Molecular Discovery
Molecular Discovery Ltd. provides proprietary GRID-based computational chemistry and cheminformatics software — including MetaSite, Mass-MetaSite, GRID, FLAP, MoKa, VolSurf+, and BioGPS — to pharmaceutical, biotech, academic, and forensic customers for drug design, ADME prediction, metabolite identification, and binding-site analysis.
- Company typePrivate
- Founded1984
- HeadquartersBorehamwood, United Kingdom
- Headcount1–10
- GTM typeB2B
- OfferingSoftware
What Molecular Discovery does
Molecular Discovery Ltd. is a privately held UK-based computational chemistry and cheminformatics software company founded in 1984 and headquartered in Borehamwood, with its primary R&D and software development operations based in Perugia, Italy, and a training site in Sant Cugat del Vallès, Barcelona. The company's product portfolio is built on a single proprietary foundation, the GRID forcefield for Molecular Interaction Fields (MIFs), originally created by Peter Goodford and used in the discovery of Glaxo's anti-flu drug Relenza. Around this core engine, Molecular Discovery ships a suite of more than 15 software products spanning structure-based drug design (GRID, FLAP, SHOP), metabolism prediction (MetaSite/MetaSite 7, Mass-MetaSite), physicochemical and ADME modelling (MoKa, VolSurf+), bioisosteric fragment replacement (MetaDesign), metabolomics and lipidomics (MARS, Lipostar/Lipostar2), protein pocket comparison (BioGPS), forensic imaging (iFIS), and a unified web container platform (ONIRO), with WebMetabase serving as the metabolite database and design environment. The flagship MetaSite algorithm is training-set independent, claims approximately 85% accuracy in site-of-metabolism prediction and over 95% top-ranked success in Mass-MetaSite automated metabolite identification, while BioGPS provides a curated database of approximately 800,000 protein binding pockets.
The business model combines quote-based commercial software licensing (Solo single-user and Site-wide Unlimited Suite editions, with multi-year contracts), a less profitable Academic License tier, fee-based training courses priced at $250–$500 per person-day, a deliberately limited number of consulting agreements, and an annual Cytochrome P450 Consortium membership that gives participating pharmaceutical companies access to proprietary homogeneous human CYP metabolism data and predictive in silico models. Molecular Discovery's go-to-market is sales-led, with direct licensing to pharmaceutical, biotech, academic, and contract research users; channel distribution for MARS metabolomics through Mass Analytica; and OEM integrations via the Accelrys/BIOVIA Pipeline Pilot ISV Program and the Waters UNIFI platform. The customer base is anchored by a roster of top-tier pharmaceutical companies (AstraZeneca, Novartis, Pfizer, Merck, Roche, BMS, Vertex, Sanofi-Aventis, Servier, among others) and is supplemented by academic, food (Nestlé Research Center), GPCR-focused biotech (SoseiHeptares), and forensic/law enforcement users of iFIS.
Molecular Discovery firmographics
Firmographics- Name
- Molecular Discovery
- Legal name
- Molecular Discovery Ltd.
- Website
- https://www.moldiscovery.com
- Company type
- Private
- Founded year
- 1984
- Operating status
- Operating
- Headcount range
- 1–10 employees
- Short description
- Molecular Discovery Ltd. provides proprietary GRID-based computational chemistry and cheminformatics software — including MetaSite, Mass-MetaSite, GRID, FLAP, MoKa, VolSurf+, and BioGPS — to pharmaceutical, biotech, academic, and forensic customers for drug design, ADME prediction, metabolite identification, and binding-site analysis.
