- Boltz-2
Accurate in silico screening for early-stage drug discovery
- BoltzGen
Design proteins and peptides to bind biomolecular targets
- DiffDock
Protein-ligand docking with diffusion models and confidence-ranked poses
- DrugFlow
Generate candidate ligands from a protein target and reference ligand using flow matching
- Sequence Mutator
Apply point mutations such as T315I to a protein sequence, checking each wild-type residue
- Antibody Numbering & Humanization
Number antibody, nanobody and TCR variable domains (IMGT, Kabat, Chothia), mark CDRs and assign the nearest human germline
- Binding ΔΔG
Rank antibody variants by predicted change in binding free energy on an antibody-antigen complex
- Stability ΔΔG Predictor
Rank point variants of a protein by predicted change in folding stability, or scan residues to alanine
- MPNN Sequence Design
Design amino-acid sequences for a fixed protein backbone with ProteinMPNN, LigandMPNN or SolubleMPNN
- RFdiffusion3
Generate all-atom protein backbones under motif, ligand, binder and symmetry constraints
- RFdiffusion3NA
Design protein, RNA and DNA backbones, and protein-nucleic-acid complexes, under motif, ligand and symmetry constraints
- RoseTTAFold3
Predict the structure of protein, DNA, RNA and ligand complexes with all-atom RoseTTAFold3 and an independent confidence score
- RFOptimization
Improve a protein binder design by cycling RoseTTAFold3 or Boltz-2 prediction with LigandMPNN redesign
- ESMFold2
Predict protein, DNA, RNA, and ligand complex structures with evolutionary scale modeling
- Evo 2
Genome modeling and design across all domains of life with the Evo 2 DNA language model
- AutoDock Vina
High performance molecular docking and virtual screening for drug discovery
- Binding-Site Detector
Find ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflows
- Lacuna
Find cryptic pockets that open across a normal-mode conformational ensemble and rank their druggability
- Docking Protocol Validator
Redock co-crystallized ligands and score pose RMSD and enrichment to validate a docking setup before screening
- Protein Preparer
PDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvation
- Protein / Antibody Developability Screen
Screen protein and antibody chains for pI, charge, GRAVY, instability, and sequence liability motifs
- OpenDDE
Predict protein, nucleic acid, and small-molecule complex structures with OpenDDE
- OpenMM MD
Prepare, solvate, and equilibrate proteins, small molecules, or membrane systems with OpenMM molecular dynamics
- MD Trajectory Analyzer
Compute RMSD, Rg, RMSF, ligand H-bond occupancy, and representative frames from OpenMM trajectories
- RFAntibody
Antibody and TCR design with RFdiffusion, ProteinMPNN, and RF2 (stages or full pipeline)
- FreeBindCraft
Design miniprotein and peptide binders against a target structure using open-source scoring
- GNINA
Protein–ligand docking and pose rescoring with convolutional neural network scoring functions
- Interaction Profiler
Enumerate hydrogen bonds, hydrophobics, salt bridges, and π-stacking in docked complexes
- Protein Structure Ensemble Comparator
Compare predicted or designed protein structures by TM-score and RMSD, cluster them, and pick one representative per fold
- Structure QC Report
Grade protein model geometry: Ramachandran and rotamer outliers, atomic clashes, cis-peptides, C-beta deviation and ligand bond geometry
- MM-GBSA Rescoring
End-point implicit-solvent MM-GBSA rescoring of docked poses or protein–ligand complexes
- Relative Binding Free Energy
Alchemical relative binding ΔΔG across ligand perturbation networks, absolute hydration ΔG, and REST2 replica-exchange sampling of protein–ligand complexes
- SurfDock
Surface-informed diffusion docking with a reference-ligand pocket and screen-model rescoring
- SURFMAP
2D projections of protein surface features from PDB structures or SURFMAP matrix files
- Thompson Sampling
Active-learning virtual screening of un-enumerated combinatorial libraries via Thompson Sampling
