What MODSIM Pharma does

MODSIM Pharma AB is a Swedish private pharmaceutical software company founded in late 2018 as a spin-off from Uppsala University. The company develops physics-based molecular simulation software for Structure-Based Drug Design (SBDD), with proprietary Free Energy Perturbation (FEP) technology as its core engine. Its stated accuracy is <1 kcal/mol—comparable to or better than established proprietary alternatives such as FEP+—while reportedly running up to 10x faster at a fraction of the cost, with benchmarking on the Wang and Merck standard datasets. AI/ML methods are integrated for cheminformatics, predictive analytics, and hardware adaptation, and the company has an academic publication record supporting its technology.

The product portfolio is modular and stackable. GPCR-ModSim provides web-based 3D structural modeling of G Protein-Coupled Receptors; QligFEP and QresFEP are automated FEP workflows for ligand series and in silico mutagenesis respectively; QmapFEP optimizes ligand-series mapping via a minimum-spanning-tree algorithm; QGPU is the next-generation MD engine optimized for CPU/GPU hardware; the Reaction Enumeration Builder generates billions of virtual molecules via multicomponent reactions; and the MODSIM Suite bundles the pipeline into an end-to-end SBDD platform. Distribution is via direct enterprise sales with modular software licensing, optional cloud or on-premise HPC deployment, and integration through technology partnerships (notably Pharmacelera).

The company monetizes through four streams: software licensing (modular), high-performance computing services, custom scientific development, and expert consulting at the Hit Identification, Hit-to-Lead, and Lead Optimization stages. Customers include pharmaceutical and biotech firms (most notably Sosei-Heptares on an A2A antagonist program) and academic drug discovery groups (Sotelo Lab USC, ComBioMed Lab USC, and LACDR at Leiden University). Operating geographies span Sweden, Spain, the Netherlands, and the United States via collaborations. The team is small (1–10 employees) including two co-founders with academic appointments at Uppsala and Leiden.

Name

MODSIM Pharma

Legal name

MODSIM Pharma AB

Website

https://modsim-pharma.com

Company type

Private

Founded year

2018

Operating status

Operating

Headcount range

1–10 employees

Short description

MODSIM Pharma AB is a Swedish pharmaceutical software company providing physics-based molecular simulation and FEP tools for Structure-Based Drug Design, serving pharmaceutical, biotech, and academic drug discovery customers across Europe and the US.

Ownership category

akta.pro rank

Product category

Computational Drug Discovery Software

NAICS

Computer Systems Design and Related Services (54151), Research and Development in Biotechnology (except Nanobiotechnology) (541714), Scientific Research and Development Services (5417)

SIC

Services-Commercial Physical & Biological Research (8731)

akta.pro primary industry

Cheminformatics & Molecular Modeling / CADD (HLAGAJAE)

akta.pro secondary industry

AI/ML Platforms for Drug Discovery & Experiment Optimization (HLAGAJAO)

Keywords

• Molecular dynamics simulation
• Structure-based drug design
• Free energy perturbation
• Computational drug discovery
• GPCR modeling software

Headquarters

HQ city

Uppsala

HQ country

Sweden

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

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

Revenue model

1. Software Licensing: Flexible software licensing for proprietary computational tools. Modules can be purchased separately.
2. Computing Services: High-performance computing services for running molecular simulations and FEP calculations on HPC infrastructure.
3. Scientific Development: Custom scientific development and integration services to include approaches in customer workflows.
4. Expert Consulting: Expert consulting services for Hit Identification, Hit-to-Lead and Lead Optimization stages of drug discovery.

Go-to-market motion1 record

Distribution channels5 records

Marketing channels5 records

Core offering

MODSIM Pharma provides a modular computational platform for Structure-Based Drug Design that combines proprietary physics-based Free Energy Perturbation (FEP) methods with molecular dynamics simulations to predict ligand–protein binding affinities. The offering includes the GPCR-ModSim web service for 3D modeling of G-protein coupled receptors and membrane proteins, the QligFEP/QresFEP/QmapFEP simulation engines for ligand series and residue mutagenesis, the QGPU underlying MD engine, the Reaction Enumeration Builder for virtual compound generation, and the integrated MODSIM Suite workflow. Sales channels include software licensing, HPC computing services, custom scientific development, and expert consulting for pharmaceutical and biotech drug discovery teams.

