What Bio-Prodict does

Bio-Prodict B.V. is a private Dutch bioinformatics software company founded in 2008 and headquartered in Nijmegen, Netherlands. It develops the 3DM platform — a set of protein super-family information systems that integrate sequence, structure, function, literature, and patent data into unified analytical environments used for protein engineering, molecular design, and DNA diagnostics. Its product portfolio includes 3DM Discovery for protein target identification, 3DM Engineering for AI-driven protein optimization, 3DM Antibodies (NPI) for therapeutic antibody development, and Helix Pathogenicity for missense variant pathogenicity prediction, with APIs available for pipeline integration and bespoke custom development engagements.

Underlying the products is a proprietary structure-based multiple sequence alignment database accumulated over more than 15 years, complemented by in-house machine learning models covering predictive analytics, optimization, and knowledge retrieval across multimodal data inputs. Bio-Prodict monetizes primarily through annual subscription licenses sold to commercial pharmaceutical and biotechnology customers (quote-based pricing) alongside discounted academic licenses priced at €500/year, supplemented by custom development services. The customer base spans major pharmaceutical companies (Merck, Roche, Pfizer, Novartis, J&J, Sanofi, GSK), industrial biotechnology firms (DSM, Novozymes, DuPont, BASF, Henkel, IFF/Genencor, BRAIN Biotech, METGEN), clinical and academic partners (LUMC, Radboudumc, RWTH Aachen, Greifswald University), and newer biotech entrants (BioCopy, Keros Therapeutics, Aminoverse, Ipsen). The company operates with regional sales coverage across Europe and the United States, is ISO 27001 certified, and participates in multiple EU-funded research collaborations that expand its scientific footprint and data assets.

Name

Bio-Prodict

Legal name

Bio-Prodict B.V.

Website

https://bio-prodict.com

Company type

Private

Founded year

2008

Operating status

Operating

Headcount range

11–50 employees

Short description

Bio-Prodict is a Dutch bioinformatics software company founded in 2008 that provides AI-driven 3DM protein information systems for target discovery, protein engineering, antibody development, and variant pathogenicity prediction, serving pharmaceutical, biotechnology, and academic customers globally.

Ownership category

akta.pro rank

Product category

Bioinformatics Software

NAICS

Software Publishers (51321), Research and Development in Biotechnology (except Nanobiotechnology) (541714), Scientific Research and Development Services (5417)

akta.pro primary industry

Protein Engineering & Directed Evolution Platforms (enzyme/therapeutic protein optimization) (HLAAAIAC)

akta.pro secondary industries

Antibody Discovery & Engineering Platforms (display tech, bispecifics, Fc engineering) (HLAAAIAB), AI/ML Platforms for Drug Discovery & Experiment Optimization (HLAGAJAO), AI/ML-Enabled Biologic Discovery Platforms (computational design, in silico screening) (HLAAAIAE), Target Identification & Validation Platforms (omics-driven, chemoproteomics, genetic validation) (HLAAAIAI)

Keywords

• Protein engineering software
• Bioinformatics platform
• Variant pathogenicity prediction
• Antibody development tools
• Sequence-structure analysis

Headquarters

HQ city

Nijmegen

HQ country

Netherlands

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Marketing or Sales, Operations, Infrastructure

Revenue model

1. Software Licenses (Commercial): Annual subscription licenses for 3DM Systems sold to commercial organizations. Pricing based on protein family systems and access levels. Supports enterprise-wide deployment with API integration.
2. Academic Licenses: Discounted annual licenses for academic institutions at €500/year per license. Provides full access to 3DM protein family information systems tailored to research needs.
3. Custom Development Services: Bespoke 3DM solutions created in collaboration with clients for specific research needs. Custom development engagement for organizations requiring tailored tools.

Pricing tiers

Go-to-market motion3 records

Distribution channels4 records

Marketing channels4 records

Core offering

Bio-Prodict develops and licenses the 3DM protein family information systems — software platforms that integrate protein sequence, 3D structure, scientific literature and patent data into unified views of protein super-families — together with Helix Pathogenicity for AI-driven missense variant pathogenicity prediction. The portfolio covers protein target discovery (3DM Discovery), protein engineering and optimization (3DM Engineering), therapeutic antibody development (3DM Antibodies/NPI), and genetic variant interpretation (Helix Pathogenicity), sold as annual subscriptions to pharmaceutical, biotech and academic customers, supplemented by bespoke custom development services.

Product overview

Bio-Prodict offers a suite of protein R&D software products centered on the 3DM platform, a protein super-family information system that integrates sequence, structure, literature, and patent data. The product portfolio includes 3DM Discovery for target identification in drug development, 3DM Engineering for protein optimization through AI-driven variant prediction, 3DM Antibodies for therapeutic antibody development, and Helix Pathogenicity for missense variant pathogenicity prediction. Custom Development services are available for bespoke solutions tailored to specific research requirements.

