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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.
OpenDDE
Open-source all-atom co-folding model for proteins, nucleic acids, ligands, and ions.
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.
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.
FKSFold-Chai
Chai-1 fork with Feynman-Kac steering for molecular-glue ternary complexes.
LMI4Boltz
Boltz-2-compatible low-memory fork with extra chunking and bfloat16 controls.
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.
Caliby
Structure- and ensemble-conditioned protein sequence design, scoring, and sidechain packing.
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.
DISCO
Joint protein sequence-structure co-design with ligand, RNA, and DNA conditioning in one diffusion workflow.
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.
BETA
Lacuna Cryptic Pocket Discovery
Discover and rank cryptic protein pockets through conformational ensemble analysis.
ColabDock
Accurately predict protein complexes with specialized restraints.
RoseTTAFold3
Open-source all-atom foundation model for structure prediction and generative design.
RoseTTAFold2
Protein structure prediction that's faster than AlphaFold2 and just as accurate.
RoseTTAFold All-Atom
Protein folding model that supports proteins, nucleotides, ligands, metal ions, and other small molecules.
GenMol
Generative AI for small molecule design and optimization.
PocketFlow
PocketFlow is a Deep Generative Model that generates ligands for target protein binding pockets.
PocketXMol | Dock
Pocket-conditioned docking for small molecules or peptides.
PocketXMol | Protein Design
Pocket-conditioned peptide generation and redesign.
PocketXMol | Small Molecule Design
Pocket-conditioned small-molecule generation and fragment expansion.
EvoEF2
Protein stability and binding energy analysis using EvoEF2.
EvoEF2 Mutant Stability Analysis
Analyze the impact of mutations on protein stability using EvoEF2.
BETA
IFACE Surface Comparison
Compare two protein structures through their geometric and chemical surfaces.
Isoelectric Point Calculator
Sequence-only pI/pKa prediction (IPC 1/2).
QEPPI
Screen and evaluate early-stage PPI-targeting compounds with a tailored drug-likeness index.
ChemBounce
Fragment-based molecular generation and optimization tool.
Transcript Assembly
Easily perform transcript quantification using an input fastq file.
Interleaved FASTQ Splitter
Split interleaved FASTQ into left/right FASTQ with validation.
Evo 2
Score genomic variants and generate DNA with Evo2.
LightDock
Powerful molecular docking algorithm for proteins and nucleotides.
ESMFold
Accurately predict protein structures at the atomic level using its amino acid sequence.
LigandMPNN
Predict alternative sequences for an input protein structure with high accuracy. Also supports ProteinMPNN and SolubleMPNN.
ProteinMPNN
Predict alternative sequences for an input protein structure with high accuracy. Also supports SolubleMPNN.
NetSolP-1.0
Accurately predict protein solubility and expression / usability from amino acid sequence.
DEAnalysis
Differential Expression Analysis pipeline configured for two-condition experiments.
ESM-IF1
Predict alternative sequences for an input protein structure with high accuracy.
MIF-ST
Predict alternative sequences for an input protein structure with high accuracy.
AfCycDesign
Generates improved cyclic protein structures using a modified AlphaFold network.
AF2Bind
Accurately predict small-molecule-binding residues using AlphaFold2 pairwise representation.
ScanNet Protein Binding Site Prediction
A geometric deep learning model for predicting binding site probability from a structure.
AFcluster
Predict conformational substates using AlphaFold2 on multiple sequence alignments.
Prodigy Binding Affinity Prediction
PRODIGY predicts binding affinity and dissociation constants for protein–protein complexes based on their 3D structures.
PPAP
A structure-aware deep learning model for high-accuracy protein-protein binding affinity prediction (Kd).
Interaction Analysis
Detect and summarize molecular interactions across uploaded structures.
Interaction Fingerprint
Compare protein-ligand interaction fingerprints across compounds with ProLIF.
SPRINT
SPRINT is a fast, accurate, and scalable deep learning framework for virtual screening of thousands of molecules.
DNA Chisel Sequence Optimizer
DnaChisel edits DNA sequences to satisfy biological constraints and optimize properties like codon usage, motif distribution, and GC content.
CodonTransformer
A deep learning-based tool for multispecies codon optimization.
TIsigner Expression Optimization
A nucleotide sequence based method for optimizing protein expression.
SoDoPE Solubility Optimization
A sequence based method for optimizing protein solubility.
Razor Signal Peptide Detection
A sequence based method for detecting signal peptides.
WoLF PSORT Protein Localization
Predicts subcellular localization sites from protein sequence.
ProtNLM
Predict protein annotations from sequence using ProtNLM.
ESM-2 for PTMs
Predict potential post translational modification sites from sequence data.