- Ownership category
- akta.pro rank
Molecular Discovery industry classification
Industry- Product category
- Computational Chemistry / Drug Discovery Software
- NAICS
- Research and Development in Biotechnology (except Nanobiotechnology) (541714), Research and Development in the Physical, Engineering, and Life Sciences (except Nanotechnology and Biotechnology) (541715)
- SIC
- Laboratory Analytical Instruments (3826), Services-Commercial Physical & Biological Research (8731)
- akta.pro primary industry
- Cheminformatics & Molecular Modeling / CADD (HLAGAJAE)
- akta.pro secondary industries
- AI/ML Platforms for Drug Discovery & Experiment Optimization (HLAGAJAO), Metabolomics & Lipidomics Services (HLAGANAG), Biomarker Discovery & Validation (omics, assay feasibility, clinical validation) (HLAAAMAA), Material Characterization & Spectroscopy (NMR/FTIR/MS) (HLAGADAK)
Keywords
Where Molecular Discovery is headquartered
LocationHeadquarters
- HQ city
- Borehamwood
- HQ country
- United Kingdom
- HQ region
- Europe
Offices3 records
Markets served
Molecular Discovery business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Personnel, Technology or R&D, Marketing or Sales, Operations
Revenue model
- Software Licensing: Commercial software licenses sold directly to pharmaceutical companies and research institutions. All software products require login/registration to download. Academic licenses available with limited support. Site-wide unlimited license options (Suite editions) provide broader enterprise deployment.
- Training Courses: In-person and online training workshops on Molecular Discovery software and Drug Design methodologies. Training courses held at MD facilities (Perugia, Italy; Sant Cugat del Vallés, Barcelona, Spain) and at customer sites. Pricing at 250 USD/day or 500 USD for multi-day packages.
- Consulting Agreements: Consulting agreements in research areas related to chemometrics and drug discovery, potentially involving scientific software development with limited exclusive rights. MD accepts a very limited number of such collaborations annually.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Subscription | Annual | Academic License |
| One time/ perpetual license | Multi-year contract | Commercial License (Solo/Suite editions) |
| Unit Pricing | Multi-year contract | Training Course Fee |
| Other | Annual | Cytochrome P450 Consortium Membership |
Go-to-market motion2 records
Distribution channels6 records
Marketing channels6 records
Molecular Discovery product offering
Product offeringCore offering
Molecular Discovery sells computational chemistry and cheminformatics software used by pharmaceutical companies and academic researchers for drug discovery. The portfolio covers metabolism prediction (MetaSite), high-throughput metabolite identification from LC-MS/MS data (Mass-MetaSite), physicochemical property prediction (MoKa, VolSurf+), virtual screening and docking (FLAP, BioGPS), lipidomics and metabolomics (Lipostar, MARS), 3D-QSAR (Pentacle), scaffold hopping (SHOP), forensic fingermark imaging (iFIS), and the ONIRO web container platform. All products are built on the proprietary GRID forcefield that calculates Molecular Interaction Fields via 74 chemical probes.
Product overview
Molecular Discovery offers a comprehensive computational chemistry and cheminformatics software suite built on the proprietary GRID forcefield for Molecular Interaction Fields (MIFs). The portfolio includes MetaSite/MetaSite 7 as the flagship metabolism prediction platform (Phase I/II CYPs, FMO, AOX, and 40+ other enzymes), Mass-MetaSite for high-throughput automated metabolite identification from LC-MS/MS data, WebMetabase as a web-based metabolite database and design platform, ONIRO as the unified web container platform, and Mass-ChemSite for organic synthesis product elucidation. Structure-based design is supported by GRID (core MIF calculation engine with 74 probes), FLAP (virtual screening, docking, pharmacophore elucidation, WaterFLAP, FLAPdock), and BioGPS (protein pocket comparison with ~800,000 curated pockets). Physicochemical property prediction is handled by MoKa (pKa, logP/D, logS, tautomers, PROTAC mode) and VolSurf+ (128 ADME descriptors with built-in models). The lipidomics/metabolomics suite includes Lipostar 2 (LC-MS/MS lipidomics) and MARS (untargeted/semi-targeted metabolomics and exposomics). Additional tools include Pentacle (alignment-independent 3D QSAR), SHOP (scaffold hopping), iFIS (forensic fingermark imaging with AI grading), and MetaDesign (bioisosteric replacement). All products integrate with Pipeline Pilot via Accelrys ISV Program, and Mass-MetaSite connects to Waters UNIFI platform.
Differentiator
Problem solved
Functional benefit
Products and services
- GRID Computational procedure for determining energetically favourable binding sites on molecules of known structure through Molecular Interaction Fields (MIFs) using 74 chemical probe types. Foundation technology underlying all Molecular Discovery products including ADME prediction, site of metabolism prediction, virtual screening, pharmacophore elucidation, water prediction, and 3D-QSAR. Used by medicinal chemists and computational chemists for structure-based drug design.
