Sodatana is your partner for bioinformatics outsourcing. We offer services in protein, peptide & RNA engineering, modeling and design; vaccine design; decision support, consulting and solutions in computational and molecular biology; mining & database integration of biological data; support for pre-clinical R&D and IP.

=> Protein engineering, peptide selection & RNA design

  • You have a gene/protein and want to alter certain properties such as glycosylation or solubility or need to identify fusions or variants with extended stability or better IP position? We are happy to help.
  • You have a protein or RNA and want to optimized the coding sequence and UTRs for specific tissues? We may have a solution for you.
  • You want to build your own mRNA platform? Go contact us, we have a database of design elements to help.

Most biotechnological developments require some sort of protein engineering. Be it generation of mutants with altered phys-chem properties or glycosylation, fragments for epitope mapping, or fusions for combining antigenic regions or functionalities. With long-standing experience in selecting peptides and protein regions, modelling, fusing and altering them, sodatana adapts to your needs towards the goals you define. Recently, due to the prominent success of mRNA encoded vaccines and therapeutics, we have also added proprietary methods such as tissue specific bicodon optimization and UTR selection to our technological portfolio.
Whatever the method, whether therapeutic protein, vaccine or delivered RNA, if the goal is to identify or optimize a molecule by biological rationale for improved pharmacological properties, production & quality requirements or patient benefit, we are apt to assist.
=> Immunoinformatics, vaccines, vaccine workflows and monoclonal antibodies
  • Need to choose optimal peptides or engineering of your antigens / fusion antigens towards immunogenic, production or IP optimization? This has been our core business for a long time. 
  • Need assistance in identifying the optimal candidate from your screen, strain coverage, patient HLA coverage or design population centroid and consensus antigens? We have probably done this before.
  • Do you think your project may benefit  from assistance converting your existing protein design to tissue optimized mRNA or want to build an entire mRNA platform? Go contact us, we may have what you need.
  • Need the construction of a computational reverse vaccinology pipeline or additional predictions/data to narrow down your list if candidate antigens? We can probably help.
  • Background and preferred strategies including IP vary immensely among vaccine developers, do not hesistate to challenge us, we adapt to your needs and perspectives!
In short, if it is related to vaccine design we can probably help. In the case of antibody humanization based on template selection and mutating key residues for maintaining heavy/light chain angle, our experience is limited but we will be happy to find a collaborative solution.

For an example how (reverse) vaccinology workflows can be supported by integrated knowledge flows, tools and visualisation, please consider the paper below. Very commonly far less extensive solutions and only selective improvements and data connections using bio- or immunoinformatical methods may be needed for individual projects, though.

Söllner J, Heinzel A, Summer G, Fechete R, Stipkovits L, Szathmary S, Mayer B. Concept and application of a computational vaccinology workflow. Immunome Res. 2010 Nov 3;6 Suppl 2:S7. doi: 10.1186/1745-7580-6-S2-S7. PubMed PMID: 21067549; PubMed Central PMCID: PMC2981879. Freely access paper at PubMed Central

=> Consulting, innovation support, literature reviews & reporting, identifying and avoiding IP conflicts
  • Need help identifying or avoiding conflicting IP? We offer IP background searches and can, where possible, suggest designs to reach freedom to operate.
  • Lacking time or resources to cover all bases in biomedical background analysis? We offer custom literature reviews of diverse biomolecular  areas including or excluding computational analysis.
  • Need translation what existing computational results actually mean? We offer consulting regarding the scope and utility of bioinformatical methods, including translation of results into biomedical decisions (considering e.g. the uncertainties associated with models / predictions). 
  • Appreciate another innovation oriented perspective on your biomedical product design or R&D? We include molecular biology and bioinformatics backgrounds interweaved, contributing to scientific processes / decision making.
  • Experienced in working with IP attorneys directly.

Practice has shown that particularly small entities such as start-ups can benefit from outsourcing some of the background searches, especially biomedial & patent literature reviews. For such purposes molecular biology and biomolecular know-how available at sodatana can be used to create custom reports for many areas of biomedical interest. Particularly where the background of genes, proteins and protein engineering, small-molecules, pathways or associations with diseases or IP relevant matter are concerned.

Bioinformatical analysis is usually neither the beginning nor the end.  So our starting point is usually to identify the status quo, optionally propose and discuss computational results and point out where practical certainties, uncertainties and unknowns of applied methods reside.

Also, frequently analysis leads to follow up questions where our biomolecular expertise can help in the scientific process, optionally also with follow-up questions to be answered computationally or experimentally. This, also in cycles, is often part of the innovation process.

The image shows an example extracted from a search in the field of endogenous and exogenous cannabinoids and other selected compounds found in medical cannabis, including THC, CBD and beta caryophyllene. It is a visualization of publicly accessible knowledge of compunds, their receptors and cannabinoid effects on these, as well as synergistic and antagonistic effects of receptors on cellular processes and their effects on health and disease. The goal was a more reaction network based, comprehensive understanding of cannabis effects to guide decision making.
=> Data Integration & knowledge mining
Do you have experimental data and want to connect them to public identifiers and datasets such as literature abstracts, genes, proteins, drugs or diseases and patents? We have done this before and may already have what you need.

Basically we can automate the process of interest or integrate the data you are interested in, into a custom database meeting your needs. We usually do not build pretty interfaces, but can can help by building or providing the backend or simply a report for expanding your knowledge based on what you already have.

People at sodatana have significant expertise in the integration particularly of heterogeneous public, biomedical data and entities such as genes, proteins, drugs, diseases and small molecules. We have repeatedly integrated sources such as PubMed abstracts, MeSH terms (controlled dictionaries), small-molecule targets, drug databases and the US patent full-text database etc., either by pre-existing links or conducting automated full-text keyword searches.

Let us discuss how sodatana can help develop your project


Biomedical Background

Johannes Söllner, PhD, is a molecular geneticist with longstanding experience in the pre-clinical commercial development of vaccines and diagnostics (protein subunits and peptides), protein and RNA engineering and innovation most commonly with an infectious disease focus as well as the repositioning of drugs using protein/drug/disease networks.

Technical expertise

Many years of experience in programming, data analysis & workflow automation, building of machine-learning models, integration of large heterogeneous datasets into relational databases, text mining, work with protein / drug networks and typical applications in bio-informatics and immuno-informatics such as sequence databases, B- and T-cell epitope prediction, working with large sequence sets, protein and genome annotation and protein homology modeling.

Tailored to your needs

Independent whether "just having an analysis run", early conceptualization of a workflow, practical issues in analysis, scaling of an analysis process or biomedical interpretation. We integrate technical, scientific and business perspectives and help your processes where needed. Whether technical setup, analysis, knowledge integration or communication of concepts to third parties  including IP attorneys, we help our clients strengthen their R&D, IP and market position.