Virtually limitless protein engineering

Protabit combines state of the art computational tools for protein design and modeling with experimental methods for high throughput expression and screening in an iterative process to rapidly yield new and improved proteins for industrial, agricultural, and therapeutic applications.  The Triad software platform can utilize a variety of structural inputs; designs typically start with X-ray crystal structures, but NMR ensembles or homology models can also be employed. Data from multiple sequence alignments can also be used to guide the design. Triad’s ability to incorporate experimental assay data directly into the design process provides a uniquely powerful capability for rapid optimization of any protein property that can be measured. Other features include multi-state design, which can be applied to design multiple conformational or chemical states or used with explicit negative design to suggest sequences with altered structural, binding, or catalytic specificity.

Triad’s CPD tools can also serve as a complement to evolutionary engineering strategies. These include the design of focused combinatorial libraries as well as tools to improve the efficiency of directed evolution or recombination experiments.  Protein variants obtained with CPD, such as the de novo design of enzymatic activity, can be further optimized using in vitro evolution techniques.

Uses a variety of inputs

  • X-ray crystal structures
  • NMR ensembles
  • Homology models
  • Multiple sequence alignments
  • Assay data

State of the art computational tools

  • Structure-based design
  • Homology modeling, ligand modeling
  • Loop design/prediction
  • Assay data-based design
  • Multi-state design
  • Molecular dynamics

Complements evolutionary engineering strategies

  • Degenerate codon library design
  • Focused combinatorial libraries
  • Improve compatibility and diversity of recombination experiments
  • Create new activity than can be improved with directed evolution