Differentiator

Problem solved

Functional benefit

Brands

• 3DM Discovery: Protein target discovery and drug design platform providing sequence-structure-function relationship insights for innovative drug development.
• 3DM Engineering
• 3DM Antibodies
• Helix Pathogenicity

Products and services

• 3DM Discovery Protein target discovery platform that accelerates drug and therapeutic development by screening proteins quickly for target discovery and drug design through integrated sequence-structure-function relationship insights.
• 3DM Engineering Protein engineering platform that identifies promising starter proteins and strategically introduces functional diversity through AI-driven variant prediction across the in-silico engineering pipeline, with integrated IP navigation for freedom-to-operate analysis.
• 3DM Antibodies (NPI) Antibody development platform that accelerates antibody R&D by providing sequence-property insights, annotation pipelines, developability filtering, CDR/germline/patent annotations, and large-scale sequence clustering for lead selection and key residue identification.
• Helix Pathogenicity AI-driven platform for predicting missense variant pathogenicity with high accuracy and confidence estimates, combining machine learning with sequence, structure and literature data, supported by interactive variant reports and API integration for clinical and biomedical research pipelines.
• Custom Development Services Bespoke 3DM solutions created in collaboration with clients when off-the-shelf software does not meet specific research needs, delivered as a professional-services engagement.

Quantifiable outcome

• Substantially saving time and efforts to identify desired improved enzyme variants
• +4 more outcomes

Named customers6 records

Segments5 records

Ideal customer profiles5 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

AI capability6 records

Feature6 records

Partnerships

Twelve partnerships are on record, tiered core and minor.

• RadboudumccoreStrategic or Co-development PartnerCollaboration in the EFRO-funded 'Diagnostics-in-3D' project focused on improving diagnostics for rare diseases through AI-based Helix platform, combining patient data, deep learning architecture, and computing infrastructure. Project aims to automate and accelerate diagnostics for rare diseases causing intellectual disabilities.
• VartioncoreStrategic or Co-development PartnerPartner in the 'Diagnostics-in-3D' project providing innovative computing infrastructure for protein 3D structure and mutation effect predictions.
• ScienceExchangeminorOthersAssociate and data supplier providing research services platform.
• Tungsten NetworkminorOthersAssociate providing electronic invoice network services.
• Scientist.comminorOthersAssociate providing research services marketplace.
• Lens.orgminorOthersData supplier providing patent and scholarly citations database.
• RWTH Aachen UniversitycoreStrategic or Co-development PartnerAcademic collaborator in enzyme engineering and protein research. Major German technical university with active research in biotechnology.
• acib (Austrian Centre of Industrial Biotechnology)coreStrategic or Co-development PartnerEU research partner in biocatalysis and industrial biotechnology.
• BRAIN Biotech AGcoreStrategic or Co-development PartnerActive collaboration in enzyme engineering. BRAIN Biotech provides protein engineering services and uses Bio-Prodict's 3DM systems for hotspot selection and library design.
• BioCopy AGcoreStrategic or Co-development PartnerLong-standing collaboration in antibody engineering with impressive testimonials about 3DM system capabilities. BioCopy uses 3DM for protein engineering and AI-driven mutation prediction.
• LUMC (Leiden University Medical Center)coreStrategic or Co-development PartnerCollaboration in clinical genetics research. LUMC provides validation and endorsement of Helix Pathogenicity for clinical variant interpretation.
• METGEN OycoreStrategic or Co-development PartnerEnzyme manufacturing company that used 3DM to develop a novel xylose isomerase that was commercialized. Provides case study validation of technology effectiveness.

Scale indicators2 records

Recent moves6 records

Expansion highlights6 records

Direct peers

• Benchling: Benchling is a cloud R&D platform for biotech that captures sequence, structure and registration data for protein and antibody workflows — comparable to Bio-Prodict's integrated protein family information systems.
• AbCellera Biologics: AbCellera runs an AI/ML-powered antibody discovery engine for therapeutic antibodies, directly comparable to 3DM Antibodies for sequence-property insight, developability filtering and germline/CDR annotations.
• Cradle Bio: Cradle provides AI-driven protein engineering models and a design-make-test platform for industrial biotech and pharma, overlapping head-on with 3DM Engineering's AI-driven variant prediction.
• Schrödinger: Schrödinger operates a physics-based computational platform for molecular design, protein structure analysis and predictive chemistry, directly overlapping with Bio-Prodict's 3DM protein family systems for structure-based engineering and variant prediction.
• Absci: Absci offers generative AI antibody design and an integrated protein engineering wet/dry stack that competes directly with 3DM Antibodies and 3DM Engineering for pharma and biotech customers.
• Dotmatics: Dotmatics delivers scientific R&D informatics (including biologics registration and analysis tools) used by pharma and biotech R&D teams, intersecting with 3DM's protein family and antibody annotation use cases.

Broad incumbents

• Generate Biomedicines: Generate Biomedicines builds proprietary generative AI foundation models for protein therapeutics; while broader in scope (internal therapeutic pipeline) it shares the AI-driven protein design base with 3DM Engineering.
• Insitro: Insitro operates an AI-driven drug discovery platform combining ML with high-throughput biology; a broad incumbent whose ML+biology thesis overlaps with Bio-Prodict's protein informatics and variant prediction positioning.

Emerging players

• DNAnexus: DNAnexus provides a cloud genomics and clinical data platform used by clinical genetics labs and pharma; overlaps with Helix Pathogenicity for variant interpretation workflows and precision medicine.
• ProteinQure: ProteinQure applies AI/ML to the computational design of therapeutic proteins, an emerging competitor whose protein design capabilities overlap with 3DM Engineering and 3DM Discovery.

Market position

Strengths5 records

Weaknesses4 records

Competitive moat5 records

Key risks5 records

Key highlights7 records

Customer concentration

• Xx.com/bioprodict

Compliance1 record

Revenue estimate

Valuation estimate

Number of profiles

Profiles4 records

Funding overview

Funding rounds

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about Bio-Prodict