- MetaSite / MetaSite 7 Computational procedure predicting metabolic transformations related to cytochrome P450 (CYP) and flavin-containing monooxygenase (FMO3) mediated reactions in Phase I metabolism, extended in version 7 to Phase II. Uses GRID Molecular Interaction Fields combined with chemical reactivity and reaction mechanism propensity; training-set independent with ~90% accuracy for top-3 predictions. Used by medicinal chemists and DMPK scientists during lead optimisation.
- Mass-MetaSite High-throughput automatic metabolite identification software for small molecules and peptides using LC-MS/MS, UV, fluorescence, and radio-chromatogram data. Reduces manual analysis from hours to minutes per compound. Supports Waters, Agilent, Bruker, Sciex, and Thermo instruments with multiple acquisition modes (DDA, MSE, HDMSE, SWATH, SONAR, AIF). Integrates with the Waters UNIFI platform. Used by DMPK and metabolite identification scientists.
- FLAP Comprehensive virtual screening, docking, water prediction, pharmacophore elucidation, and 3D-QSAR software using GRID Molecular Interaction Fields. Provides ligand-ligand, ligand-receptor, and receptor-receptor comparison via pharmacophoric quadruplet fingerprints. Includes WaterFLAP for binding site water prediction and FLAPdock for structure-based pose prediction. Used by computational chemists and medicinal chemists for hit finding and lead optimisation.
- BioGPS Protein binding site comparison software for drug repurposing, off-targeting prediction, and ligand selectivity. Uses GRID MIFs and pharmacophoric fingerprints for pocket-pocket virtual screening against a curated database of ~800,000 pockets with pre-computed MIFs and biological annotation. Supports the Runaway cloud service for large computations. Used by computational chemists and structural biologists.
- MoKa Physicochemical properties prediction software for pKa, logP, logD, logS0, tautomer enumeration/stability, and ionization states. Trained on 25,000+ pKa values with 0.4 log unit prediction error. Self-trainable with in-house experimental data. Includes PROTAC mode for Proteolysis Targeting Chimeras. Available in Solo (interactive GUI) and Suite (unlimited interface + command-line + training module) editions. Used by medicinal chemists and computational chemists.
- VolSurf+ ADME and pharmacokinetic modeling software calculating 128 molecular descriptors from GRID MIFs. Predicts passive intestinal absorption, blood-brain barrier permeation, solubility, protein binding, volume of distribution, and metabolic stability. Includes VolSurf+ Selector (virtual screening), Modeller (statistical modelling), and Designer (interactive optimisation). Available in Solo and Suite editions. Used by DMPK scientists and computational chemists.
- ONIRO Web container platform encapsulating Molecular Discovery solutions for structure elucidation, in-silico predictions, spectral database, search, and reporting. Distributes WebMetabase, Compound Library, WebChembase, and WebQuant applications with unified user access, workgroup management, and licensing control. Used by enterprise customers requiring centralised deployment of MD's web applications.
- Mass-ChemSite Software for structure elucidation of organic molecules from chemical reactions using High Resolution Mass Spectroscopy (HRMS). Applications include C-H functionalisation synthesis, forced degradation studies, agroscience, by-products identification, and targeted analysis. Covers small molecules and peptides up to 5,000 MW. Used by synthetic chemists and structure elucidation experts.
- Lipostar 2 Comprehensive vendor-neutral software for LC-MS/MS-based lipidomics (DDA and DIA). Includes DB Manager for lipid database generation, spectral matching identification, oxidized species detection, gap-filler algorithm, multivariate statistical analysis, and lipid pathways. Supports Agilent, Waters, Thermo, Sciex, Bruker, and Shimadzu instruments. Used by lipidomics and metabolomics researchers in pharma and academia.
- MARS Vendor-neutral desktop application for untargeted and semi-targeted LC-MS-based metabolomics and exposomics. Covers data conversion, peak detection, statistical analysis, automated MS/MS-based metabolite annotation, quantification, and biopathway analysis. Supports databases from HMDB, MassBank of North America, and Microbial Metabolites Database. Distributed exclusively through Mass Analytica. Used by metabolomics and exposomics researchers.
