Bioinformatics & Analytics
In addition to routine data analyses like heatmaps or boxplots, JPT's bioinformatic department also offers complex, statistical data evaluations and visual analytics. In this way, they can help you to create scientifically high-quality figures for publications from large data sets.
When designing peptide libraries based on the customer's protein sequences, various cutting-edge analysis and prediction tools are used to optimally implement customer requirements. Please feel free to contact us with your requests.
Peptide Library Design
- Overlapping Peptide Library
- Neo-Epitope Library
- Cyclization Library
- Antigen Discovery Pool
- Matrix Pools
- ULTRA Library & Pools
- Selected Epitope Pool
- Truncation Library
- Alanine Scanning Library
- Random Library
- Scrambled Library
JPT has developed an algorithm called PepSelector that performs an evaluation of manufacturability and feasibility ranking of peptide sequences. The PepSelector applies its algoritm based on literature and experimental data from several tens of thousands of synthetic peptides. It considers amino acid coupling efficiencies,Examples for peptide libraries are Positional Scanning Library side reactions during the synthesis process, peptide stability, peptide solubility, correlation of physicochemical properties and secondary structure propensities with manufacturability, the ability to be purified and reconstituted in aqueous buffers.
The goal is to predict potential difficulties, and rank peptides to their overall manufacturability. Although the PepSelector does not provide a go/no go differentiation of peptides for production it enables a selection of peptides with higher success probabilities against peptides with an increased risk to fail. As a consequence it is an efficient tool to help ranking peptides for the fast, efficient and successful synthesis in turnaround sensitive studies such as neo-epitope based individualized immunotherapies. In addition to manufacturability evaluation the program may provide access to potential optimization of sequences that can be performed by simple shortening, extension or frame-shifting the peptide sequences along their parental antigen sequences.
Peptide solubility is a crucial factor in nearly all peptide based projects. These include in vitro assay robustness and in vivo bioavailability. In both cases, lack of complete solubility at the desired effective concentration will lead to decreased activity and/or false negative results. A prerequisite for effective solubility assessment and optimization is the availability of a fast and sensitive solubility assay.
Turbidimetric Solubility Assay (TSA) allows a rapid determination of solubility using only small peptide amounts. Depending on applications of the target peptides, different organic and inorganic solvents and solvent additives can be applied.
JPT has a long standing and focused expertise to assist biomedical screening and peptide lead optimization programs with its comprehensive bioinformatic and cheminformatic capabilities. Statistical evaluation as well as visualization and presentation of complex data are performed using state of the art tools. We offer this unique know-how and expertise as part of our services or in R&D collaborations.
- Detailed discussion of your project and definition of a suitable strategy based on scientific feasibility and experience
- Receive project proposal on how our bioinformatics and cheminformatic expertise can support your project
- Obtain detailed and comprehensive service reports
- Design of peptide content for high-density peptide microarrays and complex peptide libraries
- Design of peptide libraries based on biological pathways, literature data or complex database search strategies
- Generation of homology models and use of available structural information for peptide selection
- Support for optimization of hit and lead structures (affinity, physicochemical properties, ADME)
- Prediction and modeling of data
- Interpretation, management and integration of data
- Visualization and presentation of complex data sets
- Long-term track record in the discovery and development of peptides in drug discovery and diagnostic development
- State-of-the-art prediction, data interpretation and data mining algorithms and software paired with chemical and biological know-how
- Expertise available as a fee-for-service or in collaborative partnerships