Product overview

MODSIM Pharma offers a modular computational platform for Structure-Based Drug Design combining physics-based proprietary methods with molecular simulations. The core platform consists of the MODSIM Suite, which integrates GPCR-ModSim for receptor modeling, QligFEP and QresFEP for free energy perturbation calculations, QmapFEP for ligand series optimization, QGPU for accelerated MD simulations, and the Reaction Enumeration Builder for virtual compound generation. The Q engine (QGPU) serves as the underlying MD engine powering the platform, enabling accurate binding affinity predictions at <1 kcal/mol accuracy while achieving 10x faster performance than alternatives.

Differentiator

Problem solved

Functional benefit

Brands

• GPCR-ModSim: A centralized and easy-to-use service dedicated to the structural modeling of G Protein-Coupled Receptors (GPCRs).
• QligFEP
• QresFEP
• QmapFEP
• QGPU
• MODSIM Suite
• Reaction Enumeration Builder

Products and services

• GPCR-ModSim One-stop web-based service for 3D modeling of G Protein-Coupled Receptors (GPCRs) and other membrane proteins, generating homology models from amino acid sequences for pharmaceutical and academic drug discovery teams.
• QligFEP Automated workflow for high-throughput Free Energy Perturbation simulations across ligand series, supporting scaffold hopping, linker length changes, and pose ranking via a dual topology approach for medicinal chemists and computational chemists.
• QresFEP In silico mutagenesis protocol using FEP with a smooth annihilation method to predict the effect of single point mutations on protein–ligand binding affinity, thermal stability, or conformational equilibrium for structure-based drug design teams.
• QmapFEP Proprietary algorithm based on Jarnik's minimum spanning tree approach that maps ligand series into FEP pair comparisons with an efficiency of approximately 1.5 nodes per ligand for chemistry and computational chemistry users.
• QGPU Next-generation molecular dynamics engine optimized for CPU/GPU mixture hardware using spherical boundary conditions and embarrassingly parallel replicate system representation to enable fast, high-throughput MD for HPC and cloud customers.
• MODSIM Suite Complete modular workflow platform for the structure-based drug design pipeline that brings together GPCR-ModSim, QligFEP, QresFEP, QmapFEP, QGPU, and Reaction Enumeration Builder into a flexible, customizable solution for pharmaceutical and biotech R&D teams.
• Reaction Enumeration Builder Tool for rapidly generating virtual molecules through scaffold hopping and enumeration of multicomponent reactions to expand into novel, synthesizable chemical space for medicinal chemistry and library design.
• Expert Consulting Services Expert consulting services for pharmaceutical and biotech clients covering hit identification, hit-to-lead, and lead optimization phases of drug discovery, leveraging MODSIM's physics-based simulation expertise.
• Computing Services High-performance computing services that run molecular simulations and Free Energy Perturbation calculations on HPC infrastructure on behalf of customers without in-house compute capacity.
• Scientific Development & Integration Services Custom scientific development and integration services that adapt and embed MODSIM's proprietary simulation approaches into customer drug discovery workflows and pipelines.

Quantifiable outcome

• 10x faster drug discovery simulations compared to existing alternatives
• +3 more outcomes

Named customers4 records

Segments4 records

Ideal customer profiles2 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

AI capability2 records

Feature7 records

Partnerships

Four partnerships are on record, tiered core.