- Pentacle Advanced alignment-independent 3D QSAR software calculating GRID Independent Descriptors (GRIND and GRIND2) from Molecular Interaction Fields. Automatically aligns structures using the CLACC algorithm for model interpretation. Builds and validates 3D QSAR models in minutes with multivariate analyses linked to 3D MIFs. Used by computational chemists and medicinal chemists for SAR analysis.
- SHOP Scaffold hopping software guiding scaffold replacement during drug discovery. Uses client/server architecture with GRID forcefield interaction patterns and shape criteria to search scaffold databases for bioisosteric replacements considering synthetic feasibility and ADME profiles. Includes a sample combichem database. Used by medicinal chemists exploring chemical diversity and intellectual property space.
- iFIS Intelligent Fingermark Imaging System for mass spectrometry experts and law enforcement. Visualises fingermarks from a chemical perspective to improve biometric recognition and co-localise chemicals. Available in iFIS Ultra (for MS experts) and iFIS (for law enforcement). Features AI-based automated quality grading using Scotland Yard grades, image stitching, superimposition, and overlapping fingermark separation. Used by forensic labs and law enforcement agencies.
- WebMetabase Web-based metabolite identification database, reviewing system, and design platform. Tracks metabolic schema, chromatograms, spectra, and fragmentation. Enables kinetic data analysis (half-life, clearance), matrix analysis (cytochrome reaction phenotyping), compound series analysis (SMRt), and design tools including MetaDesign via web interface. Distributed through ONIRO. Used by DMPK scientists for collaborative MetID workflows.
- Software Training Courses In-person and online training workshops covering Molecular Discovery software and drug design methodologies. Courses held at MD facilities (Perugia, Italy; Sant Cugat del Vallès, Barcelona, Spain) and at customer sites. Priced at 250 USD/person per day, 500 USD for multi-day packages (e.g., 3-day course), with optional computer rental at 100 USD/day. Lunch and coffee included.
- Research Consulting Agreements Consulting agreements in chemometrics and drug discovery research areas, potentially involving scientific software development with limited exclusive rights. Molecular Discovery accepts a very limited number of such collaborations annually. Intended for pharmaceutical and academic clients needing bespoke cheminformatics work.
- Cytochrome P450 Consortium Membership Consortium-led data and in silico model initiative led by Molecular Discovery, generating large homogeneous experimental datasets for human CYP metabolism (metabolic rate, substrate likelihood, inhibitor classification, isoform selectivity, metabolic stability, sites of metabolism, metabolic pathway elucidation). Pharmaceutical members gain access to the proprietary dataset and consortium-developed predictive models; managed by Dr. Martin Bohl.
Quantifiable outcome
- Reduces manual metabolite identification from several hours to minutes per compound (Mass-MetaSite)
- +6 more outcomes
Companies that use Molecular Discovery
Customer profileNamed customers17 records
Segments4 records
Ideal customer profiles4 records
Molecular Discovery technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- No
- API docs
- API detail
Core technology
AI maturity
App detail
Integration2 records
AI capability25 records
Feature14 records
Molecular Discovery partnerships and signals
Strategic signalPartnerships
16 partnerships are on record, tiered minor and core.
- Molecular Horizon srlminorMolecular Horizon srl is a partner organisation of LightDyNAmics European Training Network and co-organised a training workshop with Molecular Discovery in December 2020 on Design, Development and Commercial Release of Computational Software for Pharmaceutical Research.
- LightDyNAmics (European Commission)minorLightDyNAmics is a multidisciplinary European Training Network funded by the European Commission under the Horizon Marie Sklodowska-Curie Action. Molecular Discovery Ltd and Molecular Horizon srl are partner organisations. MD staff participate in practical tutorials for early stage researchers (ESRs) within the project.
- Waters CorporationcoreMass-MetaSite 3.4 directly interacts with the UNIFI platform from Waters Corporation. This new version reads and processes data obtained from UNIFI including the non-targeted approach based on Ion Mobility acquisition mode, HDMSE. This collaboration between Molecular Discovery, Waters, and Lead Molecular Design produced one of the first commercial approaches for metabolite identification using a 3rd party API implemented in UNIFI.
