Molsoft
MolSoft is a privately held San Diego-based developer of ICM, a physics-based and AI-enhanced molecular modeling platform serving pharmaceutical and biotech companies, academic institutions, and government research agencies through software licensing, GPU-accelerated screening tools, and contract research services.
- Company typePrivate
- Founded1994
- HeadquartersSan Diego, United States
- Headcount11–50
- GTM typeB2B
- OfferingSoftware
What Molsoft does
Molsoft L.L.C. is a privately held, founder-controlled computational drug discovery software and services company headquartered in San Diego, California. Founded in 1994 by Ruben Abagyan (originally as Biosoft, renamed 1995), the company develops the proprietary ICM (Internal Coordinate Mechanics) platform, a physics-based molecular modeling framework that operates in internal coordinate space rather than Cartesian coordinates, enabling approximately 1,000x faster convergence for conformational optimization versus traditional methods. ICM serves as the foundation for a modular product portfolio spanning molecular modeling (ICM-Pro), cheminformatics (ICM-Chemist, ICM-Chemist-Pro, MolCart, ICM-Scarab), ML-based target profiling (MolScreen with ~2,500 models across 1,200 targets), and a growing suite of GPU-accelerated tools for ultra-large library virtual screening (GINGER, RIDGE, RIDE, CombiRIDGE, V-SYNTHES, GigaSearch, GigaScreen). Newer AI-native additions released in 2025-2026 include groupGen (generative R-group design) and Ligand AIDE (de novo ligand generation), alongside the RTCNN graph-neural-network scoring function.
The company monetizes through annual software subscriptions (ICM-Pro floating and node-locked licenses, separate GPU add-on modules for GINGER/RIDGE/RIDE), free-tier funnel tools (ICM-Browser, ActiveICM, iMolView, IcmJS), and fee-for-service or FTE-based contract research for drug discovery projects, including cloud-based high-throughput virtual screening on AWS, Azure, and Google Cloud. Molsoft sells primarily into pharmaceutical and biotechnology companies (notably Novartis with ~1,500 global users via the FOCUS collaboration, plus Eilean Therapeutics, Lomond Therapeutics, Arrakis Therapeutics, Rempex/Medicines Company, Aurigene Oncology, Syngene International), with secondary demand from academic institutions (USC, UCSD labs) and government agencies (NIH/NCI). Distribution combines direct enterprise field sales, regional channel partners (Advent Informatics in India, inCerebro in Korea), and a multi-channel marketing apparatus spanning user group meetings, scientific conferences, webinars, technical publications, and a YouTube/community-forum presence.
The company's technology is validated by repeated wins in independent D3R Grand Challenges (2017, 2018, 2020), an OpenEye/Merck/GSK docking competition win, a Pasteur Institute virtual screening comparison, and one FDA-approved drug (Vabomere, 2017) discovered using ICM-based structure design. With 11-50 employees, no documented outside investment, and a 31-year operating history, Molsoft operates as a focused, founder-led specialist serving a technically demanding segment of computational chemistry and structure-based drug design.
Molsoft firmographics
Firmographics- Name
- Molsoft
- Legal name
- Molsoft L.L.C.
- Website
- https://molsoft.com
- Company type
- Private
- Founded year
- 1994
- Operating status
- Operating
- Headcount range
- 11–50 employees
- Short description
- MolSoft is a privately held San Diego-based developer of ICM, a physics-based and AI-enhanced molecular modeling platform serving pharmaceutical and biotech companies, academic institutions, and government research agencies through software licensing, GPU-accelerated screening tools, and contract research services.
- Ownership category
- akta.pro rank
Molsoft industry classification
Industry- Product category
- Computational Drug Discovery Software
- NAICS
- Software Publishers (5132), Scientific Research and Development Services (5417), Research and Development in Biotechnology (except Nanobiotechnology) (541714)
- 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
Where Molsoft is headquartered
LocationHeadquarters
- HQ city
- San Diego
- HQ country
- United States
- HQ region
- North America
Offices1 record
Markets served
Molsoft business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Technology or R&D, Personnel, Infrastructure, Marketing or Sales, Operations
Revenue model
- Software Licensing: MolSoft licenses ICM software products including ICM-Pro, ICM-Chemist, ICM-Browser, and various add-on modules. Licenses are available as floating (server-based, multi-user) or node-locked (single machine). Options include annual, multi-year, perpetual, site, and teaching licenses. GPU-specific license keys available for GINGER, RIDGE, and RIDE modules.
