Levitate Bio offers two fully managed protein modeling and design products: Levitate Bench, which is an easy to use browser based GUI tool, and Levitate Engine which is a powerful and flexible API system for building sophisticated protein modeling and design pipelines.
Levitate Bench
Cloud-run Rosetta & Artificial Intelligence protocols accessible via an easy-to-use web-based software
- No Computational Biology experience needed
- No Installation required
- Runs in a web browser
- Full-time professional support
- Unlimited users
- Flexible subscription tiers based on compute usage
Levitate Bench Tools
| Category | Protocol | Function |
|---|---|---|
| Protein Structure Prediction | Single Chain Homology Modeling (HM) | Monomer |
| HM for Variable Region (RosettaAb) | Antibody Variable Region | |
| HM for Variable Region (High Res) | Antibody Variable Region | |
| HM for Full Length Antibody (High Res) | Antibody Full Length | |
| AlphaFold2 | AI Folding, Monomer | |
| AlphaFold2 Multimer | AI Folding, Multimer | |
| OpenFold | AI Folding, Monomer | |
| ESMFold | AI Folding, Monomer, (fast) | |
| Protein Structure Optimization | Relax | Find More Favorable Conformations |
| Prepare | Constrained Relax | |
| Loop Remodel | Find More Favorable Loops | |
| Minimize | Find Closest Favorable Conformations | |
| Repack | Optimize Side Chains | |
| Protein Design/Mutation Sampling | Relax Design (region redesign with Relax) | Suggest Sets of Mutations |
| Flex Design (region redesign with local flex) | Suggest Sets of Mutations | |
| Fixed Backbone Design (region redesign) | Suggest Conservative Mutations | |
| Single Point Mutation Scan (Cartesian DDG) | Scan Point Mutations | |
| Single Point Mutation Scan (ThermoMPNN) | Scan Point Mutations | |
| Sequence Analysis | Immunogenicity Scan | Predict MHCII Display |
Levitate Engine
Cloud-Run Rosetta & Artificial Intelligence protocols accessible via APIs. 4 Different API packages are provided based on use case. The packages are focused on Rosetta modeling methods, AI/ML modeling methods, Analysis and liability prediction, and De Novo design.
Rosetta Package
The Rosetta Package has physical-based tools from the Rosetta Modeling Suite, including the most used tools with optional flags for flexible modeling of broad protein types and for diverse types of modeling goals.
This package requires a Rosetta license from the University of Washington
| Category | Protocol | Function |
|---|---|---|
| Protein Structure Prediction | Single Chain Homology Modeling (HM) | Monomer |
| HM for Variable Region (High Res) | Antibody Variable Region | |
| HM for Full Length Antibody (High Res) | Antibody Full Length | |
| HM with Disulfide Constraint | Monomer w/ Disulfide | |
| HM Accessory Tools (Fragments, BLAST, PatentBLAST) | Extra Tools | |
| Protein Structure Optimization | Relax | Find More Favorable Conformations |
| Loop Remodel | Find More Favorable Loops | |
| Protein Design/Mutation Sampling | Relax Design (region redesign with Relax) | Suggest Sets of Mutations |
| Single Point Mutation Scan (Cartesian DDG) | Scan Point Mutations | |
| Disulfidizer (Creates each favorable disulfide) | Suggest Disulfide Positions | |
| Epitope Redesign (Reduce MHC II display) | Select Less Immunogenic Mutations | |
| Structure Analysis | RosettaHoles (Check core for gaps) | Show Holes in Core |
| Interface Analysis (Energy, SASA, and more) | Analyze Protein-Protein Interface |
Artificial Intelligence Package
The Artificial Intelligence Packages provide the newest protocols for structure prediction and Rosetta community’s recent cutting-edge sequence design and structure generation tools.
| Folding | Sequence | Structure | Protocol | Function |
|---|---|---|---|---|
| ✔️ | AlphaFold2 | Monomer AI | ||
| ✔️ | AlphaFold2 Multimer | Monomer AI | ||
| ✔️ | Openfold for Single Chain | Monomer AI | ||
| ✔️ | ESMFold for Single Chain | Monomer AI Fast | ||
| ✔️ | Molprobity | ID Structure Problems | ||
| ✔️ | Single Point Mutation Scan (ThermoMPNN) | Scan Point Mutations | ||
| ✔️ | ProteinMPNN (sequence generation) | Generate sequences from structures | ||
| ✔️ | LigandMPNN (sequence generation) | Generate sequences from structures including ligands | ||
| ✔️ | RosettaFold Diffusion (RFDiffusion, structures) | Generate de novo structures | ||
| ✔️ | RosettaFold All Atom (RFAA, structures) | Generate de novo structures including ligands | ||
| ✔️ | Radius of Gyration (for RFDiffusion filtering) | Protein Compactness |
Analysis Package
The Analysis Package has machine learning-based predictions for developability
| Category | Protocol | Function |
|---|---|---|
| Structure/Sequence Analysis | N-linked Glycosylation Prediction | Predict Glycosylation |
| PTM prediction (deamidase, isomerization, oxidation, etc) | Predict Degradation | |
| Immunogenicity Scan (MHC II affinity) | Predict Immunogenicity | |
| Solubility/Aggregation Prediction | Predict Solubility |
De Novo Package
The De Novo Package has a full set of tools that facilitate end to end de novo protein design, featuring the Rosetta community’s AI protocols. The Lite version excludes tools that require a Rosetta license from the University of Washington.
| Category | Protocol | Function | Lite Version |
|---|---|---|---|
| Protein Structure Prediction | AI Folding | Monomer/Multimer Structure Prediction | ✔️ |
| Structure Optimization | Relax | Find More Favorable Conformations | |
| Loop Remodel | Find more favorable loops | ||
| De Novo Design | ProteinMPNN (sequence generation) | Generate Sequence from structure | ✔️ |
| RosettaFold Diffusion (RFDiffusion) | Generate de novo structures | ✔️ | |
| De Novo Design | Molprobity (for AIFolding structure analysis | Identify Structure Problems | ✔️ |
| Radius of Gyration (for RFDiffusion filtering) | Generate de novo structures | ✔️ | |
| Interface Analysis (Energy, SASA, and more) | Analyze Protein-Protein interfaces | ||
| Solubility/Aggregation Prediction | Predict solubility | ✔️ |