- AstraZenecacoreAstraZeneca joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models. Seven pharmaceutical companies initially signed up. Consortium data and models are made available to all members.
- NovartiscoreNovartis joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models.
- PfizercorePfizer joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models.
- Sanofi-AventiscoreSanofi-Aventis joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models.
- ServiercoreServier joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models.
- AcceleracoreAccelera joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models.
- Solvay PharmaceuticalscoreSolvay Pharmaceuticals joined the Cytochrome P450 Consortium led by Molecular Discovery. The consortium generates comprehensive experimental data for human CYP metabolism and develops predictive in silico models.
- Accelrys (BIOVIA)coreThrough the Accelrys Independent Software Vendors (ISV) Program, Molecular Discovery provides a full set of Pipeline Pilot components for MoKa, MetaSite, and VolSurf+. This embeds MD's cheminformatics capabilities into Accelrys/BIOVIA Pipeline Pilot enterprise workflows.
- Mass AnalyticacoreMARS (MetAbolomics ReSearch) software is distributed exclusively through Mass Analytica. Customers interested in MARS are directed to mass-analytica.com for download, evaluation, and purchase.
- Nestlé Research CenterminorCollaboration with BioGPS for ligand-protein binding screening across the full proteome to identify new molecular initiating events (MIEs) for food chemicals.
- SoseiHeptaresminorCollaboration with BioGPS for building the GPCRome platform — a GPCR binding site platform for similarity assessments and screening/ligand repurposing efforts.
- GoogleminorMolecular Discovery uses Google Analytics for web analytics and Google services for sending email. Google Analytics uses cookies to help analyze website usage. IP addresses are transmitted to and stored by Google on servers in the United States.
- MailChimp (Intuit)minorMailChimp is used to send Molecular Discovery's newsletter to registered users who have opted in. Personal information (name, email address) may be shared with MailChimp for this purpose.
Scale indicators9 records
Recent moves6 records
Expansion highlights5 records
Molecular Discovery competitors and assessment
Company assessmentMarket position
Competitive moat5 records
Key risks5 records
Key highlights7 records
Customer concentration
Molecular Discovery social profiles
Digital presenceMolecular Discovery financial estimates
Financial estimateRevenue estimate
Valuation estimate
Molecular Discovery leadership team
Management profileNumber of profiles
Profiles16 records
Molecular Discovery funding detail
Funding detailFunding overview
Funding rounds
Investors
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
Molecular Discovery M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about Molecular Discovery
What does Molecular Discovery do?
Molecular Discovery sells computational chemistry and cheminformatics software used by pharmaceutical companies and academic researchers for drug discovery. The portfolio covers metabolism prediction (MetaSite), high-throughput metabolite identification from LC-MS/MS data (Mass-MetaSite), physicochemical property prediction (MoKa, VolSurf+), virtual screening and docking (FLAP, BioGPS), lipidomics and metabolomics (Lipostar, MARS), 3D-QSAR (Pentacle), scaffold hopping (SHOP), forensic fingermark imaging (iFIS), and the ONIRO web container platform. All products are built on the proprietary GRID forcefield that calculates Molecular Interaction Fields via 74 chemical probes.
Is Molecular Discovery a public or private company?
Molecular Discovery is a private company. It is classified as founder individual operated bootstrapped and is currently operating.
When was Molecular Discovery founded?
Molecular Discovery was founded in 1984. It employs 1 to 10 people.
Where is Molecular Discovery based?
Molecular Discovery is headquartered in Borehamwood, United Kingdom, in the Europe region.
How does Molecular Discovery make money?
Three revenue lines are on record. Software Licensing is the primary driver. The others are training Courses and consulting Agreements.
Does Molecular Discovery have an API?
No public API is recorded for Molecular Discovery.
What industry is Molecular Discovery in?
Molecular Discovery's product category is Computational Chemistry / Drug Discovery Software. Its primary akta.pro industry code is HLAGAJAE, Cheminformatics & Molecular Modeling / CADD, with a secondary code of HLAGAJAO, AI/ML Platforms for Drug Discovery & Experiment Optimization. Its NAICS code is 541714 and its SIC code is 3826.