• Leiden Academic Center for Drug Research (LACDR)coreStrategic or Co-development Partner · 27 June 2024Collaboration on CCR2 receptor hit identification project combining ultra-large virtual screening with FEP optimization. LACDR performs experimental validation using radioligand binding assays. This collaboration reinforces the existing partnership with Pharmacelera and demonstrates integrated resources, expertise, and capabilities for speeding up drug discovery.
• PharmaceleracoreTechnology or Integration · 2 March 2023Technology and business partnership to jointly provide an efficient in-silico platform from Hit Finding up to Lead Optimization. Combines Pharmacelera's virtual screening expertise with MODSIM's Free Energy Perturbation (FEP) technology for in silico mutagenesis and ligand ranking. Enables integrated resources for academia, biotech, and pharmaceutical industry customers.
• Uppsala UniversitycoreStrategic or Co-development Partner · 1 January 2018MODSIM Pharma was founded as a spin-off from Uppsala University, stemming from state-of-the-art research in a leading academic lab. Johan Åqvist, Professor of Theoretical Chemistry at Uppsala University, serves on the Scientific Advisory Board.
• Sotelo Lab (Universidad de Santiago de Compostela)coreStrategic or Co-development PartnerLong-term academic collaboration for GPCR drug design research. Developed Reaction Enumeration Builder technology together. Multiple published studies on adenosine receptor antagonists (A2A, A2B, A3) with synthesis support from the Sotelo lab.

Scale indicators3 records

Recent moves7 records

Expansion highlights6 records

Direct peers

• Pharmacelera: Barcelona-based provider of computational tools for ultra-large virtual screening and hit discovery (Pharmacelera platform). Direct peer and current technology partner of MODSIM Pharma, with a complementary product set covering hit ID that MODSIM does not natively address.
• Cresset: UK-based computational chemistry company offering ligand-based and structure-based design tools (Flare, Spark) used by medicinal chemists. Direct peer in computational chemistry with overlapping customers in pharma and biotech and a similar mid-size footprint.
• Schrödinger: Publicly traded provider of physics-based molecular simulation software, including the FEP+ product widely regarded as the enterprise standard for binding affinity prediction. Most directly comparable competitor to MODSIM on physics-based FEP for structure-based drug design, serving the same big-pharma and biotech customer base at much larger scale.
• Chemical Computing Group (CCG): Developer of the Molecular Operating Environment (MOE), a longstanding integrated computational chemistry platform for drug discovery including docking, FEP, and protein modeling. Direct peer offering a comprehensive suite of cheminformatics and molecular simulation tools to pharma and academic users.
• Optibrium: Provider of the StarDrop drug discovery platform that integrates ADMET prediction, multi-parameter optimization and decision support with computational chemistry modules. Comparable as a focused, mid-sized computational drug discovery software vendor serving similar pharma and biotech customers.
• OpenEye Scientific (Cadence): Provider of molecular modeling and cheminformatics software (e.g., OMEGA, FEP+, ROCS) used in pharmaceutical drug discovery. Direct competitor in computational chemistry tooling for structure-based and ligand-based design.

Emerging players

• Insilico Medicine: AI-driven drug discovery company combining generative AI, target identification and computational chemistry. Emerging player partially overlapping with MODSIM in computational binding-affinity prediction but pursuing a more AI-native, end-to-end discovery approach.

Broad incumbents

• Certara: Publicly traded biosimulation and drug development software and services company serving global pharma with PBPK, QSP, regulatory and discovery modeling tools. Broad incumbent with adjacent modeling capabilities and an established enterprise customer base.
• Dotmatics: Scientific R&D informatics platform (now part of Siemens) covering data management, ELN, and analysis workflows for drug discovery. Adjacent incumbent offering broader lab informatics with some overlap in computational chemistry integrations at pharma customers.
• Dassault Systèmes BIOVIA: Division of Dassault Systèmes offering BIOVIA Discovery Studio and a broad scientific informatics portfolio spanning modeling, simulation, lab informatics and manufacturing. Broad incumbent with overlapping capabilities in molecular simulation but a much wider platform footprint than MODSIM.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/modsim_pharma
• LinkedInlinkedin.com/company/modsim-pharma-ab

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 MODSIM Pharma