ProPHECY™ - in silico Protein and Peptide Optimization

Protein and peptide optimization has wide applications in biotechnology and the structure-based design of biological drugs (biologics). By modifying and optimizing the amino acid sequence of a protein (e.g., an antibody) or a peptide, it is possible to build a model for its quantitative structure-activity relationships (QSAR). This knowledge can subsequently be used to control and modify reactivity and other properties. Our proprietary software package ProPHECY™ works similarly to that of the well-known QSAR methodology widely used in small molecule drug design.
in silico protein optimization services

QSAR optimization

The software package ProPHECY™ for QSAR-analysis of protein modifications is based on a novel algorithm, which uses experimentally determined protein parameters to predict amino acid replacements required for a rational design of new protein or peptide variants.
The algorithm is based on analyzing and discovering hidden information in large and complex data sets. From this analysis, detailed quantitative information on the influence of each amino acid replacement on the protein can be deduced. It may even perform simultaneous optimization of several parameters, among which is:

* biological or catalytic activity
* antigenicity (decrease or increase)
* enhancement of cell-penetrating capabilities
* protease resistance
* thermal stability
* solubility, etc.

Compared to conventional random screening, this approach dramatically reduces the effort, time, and costs required for protein and peptide optimization. Please
get in touch with us for a discussion of your project!
Bo Svensson,  Protein Oprimization, SARomics Biostructures
On the image: Bo Svensson, PhD, Director, in silico discovery

Examples of the use of ProPHECY™ can be found in the publications below:

  1. Pasupuleti, M. Walse, B., Svensson, B., Malmsten, M. and Schmidtchenet, A. (2008). Rational design of antimicrobial C3a analogues with enhanced effects against Staphylococci using an integrated structure and function-based approach. Biochemistry, 47, 9057-9070.
  2. Kassetty, G. Papareddy, P., Kalle, M., Rydengård, V., Walse, B., Svensson, B., Mörgelin, M., Malmsten, M. and Schmidtchen, A. (2011). The C-terminal sequence of several human serine proteases encodes host defense functions. J Innate Immun, 3, 471-482.

For other services please follow the respective links

protein X-ray crystallography services, gen-to-structure and off-the-shelf structures

X-ray crystallography

protein NMR spectroscopy services, fragment screening and ligand binding

Protein NMR spectroscopy

antibody and antibody-antigen complex strucure

Antibody and antibody-antigen complex structures

weak-affinity chromatography, fragment-based drug design

Weak-affinity chromatography

integrated lead discovery services

Integrated drug discovery

computational chemistry services, in silico screening and drug design

in silico lead discovery