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De Novo Miniprotein Design

Miniproteins are a class of small, highly stable proteins (~75-100 AAs), shown to have good binding (nanomolar) and specificity against a diverse set of targets.

De novo miniprotein design involves creating new protein binders from scratch to target specific molecules or surfaces.

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Antibody CDR Design

These protocols focus on engineering the variable regions of antibodies to improve binding affinity, specificity, and developability. Inverse folding methods such as IgDesign from Absci and AntiFold from OPIG start from structures of AbAg complexes and redesign complementarity-determining regions for improved binding against the target. This process can be understood as more of an optimization task. Conversely, RFantibody represents the de novo design approach. Starting from an antigen structure, RFantibody designs structures and sequences for CDRs from scratch. One note here is that RFantibody does require a framework structure as input, whose CDRs fill be filled with de novo designs generated from the protocol.

Both of these approaches are applicable to both scFvs and VHHs.

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Motif/Interface Scaffolding

Interface scaffolding involves designing protein scaffolds to present functional motifs or binding interfaces in specific orientations.

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Binder Optimization

Optimizing existing protein binders involves improving their binding affinity, specificity, and stability through targeted mutations and structural modifications.

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Improving Stability

Improving protein stability involves modifying sequences and structures to enhance thermal stability, resistance to aggregation, and overall robustness. We’ve found stabilizing mutations recommended by ThermoMPNN to correlate well with experimental results.

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Solubilizing membrane proteins

Engineering a target membrane protein to be soluble in solution without detergent, while keeping as much of the structural features in tact as possible.