EnzBert E.C. Prediction
Enzbert predicts enzymatic classes of protein sequences in batch or individually.
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'.
CatPred
A deep learning framework for predicting enzyme kinetic parameters (kcat, Km, Ki).
RealKcat
Predict kcat and Km class ranges from one enzyme sequence and a substrate panel.
DLKcat Kcat Prediction
Predict Kcats of complexes using a protein sequence and compounds in SMILES format.
TemStaPro Protein Thermostability Prediction
TemStaPro predicts protein thermostability from sequence at a range of temperatures.
TEMPRO Nanobody Melting Temperature Prediction
Predict nanobody melting temperature directly from amino-acid sequence.
eTox Drug Toxicity Prediction
Predict Toxicity and Synthetic Accessibility from SMILES text or file inputs.
ToxinPred Peptide Toxicity Prediction
Predict peptide toxicity from single protein sequences or in batch using an accelerated algorithm.
AlphaFlow
Use AlphaFlow to generate protein structures that closely reflect experimental and physiological conditions.
AMBER Relaxation
Relax a protein structure using an AMBER settling protocol.
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.
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.
Aggrescan3D
Structure-based aggregation profiling with Aggrescan3D
DeepViscosity
Predict high-concentration monoclonal antibody viscosity classes.
DockQ
Assess the quality of protein-protein docking models using the native and predicted structure.
Protein Fold Stability Prediction
Predict protein stability from structure using ESM-IF.
Foldseek Structural Clustering
Use the Foldseek easy-cluster algorthim to cluster structures using a representative structure.
Foldtree
Construct phylogenetic trees from protein structures using Foldseek.
EpHod Optimal Enzyme pH Prediction
EpHod is a semi-supervised language model that predicts optimal pH for enzymes from sequence alone.
Immune Builder
Design Antibodies, Nanobodies, and T-Cell Receptors using Immune Builder's state-of-the-art generative models.
ANARCI
ANARCI provides standardized numbering and chain classification for antibody and TCR domains.
ANARCII
ANARCII is a language model–based tool for scalable, accurate numbering and classification of antibody and TCR repertoires.
PDB Animator
Render animated GIF and MP4 files from multi-model PDB structures.
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.
DiffAb Antibody Design
Design Antibodies for a target Antigen using the Antigen structure. DiffAb leverages a probabalistic diffusion model.
PULCHRA
Reconstruct all-atom protein structures from C-alpha or reduced protein PDB models.
PDBFixer
Fix common issues with PDB files such as missing atoms.
PDB-mmCIF Converter
Converts PDB files to CIF / mmCIF files and vice versa
Chain Exporter
Split one structure into separate chain-level PDB or mmCIF files.
PDB-SDF Converter
Converts PDB files to SDF files and vice versa
PDB2PQR
PDB2PQR converts PDB files to PQR format, adding missing atoms and assigning charges for electrostatics calculations.
PDB2Fasta
Convert a PDB structure into FASTA sequences for each valid protein chain.
AutoDock Vina (smina)
An enhanced fork of AutoDock Vina offering customizable scoring functions, improved sampling, and better performance for molecular docking simulations.
Conformer Generator
Generate conformers for small molecules and ligands using RDkit.
mmseqs2 MSA Generation
Rapidly generate diverse and quality MSAs with support for various pairing modes.
Align Structures
Align uploaded biomolecular structures to a shared reference while preserving complete complexes.
RMSD Calculator
Calculate all-against-all backbone RMSD values between reference and mobile structure groups.
USalign Structural Alignment
Efficiently produce accurate 3D structural alignments across diverse macromolecular forms and configurations
LDDT Structural Comparison
Evaluate protein structure quality with a superposition-free local distance difference score
StaB-ddG
Fast & accurate deep learning model for predicting binding ∆∆G using folding energy principles and a ProteinMPNN-based inverse folding framework.
PAMmla
Machine learning models to predict SpCas9 PAM preference from amino acid sequence.
PAMmla Evolve
Evolve SpCas9 PAM preference using evolutionary algorithms.
AntiFold
Predict alternative sequences for an input Antibodies, Nanobodies, and Antigen-Antibody structures with high accuracy.
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.
HMMER Profile Alignment
Align protein or nucleotide sequences to a profile HMM with HMMER.
MUSCLE v5 MSA Generation
Rapidly generate high-quality multiple sequence alignments for protein sequences.
MAFFT MSA Generation
Rapidly generate multiple sequence alignments for protein sequences.
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.
FastTree
Rapidly infer maximum-likelihood phylogenetic trees for large sequence datasets.
Mordred Molecular Descriptor Calculator
High-throughput descriptor engine for ML-ready molecular fingerprints.
