also supports ProteinMPNN and SolubleMPNN.
PDBFixer
Fix common issues with PDB files such as missing atoms.
NetSolP-1.0
Accurately predict protein solubility and expression / usability from amino acid sequence.
PPAP
A structure-aware deep learning model for high-accuracy protein-protein binding affinity prediction (Kd).
RoseTTAFold3
Open-source all-atom foundation model for structure prediction and generative design.
eTox Drug Toxicity Prediction
Predict Toxicity and Synthetic Accessibility from SMILES text or file inputs.
ESMFold
Accurately predict protein structures at the atomic level using its amino acid sequence.
RoseTTAFold2
Protein structure prediction that's faster than AlphaFold2 and just as accurate.
DLKcat Kcat Prediction
Predict Kcats of complexes using a protein sequence and compounds in SMILES format.
SPRINT
SPRINT is a fast, accurate, and scalable deep learning framework for virtual screening of thousands of molecules.
RoseTTAFold All-Atom
Protein folding model that supports proteins, nucleotides, ligands, metal ions, and other small molecules.
AMBER Relaxation
Relax a protein structure using an AMBER settling protocol.
TemStaPro Protein Thermostability Prediction
TemStaPro predicts protein thermostability from sequence at a range of temperatures.
Aggrescan3D
Structure-based aggregation profiling with Aggrescan3D
ThermoMPNN
ThermoMPNN Predicts protein stability changes with precision and efficiency for mutation analysis and design.
EvoEF2 Mutant Stability Analysis
Analyze the impact of mutations on protein stability using EvoEF2.
SoDoPE Solubility Optimization
A sequence based method for optimizing protein solubility.
PocketFlow
PocketFlow is a Deep Generative Model that generates ligands for target protein binding pockets.
FlowDock
FlowDock predicts protein-ligand structures and binding affinities using geometric flow matching, enabling multi-ligand docking and fast virtual drug screening.
ScanNet Protein Binding Site Prediction
A geometric deep learning model for predicting binding site probability from a structure.
DeepImmuno Immunogenicity Prediction
DeepImmuno is a CNN-based model for peptide immunogenicity prediction with state-of-the-art accuracy across viral and cancer datasets.
EpHod Optimal Enzyme pH Prediction
EpHod is a semi-supervised language model that predicts optimal pH for enzymes from sequence alone.
ESM-IF1
Predict alternative sequences for an input protein structure with high accuracy.
USalign Structural Alignment
Efficiently produce accurate 3D structural alignments across diverse macromolecular forms and configurations
AlphaFlow
Use AlphaFlow to generate protein structures that closely reflect experimental and physiological conditions.
Conformer Generator
Generate conformers for small molecules and ligands using RDkit.
LightDock
Powerful molecular docking algorithm for proteins and nucleotides.
ColabDock
Accurately predict protein complexes with specialized restraints.
AF2Bind
Accurately predict small-molecule-binding residues using AlphaFold2 pairwise representation.
StaB-ddG
Fast & accurate deep learning model for predicting binding ∆∆G using folding energy principles and a ProteinMPNN-based inverse folding framework.
Foldtree
Construct phylogenetic trees from protein structures using Foldseek.
ProtNLM
Predict protein annotations from sequence using ProtNLM.
Immune Builder
Design Antibodies, Nanobodies, and T-Cell Receptors using Immune Builder's state-of-the-art generative models.
ToxinPred Peptide Toxicity Prediction
Predict peptide toxicity from single protein sequences or in batch using an accelerated algorithm.
RealKcat
Predict kcat and Km class ranges from one enzyme sequence and a substrate panel.
PDB-SDF Converter
Converts PDB files to SDF files and vice versa
ProteinMPNN-ddG
An unsupervised deep learning model for rapid and accurate prediction of protein stability changes upon mutation, based on an improved ProteinMPNN methodology.