- GPU License Add-ons: Specialized GPU license keys for accelerated computing tasks including molecular dynamics, RIDE-GPU, RIDGE-GPU, and GINGER. These are add-on licenses to regular ICM-Pro licenses.
- Contract Research Services: Fee-for-service or FTE-based consulting services for drug discovery including virtual screening, protein modeling, lead optimization, cheminformatics solutions, and software development. Services are tailored to customer needs and undertaken in-house by expert research scientists.
- Cloud Computing Services: Virtual screening services run on cloud infrastructure (AWS, Azure, Google Cloud) when extra capacity is needed beyond on-premise capabilities.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Subscription | Annual | ICM-Pro Desktop Modeling License |
| Subscription | Annual | GPU Accelerated Modules (GINGER, RIDGE, RIDE-GPU) |
| Freemium | Multi-year contract | ICM-Browser (Free) |
| Subscription | Annual | Academic/Teaching Licenses |
| Hybrid | Pay-as-you-go | Contract Research Services |
Go-to-market motion3 records
Distribution channels5 records
Marketing channels10 records
Molsoft product offering
Product offeringCore offering
Molsoft develops and licenses the ICM (Internal Coordinate Mechanics) software platform for computational drug discovery, offering tools for molecular modeling, flexible docking, virtual ligand screening, protein homology modeling, and cheminformatics. The platform is sold as ICM-Pro with add-on modules (VLS, Homology, GINGER, RIDGE, RIDE, CombiRIDGE, V-SYNTHES, MolScreen) and standalone cheminformatics products (ICM-Chemist, MolCart, ICM-Scarab), plus contract research and consulting services for pharmaceutical, biotech, academic, and government customers.
Product overview
MolSoft offers a comprehensive platform-plus-modules architecture centered on its proprietary ICM (Internal Coordinate Mechanics) technology. The core ICM-Pro desktop modeling software serves as the primary platform, with specialized modules including the Virtual Ligand Screening (VLS) Module, Homology Module, and ICM-Bio extending its capabilities. Specialized add-on products like GINGER (GPU-accelerated conformer generation), RIDGE (GPU docking), CombiRIDGE (combinatorial docking), GigaScreen (deep learning screening), and V-SYNTHES (synthon-based screening) target ultra-large library virtual screening workflows. Standalone cheminformatics products include ICM-Chemist/Pro, MolCart with Giga-Search, and ICM-Scarab. Free tools encompass ICM-Browser, ActiveICM, IcmJS, and iMolView mobile app. AI-powered additions include groupGen (generative R-group optimization), Ligand AIDE (de novo ligand design), RTCNN scoring function, and MolScreen (ML screening models). The portfolio serves academic labs and pharmaceutical/biotech companies across computational biology and chemistry workflows.
Differentiator
Problem solved
Functional benefit
Products and services
- ICM-Pro Desktop Modeling MolSoft's main desktop modeling software providing tools for molecular modeling using Biased Probability Monte Carlo and Molecular Dynamics, flexible docking, virtual ligand screening, homology modeling, and structure-based drug design for pharmaceutical, biotech, and academic researchers.
- ICM-Pro Virtual Ligand Screening (VLS) Module Add-on module enabling high-throughput structure- and ligand-based virtual screening of multi-million and ultra-large compound libraries on a local server or cloud, for pharmaceutical and biotech discovery teams.
- ICM-Pro Homology Module Add-on module for searching homologs, building structure-based sequence alignments, and creating single- and multi-chain homology models including loops for structural biology researchers.
- ICM-Bio Add-on module providing an environment for sequence analysis, alignments, profiles, databases, and connectivity with 3D structures with an alignment editor and annotator for bioinformatics users.
- ICM-Chemist Standalone suite for chemical drawing and editing, chemical database generation, chemical searching, clustering, and enumeration for medicinal chemists and cheminformatics teams.
- ICM-Chemist-Pro Standalone product containing 3D chemical tools, chemical superposition, 3D interactive ligand-receptor editing, and QSAR modeling for advanced medicinal chemistry users.
- MolCart Chemical cartridge enabling storage and searching of large chemical compound libraries using a fast relational database for cheminformatics and screening workflows.
- MolCart Giga-Search Add-on module enabling substructure and fingerprint search of billions of chemicals in seconds for ultra-large libraries such as Enamine REAL and ZINC database.
