A pioneering company with years of experience in bioinformatics
We are a private Dutch company founded in 2008, specialized in software design, structural biology, and protein analysis
Our Team
Experts in protein research for drug development and therapeutics
We create a dynamic, inclusive environment by integrating diverse backgrounds in biotech, bioinformatics, data science, and AI to drive innovation . Adhering to scientific methodology, we value competency, dedication, and openness, offering flexibility to our employees in return. Bio-Prodict is dedicated to fostering an inclusive and innovative atmosphere where every team member can thrive.
Executive
Publications
Scientific publications
Discover the scientific breakthroughs enabled by our products and company
- Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk. (Cancer Research)
- Breast cancer risks associated with missense variants in breast cancer susceptibility genes. (Genome Medicine)
- AmiP from hyperthermophilic Thermus parvatiensis prophage is a thermoactive and ultrathermostable peptidoglycan lytic amidase. (Protein science: a publication of the Protein Society)
- Pathogenic Variant Spectrum in Breast Cancer Risk Genes in Finnish Patients. (MDPI)
- Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk. (Nature Genetics)
- Genome-wide Association Study of Postpartum Depression Identifies a Novel Susceptibility Locus at 18q12.1. (medRxiv)
- Common Pitfalls and Novel Opportunities for Predicting Variant Pathogenicity. (Biochemistry & Physiology: Open Access)
- In-silico smart library design to engineer a xylose-tolerant hexokinase variant. (African Journal of Biotechnology)
- Fully automatized high-throughput enzyme library screening using a robotic platform. (Biotechnology and Bioengineering)
- Engineering the Amine Transaminase from Vibrio fluvialis towards Branched-Chain Substrates. (ChemCatChem)
- Bioinformatic analysis of fold-type III PLP-dependent enzymes discovers multimeric racemases. (Applied Microbiology and Biotechnology)
- Synthesis of (1R,3R)-1-amino-3-methylcyclohexane by an enzyme cascade reaction. (Tetrahedron)
- CorNet: Assigning function to networks of co-evolving residues by automated literature mining. (PLOS ONE)
- Complex phenotypes associated with STIM1 mutations in both coiled coil and EF-hand domains. (Neuromuscular Disorders)
- Two-enzyme hydrogen-borrowing amination of alcohols enabled by a cofactor switched alcohol dehydrogenase. (ChemCatChem)
- Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily. (nature.com)
- Switch in Cofactor Specificity of a Baeyer–Villiger Monooxygenase. (Wiley)
- A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications. (ScienceDirect)
- A quantitative indicator diagram for lytic polysaccharide monooxygenases reveals the role of aromatic surface residues in HjLPMO9A regioselectivity. (PLOS ONE)
- Complete switch of reaction specificity of an aldolase by directed evolution in vitro: Synthesis of generic aliphatic aldol products. (Wiley)
- Recessive variants of MuSK are associated with late onset CMS and predominant limb girdle weakness. (Am J Med Genet)
- Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase. (MDPI)
- Functional analysis of genetic variants in the high-risk breast cancer susceptibility gene PALB2. (Nature Communications)
- Mind the gap: preventing circularity in missense variant prediction. (bioRxiv)
- Going to extremes – a metagenomic journey into the dark matter of life. (FEMS Microbiology Letters)
- White paper: The Helix Pathogenicity Prediction Platform. (aRxiv)
- Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering. (Biotechnology Advances)
- The a-b-hydrolase fold 3DM database (ABHDB) as a tool for protein engineering (Chembiochem)
- Thermostabilization of an esterase by alignment-guided focussed directed evolution (PEDS)
- Natural Diversity to Guide Focused Directed Evolution (Chembiochem)
- Simulation on the structure of pig liver esterase. (J Mol Model)
- 3DM: systematic analysis of heterogeneous super-family data to discover protein functionalities. (Proteins)
- Novel tools for extraction and validation of disease related mutations applied to Fabry disease. (Human Mutation) (1 editorial note)
- Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. (BMC Bioinformatics)
- Beyond directed evolution–semi-rational protein engineering and design. (Curr Opin Biotechnol)
- Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst. (Curr Opin Chem Biol)
- Protein design in metabolic engineering and synthetic biology. (Curr Opin Biotechnol)
- Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis (PEDS)
- Integrating GPCR-specific information with full text articles. (BMC bioinformatics)
- NucleaRDB:information system for nuclear receptors. (NAR)
- 3DM Protein Engineering Super-Family systems applied to the P450 family. (Proceedings of the 17th International Conference on Cytochrome P450)
- Molecular characterization of the C-methyltransferase NovO of Streptomyces spheroides, a valuable enzyme for performing Friedel-Crafts alkylation. (J. Mol. Catal. B: Enzym)
- Drug design for ever, from hype to hope (J Comput Aided Mol Des)
- Recent advances in rational approaches for enzyme engineering (CSBJ)
- Strategies for discovery and improvement of enzyme function: state of the art and opportunities. (Microb Biotechnol)
- Hydrolases as Catalysts for Green Chemistry and Industrial Applications-Esterase, Lipase and Phytase. (PhD thesis)
- Use of ‘small but smart’ libraries to enhance the enantioselectivity of an esterase from Bacillus stearothermophilus towards tetrahydrofuran-3-yl acetate. (FEBS J)
- Mapping the acceptor site of sucrose phosphorylase from Bifidobacterium adolescentis by alanine scanning. (Elsevier)
- Consensus engineering of sucrose phosphorylase: the outcome reflects the sequence input. (Elsevier)
- Site-Directed Mutagenesis as Applied to Biocatalysts. (springer)
- Protein Engineering as a Tool for the Development of Novel Bioproduction Systems. (CDN)
- Engineering proteins for thermostability through rigidifying flexible sites (RFS). (Biotechnol Adv)
- GPCRDB: an information system for G protein-coupled receptors. (NAR)
- The NewProt Self-Service Portal for Protein Engineering (SWAT4LS)
- Simultaneous use of in silico design and a correlated mutation network as a tool to efficiently guide enzyme engineering. (ChemBioChem)
- Bioinformatic analysis of a PLP-dependent enzyme superfamily suitable for biocatalytic applications. (Biotechnology Advances)
- A structural classification of carbohydrate epimerases: From mechanistic insights to practical applications. (Biotechnology Advances)
- Alteration of the Donor/Acceptor Spectrum of the (S)-Amine Transaminase from Vibrio fluvialis. (International Journal of Molecular Sciences)
- Two Subtle Amino Acid Changes in a Transaminase Substantially Enhance or Invert Enantiopreference in Cascade Syntheses. (ChemBioChem)
- Synthesis of (1R,3R)-1-amino-3-methylcyclohexane by an enzyme cascade reaction. (Tetrahedron)
- FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. (PLOS Computational Biology)
- A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain (JMB)
- The Nuclear Receptor Ligand-Binding Domain: A Family-Based Structure Analyses. (Current Med. Chem.)
- Method of generating a protein database. (patent WO/2008/035970)
- 3DM: From Data to Medicine. (PhD thesis)
- Oxaloacetate Hydrolase, the C-C Bond Lyase of Oxalate Secreting Fungi. (JBC)
- Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method. (Proteins)
- Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member. (JMB)
- Correlated mutation analysis on super-family alignments reveal functionally important residues. (Proteins)
- Identification of a gatekeeper residue that prevents dehydrogenases to act as oxidases. (JBC)
Collaborators
Partners & projects
We are involved in multiple EU projects aimed at driving scientific discovery forward
Want to join the team?
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We are always looking for new talent. If you want to know more about our internships for students in bioinformatics and computer science, send an email to internship@bio-prodict.com.
If you’re curious about opportunities beyond internships, such as full-time positions or freelance collaborations, don’t hesitate to reach out: jobs@bio-prodict.com.