OmegaFold
Accurate de novo protein structure prediction without reliance on MSAs.
DiffAb Antibody Design
Design Antibodies for a target Antigen using the Antigen structure. DiffAb leverages a probabalistic diffusion model.
PDB2PQR
PDB2PQR converts PDB files to PQR format, adding missing atoms and assigning charges for electrostatics calculations.
WoLF PSORT Protein Localization
Predicts subcellular localization sites from protein sequence.
Mordred Molecular Descriptor Calculator
High-throughput descriptor engine for ML-ready molecular fingerprints.
FastTree
Rapidly infer maximum-likelihood phylogenetic trees for large sequence datasets.
QEPPI
Screen and evaluate early-stage PPI-targeting compounds with a tailored drug-likeness index.
AfCycDesign
Generates improved cyclic protein structures using a modified AlphaFold network.
CodonTransformer
A deep learning-based tool for multispecies codon optimization.
BioPhi
AI-driven antibody humanization + humanness scoring from natural repertoire data.
Efficient Evolution
A protein language model-based tool for efficient, task-agnostic design of high-functionality protein variants.
ProGen2
Create protein variants using nothing but the amino acid sequence.
Humatch
A CNN-based tool for rapid, gene-specific humanization and classification of antibody heavy and light chains.
DeepEMhancer
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.
ESM-2 for PTMs
Predict potential post translational modification sites from sequence data.
Razor Signal Peptide Detection
A sequence based method for detecting signal peptides.
PocketXMol | Dock
Pocket-conditioned docking for small molecules or peptides.
MUSCLE v5 MSA Generation
Rapidly generate high-quality multiple sequence alignments for protein sequences.
TIsigner Expression Optimization
A nucleotide sequence based method for optimizing protein expression.
ANARCI
ANARCI provides standardized numbering and chain classification for antibody and TCR domains.
CryoAtom Cryo-EM Model Builder
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.
Interaction Analysis
Detect and summarize molecular interactions across uploaded structures.
EnzBert E.C. Prediction
Enzbert predicts enzymatic classes of protein sequences in batch or individually.
LMI4Boltz
Boltz-2-compatible low-memory fork with extra chunking and bfloat16 controls.
DR-BERT
Efficiently annotate disordered protein regions with a compact language model.
CAR-Toner
CAR-Toner is an AI tool for rapid prediction of CAR-T tonic signaling by calculating Positively Charged Patch (PCP) scores.
AFcluster
Predict conformational substates using AlphaFold2 on multiple sequence alignments.
GenMol
Generative AI for small molecule design and optimization.
AllMetal3D
Identify likely metal and water binding sites from a protein structure.
PDB2Fasta
Convert a PDB structure into FASTA sequences for each valid protein chain.
Foldseek Structural Clustering
Use the Foldseek easy-cluster algorthim to cluster structures using a representative structure.
ImaPEp Antibody-Antigen Binding Prediction
ImaPEp predicts binding probabilities for antibody–antigen pairs by representing their binding interfaces as 2D images and leveraging convolutional neural networks.
ProSST Mutation Effect Prediction
ProSST predicts protein mutation effects and functions by integrating sequence and structural data via quantized tokens and disentangled attention.
Kluster
Protein structure clustering and visualization tool using TM-align/US-align structural alignment and dimensionality reduction techniques (UMAP, t-SNE, PCA).
Pangolin RNA Splicing Prediction
Pangolin is a deep learning model to predict splice site strength and the impact of genetic variants on RNA splicing in multiple tissues.
AntiFold
Predict alternative sequences for an input Antibodies, Nanobodies, and Antigen-Antibody structures with high accuracy.
DNA Chisel Sequence Optimizer
DnaChisel edits DNA sequences to satisfy biological constraints and optimize properties like codon usage, motif distribution, and GC content.
TEMPRO Nanobody Melting Temperature Prediction
Predict nanobody melting temperature directly from amino-acid sequence.