- ICM-Scarab Standalone software for storing and disseminating scientific data with tools for data mining, extraction, insertion, and a built-in electronic lab notebook for research organizations.
- MolScreen Add-on module providing a set of high-quality 2D fingerprint and 3D AI/ML models for approximately 2,500 pharmacology and toxicology targets across 1,200 targets, used for lead discovery or counter-screening.
- ICM-Browser Free downloadable software for browsing molecules and creating fully-interactive 3D molecule documents for embedding in PowerPoint and on the Web, for academic and individual users.
- ActiveICM Free plugin for viewing and displaying 3D ICM graphical slides and animations in Microsoft PowerPoint and web browsers without plugins, for scientists and educators.
- IcmJS (JavaScript Molecular Viewer) JavaScript/HTML5 3D molecular viewer requiring no plugin or browser extension, bringing desktop-quality graphics to web applications with Google Drive integration.
- iMolView Mobile App Mobile app for iPhone/iPad and Android enabling browsing of protein, DNA, and drug molecules in 3D with direct links to PDB and DrugBank for scientists, students, and educators.
- GINGER Conformer Generator GPU-accelerated neural-network conformer generator add-on module producing high-quality 3D conformations at 150-200 mol/sec on a single RTX 4090 GPU for medicinal chemists and screening teams.
- RIDGE Rapid Docking GPU Engine Add-on module enabling structure-based screening of ultra-large libraries with approximately 100-fold speed increase over CPU docking, processing ~100 compounds per second per GPU.
- GPU-RIDE Rapid Isostere Discovery Engine GPU-accelerated add-on module for enhanced ligand-based virtual screening using Atomic Property Fields, searching approximately 0.5 million conformers per second per GPU.
- CombiRIDGE Combinatorial Docking GPU-accelerated high-throughput combinatorial anchored docking add-on module that grows R-groups around a defined core fragment using neural networks for ultra-large chemical library screening.
- GigaScreen Deep Learning Screening Deep learning virtual screening add-on module combining ML and deep learning tools to tackle the computational intensity of screening very large chemical databases.
- V-SYNTHES Hierarchical Virtual Screening Add-on module providing a hierarchical, synthon-based virtual screening strategy for efficiently navigating gigascale make-on-demand chemical libraries by iteratively assembling and docking scaffold-synthon combinations.
- groupGen Generative R-group Optimization Generative AI add-on module proposing R-group substitutions tailored to specific protein binding sites using 3D graph neural networks, for medicinal chemistry lead optimization.
- Ligand AIDE De Novo Ligand Design AI-driven evolutionary add-on workflow for de novo ligand generation that iteratively grows and optimizes compounds over multiple generations using generative substitutions and re-docking.
- RTCNN Scoring Function Radial and Topological Convolutional Neural Network scoring add-on module combining 2D topological and 3D radial convolutions for improved ligand-receptor binding pose ranking and affinity prediction.
- ICM Molecular Dynamics Molecular dynamics simulation add-on module integrated into ICM-Pro, with GPU acceleration available for enhanced performance.
- Contract Research and Drug Discovery Services Fee-for-service or FTE-based drug discovery consulting delivered by in-house research scientists, including virtual screening, lead optimization, protein modeling, cheminformatics solutions, and custom software development for pharmaceutical and biotech clients.
Quantifiable outcome
- Achieved Ki values below 1nM in multiple drug discovery projects for oncology targets
- +4 more outcomes
Companies that use Molsoft
Customer profileNamed customers11 records
Segments4 records
Ideal customer profiles4 records
Molsoft technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- No
- API docs
- API detail
Core technology
AI maturity
App detail
Integration8 records
AI capability7 records
Feature10 records
Molsoft partnerships and signals
Strategic signalPartnerships
Eleven partnerships are on record, tiered core and minor.
- XtalPicorePartnership to unlock XtalPi's VAST Space (4.66 billion synthetically accessible compounds) for 3D docking using MolSoft's CombiRIDGE platform. Combines MolSoft's computational screening technology with XtalPi's highly curated, synthesis-aware chemical space. Enables researchers to transition computationally identified hits to experimentally testable compounds in weeks.
- inCerebro Co., Ltd.minorKorean partner that organized and delivered ICM-Pro Drug Discovery Workshop in Seoul (May 2026). Provides local hands-on training and expanding research collaboration in Korea.