ADMET-AI
Predict ADMET properties swiftly and accurately using machine learning.
PyPermM Membrane Permeability
Estimate passive membrane permeability and insertion energy from 3D molecular structure.
Permeability and Efflux Prediction
Predict Caco-2 and MDCK permeability and efflux from small-molecule structures.
Admetica
Open-source Chemprop ADMET prediction for small-molecule screening.
AllMetal3D
Identify likely metal and water binding sites from a protein structure.
Free Wilson Analysis
Interpretable R-group SAR modeling and analog prioritization for congeneric small-molecule series.
ThermoMPNN
ThermoMPNN Predicts protein stability changes with precision and efficiency for mutation analysis and design.
CAR-Toner
CAR-Toner is an AI tool for rapid prediction of CAR-T tonic signaling by calculating Positively Charged Patch (PCP) scores.
RhoDesign RNA Inverse Folding
Generates RNA sequences with precise structural fidelity and functional diversity for targeted applications
StrucTFactor
StrucTFactor leverages 3D protein structures for precise transcription factor prediction, outperforming existing methods.
SaProt
SaProt integrates sequence and structure information through a structure-aware vocabulary to predict protein properties accurately.
ProGen2
Create protein variants using nothing but the amino acid sequence.
FlowDock
FlowDock predicts protein-ligand structures and binding affinities using geometric flow matching, enabling multi-ligand docking and fast virtual drug screening.
SpatialPPIv2 Protein Interaction Prediction
Predict protein-protein interaction probability from paired structures or sequences.
AlphaBind Antibody-Antigen Affinity Prediction
Rank antibody candidates with pretrained AlphaBind, optionally fine-tuned on target-specific measurements.
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.
Efficient Evolution
A protein language model-based tool for efficient, task-agnostic design of high-functionality protein variants.
Humatch
A CNN-based tool for rapid, gene-specific humanization and classification of antibody heavy and light chains.
DeepImmuno Immunogenicity Prediction
DeepImmuno is a CNN-based model for peptide immunogenicity prediction with state-of-the-art accuracy across viral and cancer datasets.
BioPhi
AI-driven antibody humanization + humanness scoring from natural repertoire data.
DR-BERT
Efficiently annotate disordered protein regions with a compact language model.
NARDINI+ GIN IDR Grammar Analysis
Analyze IDR molecular grammar features and GIN clusters from human IDs or custom IDR sequences.
ProSST Mutation Effect Prediction
ProSST predicts protein mutation effects and functions by integrating sequence and structural data via quantized tokens and disentangled attention.
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.
Kluster
Protein structure clustering and visualization tool using TM-align/US-align structural alignment and dimensionality reduction techniques (UMAP, t-SNE, PCA).
AlphaFind
Fast structure similarity search across AlphaFold DB.
Boltz-1 (AlphaFold3)
An open-source version of AlphaFold3 developed by an MIT lab.
ABACUS-R Sequence Design
Use ABACUS-R to design protein sequences for a given backbone structure using an encoder-decoder model.
NeuroFold
Optimize enzyme thermostability, pH stability, solubility, and reaction rate with high accuracy.
PubChem Similarity Search
Find structurally similar compounds in PubChem from SMILES, SDF, or CCD queries.
SuperMetal
Predict zinc-binding sites from an uploaded protein structure.
SuperWater
Predict protein surface hydration waters from uploaded PDB or mmCIF structures.
ipSAE
Calculate interface confidence metrics from a structure and PAE matrix.
Random RNA Sequence Generator
Generate customizable RNA sequences in FASTA format.
SMILES to MOL2
Generate bulk 3D MOL2 structures from SMILES.
SMILES to InChI
Convert bulk SMILES to standard InChI and InChIKey.
Aliphatic Index
Compare the aliphatic index of protein sequences.
Reverse Complement
Convert DNA and RNA strands from text, FASTA, or FASTQ.
Molecular Descriptors
Calculate common molecular properties for small molecules.
SASA Calculator
Measure protein surface exposure by structure, chain, and residue.
Radius of Gyration Calculator
Measure protein compactness for a structure or selected chains.
RNAalifold | ViennaRNA
Predict a consensus RNA secondary structure and free energy from a prealigned RNA multiple-sequence alignment.
RNAcofold | ViennaRNA
Predict the minimum-free-energy structure of two interacting RNA strands.
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.
RNALfold | ViennaRNA
Identify locally stable RNA secondary structures within a selected window.
RNAplex | ViennaRNA
Scan for favorable RNA-RNA interaction sites and duplex energies.
RNAplfold | ViennaRNA
Estimate local RNA accessibility and base-pair probabilities along a sequence.
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.
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