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

Tab Khan, PhD

Chief Executive Officer (CEO)

Henk-Jan Joosten, PhD

Chief Commercial Officer (CCO) and Founder

Tom van den Bergh, PhD

Head of Protein Data & 3DM

Bas Vroling, PhD

Head of Machine Learning

Remko K.P. Kuipers, PhD

Senior software developer

Sergio Maduro, BSc

Software Developer

Stephan Heijl, BSc

Senior Data Scientist

Julian Koornneef

Front-end Developer

Hidde Bleeker, MSc

Bioinformatician

Jeanine Boot, MSc

Bioinformatician

Maarten Wijnhoven

System Administrator

Jochem Evers, MSc

Bioinformatician

Bastiaan Brier, BSc

Junior Data Scientist

Bram Utberg, BSc

Junior Data Scientist

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)

Our Network

Associates & data suppliers

We work with top-notch associates and suppliers dedicated to providing the best service

Collaborators

Partners & projects

We are involved in multiple EU projects aimed at driving scientific discovery forward

Virus-X

Viral metagenomics for innovation value

MicroB3

Biodiversity, Bioinformatics, Biotechnology… Innovation from the sea

CarbaZymes

Sustainable industrial processes based on a C-C bond-forming enzyme platform

Bridges

Breast Cancer Risk after Diagnostic Gene Sequencing

SuSy

Sucrose Synthase as Effective Mediator of Glycosylation

RadicalZ

The RADICALZ project unleashes the potential of enzymes for more sustainable consumer products

BIOOX

Developing a validated technology platform for the application of oxygen dependent enzymes in synthesis and transformation of alcohols

Kyrobio

Developing biocatalysts for industrial chiral chemicals

Neuromics

Integrated European Project on Omics Research of Rare Neuromuscular and Neurodegenerative Diseases

Newprot

Interactive protein engineering portal with validated software and database facilities

EFRO project

Detecting more rare diseases through analysis in three dimensions

The European Regional Development Fund (EFRO) and the province of Gelderland are financially supporting the project ‘Diagnostics-in-3D’ with more than half a million euros. The aim of the project is to improve diagnostics of patients with rare diseases through a combination of artificial intelligence, smart computing power and genetics. For this project Radboudumc, together with the companies Bio-Prodict and Vartion from the Nijmegen region will join forces.

Bio-Prodict has automated the prediction of the effect of missense mutations on proteins with the AI-based Helix platform. By using anonymous patient data and AI from Radboudumc and innovative computing infrastructure provided by Vartion, major steps can be taken in predicting the effect of mutations on the 3D structure of a protein, and thus on its function. For this, the representation of the 3D protein data, the deep learning architecture to be used and the computing power will be optimized. In the “Diagnostics-in-3D “project, Bio-Prodict, Vartion and Radboudumc aim to automate and accelerate diagnostics for rare diseases. In doing so, they will mainly focus on the rare diseases that cause intellectual disabilities, a subject in which Radboudumc in Nijmegen has already built up a great deal of expertise.

Want to join the team?

Premium tools to boost your research

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.

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