ParaSurf
ParaSurf is a deep learning framework that predicts paratope binding sites by analyzing molecular surfaces of antibodies/nanobodies to identify antigen-binding regions across the entire Fab/Fv domain.
ChemBounce
Fragment-based molecular generation and optimization tool.
FKSFold-Chai
Chai-1 fork with Feynman-Kac steering for molecular-glue ternary complexes.
BETA
Lacuna Cryptic Pocket Discovery
Discover and rank cryptic protein pockets through conformational ensemble analysis.
Caliby
Structure- and ensemble-conditioned protein sequence design, scoring, and sidechain packing.
DockQ
Assess the quality of protein-protein docking models using the native and predicted structure.
MIF-ST
Predict alternative sequences for an input protein structure with high accuracy.
Chain Exporter
Split one structure into separate chain-level PDB or mmCIF files.
PocketXMol | Protein Design
Pocket-conditioned peptide generation and redesign.
PocketXMol | Small Molecule Design
Pocket-conditioned small-molecule generation and fragment expansion.
Isoelectric Point Calculator
Sequence-only pI/pKa prediction (IPC 1/2).
CryoSAMU
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.
DeepViscosity
Predict high-concentration monoclonal antibody viscosity classes.
ANARCII
ANARCII is a language model–based tool for scalable, accurate numbering and classification of antibody and TCR repertoires.
AlphaFind
Fast structure similarity search across AlphaFold DB.
MAFFT MSA Generation
Rapidly generate multiple sequence alignments for protein sequences.
SpatialPPIv2 Protein Interaction Prediction
Predict protein-protein interaction probability from paired structures or sequences.
Interaction Fingerprint
Compare protein-ligand interaction fingerprints across compounds with ProLIF.
DISCO
Joint protein sequence-structure co-design with ligand, RNA, and DNA conditioning in one diffusion workflow.
ClusterProt
Cluster same length proteins using only their structures.
ITsFlexible
A deep learning tool that predicts the conformational flexibility of antibody and T cell receptor (TCR) CDR3 loops, classifying them as 'rigid' or 'flexible'.
StrucTFactor
StrucTFactor leverages 3D protein structures for precise transcription factor prediction, outperforming existing methods.
RhoDesign RNA Inverse Folding
Generates RNA sequences with precise structural fidelity and functional diversity for targeted applications
PubChem Similarity Search
Find structurally similar compounds in PubChem from SMILES, SDF, or CCD queries.
LDDT Structural Comparison
Evaluate protein structure quality with a superposition-free local distance difference score
Admetica
Open-source Chemprop ADMET prediction for small-molecule screening.
ABACUS-R Sequence Design
Use ABACUS-R to design protein sequences for a given backbone structure using an encoder-decoder model.
Transcript Assembly
Easily perform transcript quantification using an input fastq file.
PDB Animator
Render animated GIF and MP4 files from multi-model PDB structures.
NeuroFold
Optimize enzyme thermostability, pH stability, solubility, and reaction rate with high accuracy.
AlphaBind Antibody-Antigen Affinity Prediction
Rank antibody candidates with pretrained AlphaBind, optionally fine-tuned on target-specific measurements.
BETA
IFACE Surface Comparison
Compare two protein structures through their geometric and chemical surfaces.
DEAnalysis
Differential Expression Analysis pipeline configured for two-condition experiments.
PyPermM Membrane Permeability
Estimate passive membrane permeability and insertion energy from 3D molecular structure.
SMILES to MOL2
Generate bulk 3D MOL2 structures from SMILES.
SuperMetal
Predict zinc-binding sites from an uploaded protein structure.
Permeability and Efflux Prediction
Predict Caco-2 and MDCK permeability and efflux from small-molecule structures.
RDKit Molecular Descriptors
Calculate common molecular properties for small molecules using RDKit.
SASA Calculator
Measure protein surface exposure by structure, chain, and residue.
NARDINI+ GIN IDR Grammar Analysis
Analyze IDR molecular grammar features and GIN clusters from human IDs or custom IDR sequences.
RNAcofold | ViennaRNA
Predict the minimum-free-energy structure of two interacting RNA strands.
RNAplfold | ViennaRNA
Estimate local RNA accessibility and base-pair probabilities along a sequence.
SuperWater
Predict protein surface hydration waters from uploaded PDB or mmCIF structures.
Evo 2
Score genomic variants and generate DNA with Evo2.
Interleaved FASTQ Splitter
Split interleaved FASTQ into left/right FASTQ with validation.
PAMmla Evolve
Evolve SpCas9 PAM preference using evolutionary algorithms.
Align Structures
Align uploaded biomolecular structures to a shared reference while preserving complete complexes.
Aliphatic Index
Compare the aliphatic index of protein sequences.
DELPHI Antibody Developability Prediction
Predict antibody PSR and SEC developability from paired variable-domain sequences.
Free Wilson Analysis
Interpretable R-group SAR modeling and analog prioritization for congeneric small-molecule series.
HMMER Profile Alignment
Align protein or nucleotide sequences to a profile HMM with HMMER.
PAMmla
Machine learning models to predict SpCas9 PAM preference from amino acid sequence.
BETA
PLACER
Confidence-ranked ligand and protein side-chain ensembles.
PSSM Generation
Build a reusable protein profile from an existing MSA or generate an alignment from sequences or a query.
PSSM Profile Comparison
Align two reusable profiles using symmetric probability overlap rather than an HMM method. Scores are in bits and have no calibrated E-values.
PSSM Sequence Alignment
Align and rank protein candidates against one reusable position-specific protein profile. Scores are log-odds in bits, with no calibrated E-values or PSI-BLAST equivalence.
PSSM Sequence Scan
Find and rank ungapped profile-length windows in longer protein sequences. Scores are log-odds in bits, with no calibrated E-values or PSI-BLAST equivalence.
PULCHRA
Reconstruct all-atom protein structures from C-alpha or reduced protein PDB models.
RMSD Calculator
Calculate all-against-all backbone RMSD values between reference and mobile structure groups.
RNALfold | ViennaRNA
Identify locally stable RNA secondary structures within a selected window.
RNAalifold | ViennaRNA
Predict a consensus RNA secondary structure and free energy from a prealigned RNA multiple-sequence alignment.
RNAdistance | ViennaRNA
Compare RNA secondary structures using tree, string, or base-pair distance measures.
RNAdos | ViennaRNA
Count RNA secondary structures across discrete energy bands.
RNAduplex | ViennaRNA
Find optimal RNA-RNA hybridization duplexes and their binding energies.
RNAeval | ViennaRNA
Evaluate the free energy of a supplied RNA sequence and secondary structure.
RNAfold | ViennaRNA
Predict RNA minimum-free-energy structures and optional base-pair probabilities.
RNAinverse | ViennaRNA
Design RNA sequences that fold toward a specified secondary structure.
RNAplex | ViennaRNA
Scan for favorable RNA-RNA interaction sites and duplex energies.
RNAplot | ViennaRNA
Draw a supplied RNA secondary structure as a radial, circular, or alternative layout.
RNAsubopt | ViennaRNA
Enumerate RNA secondary structures near the minimum free energy.
RNAup | ViennaRNA
Calculate RNA-RNA interaction energies that include site accessibility.
Radius of Gyration Calculator
Measure protein compactness for a structure or selected chains.
Random RNA Sequence Generator
Generate customizable RNA sequences in FASTA format.
Reverse Complement
Convert DNA and RNA strands from text, FASTA, or FASTQ.
SMILES to InChI
Convert bulk SMILES to standard InChI and InChIKey.
ipSAE
Calculate interface confidence metrics from a structure and PAE matrix.
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