- ChemSpaceminorChemSpace used MolSoft ICM suite to successfully complete CACHE 2 Challenge, screening 176 billion chemicals for COVID target NSP13 helicase. Demonstrates robustness of MolSoft technology for ultra-large library screening.
- Liverpool Chiro Chem (LCC)corePartnership to make LCC's 1.4 Billion ultra-large, stereo-defined, diverse chemical library available for virtual screening. LCC's chirally pure, sp3-rich scaffolds converted to 3D using GINGER and screened via RIDGE and RIDE methods. Enables structure-based and ligand-based lead discovery.
- EnaminecoreCollaboration to prepare Enamine's REAL database (2 billion+ chemicals) for virtual screening using RIDE method. Enables screening of 48 billion chemical conformers from Enamine REAL database. Partnership maintained during Ukraine crisis.
- NIH/NCIcoreCollaboration to make NIH's Synthetically Accessible Virtual Inventory (SAVI) database containing 1+ billion chemicals available for screening using RIDE method. Includes development of GPU-accelerated screening methods that led to discovery of hits against K-Ras G12D and PD-L1.
- MculeminorIntegration of Mcule's ULTIMATE library (100+ million novel compounds) into ICM-Chemist and ICM-Pro. Enables 2D and 3D pharmacophore searches, substructure searches, and virtual screening for novel chemistry discovery.
- Advent InformaticscoreDistribution agreement for India market. Advent Informatics promotes and distributes ICM computational drug discovery software in India using marketing expertise and research capabilities. Provides local support for Indian customers.
- NovartiscoreOver 8-year collaboration developing FOCUS platform - a global communication and modeling environment for medicinal chemists. Novartis has ~1,500 registered users globally. FOCUS based on ICM technology and includes ICM Ligand Editor for structure-based design.
- Biovitrum ABminorCollaboration with Biovitrum AB (Sweden) to co-develop the BeeHive Cheminformatics Client System. Product used by Biovitrum and Structural Genomics Consortium as program manager and database interface.
- Eilean TherapeuticscoreOncology-focused biotech company using MolSoft's AI and physics-based molecular modeling tools as integral part of Loch Company Group. Multiple compounds (eiletoclax, lomonotinib, balamenib) have entered clinical trials.
Scale indicators7 records
Recent moves9 records
Expansion highlights4 records
Molsoft competitors and assessment
Company assessmentDirect peers
- Optibrium: Developer of StarDrop and related software for drug discovery, including ADMET prediction, multi-parameter optimization, and small molecule design. Directly comparable to Molsoft in cheminformatics, lead optimization, and decision-support for medicinal chemistry.
- Cresset: Computational chemistry and molecular design software company offering ligand-based and structure-based tools (Flare, Spark, Torch). Directly comparable to Molsoft in ligand-based virtual screening, 3D pharmacophore modeling, and field-based methods for medicinal chemistry.
- Chemical Computing Group (CCG): Developer of the Molecular Operating Environment (MOE) and related drug discovery software. Directly comparable to Molsoft's ICM-Pro in desktop molecular modeling, docking, virtual screening, and QSAR for pharma and academic customers.
- ChemAxon: Cheminformatics software platform providing chemical search, structure handling, and molecular informatics tools. Directly comparable to Molsoft in cheminformatics and chemical database management, with broader enterprise footprint and partnerships with large pharma IT systems.
- Schrödinger: Public computational chemistry and molecular simulation software company offering physics-based and AI-driven drug discovery platforms. Directly comparable to Molsoft in molecular modeling, docking, virtual screening, and cheminformatics serving pharmaceutical and biotech customers, with broader product breadth and a significantly larger R&D budget.
- OpenEye Scientific (Cadence Design Systems): Provider of molecular modeling and cheminformatics software (OEChem, OEDocking, Orion) for drug discovery. Directly comparable to Molsoft's ICM suite across virtual screening, cheminformatics, and molecular design, now backed by Cadence's enterprise scale.
Broad incumbents
- Dotmatics: Scientific R&D software platform covering data management, chemistry, and biology informatics. Listed alongside Molsoft as a key chemoinformatics player; broader scope as a full scientific R&D platform rather than a focused molecular modeling tool.
- BIOVIA (Dassault Systèmes): Dassault's life sciences software portfolio including BIOVIA Discovery Studio and pipeline of scientific R&D tools. Overlaps with Molsoft in molecular modeling, virtual screening, and cheminformatics, but is part of a much broader enterprise PLM/Scientific portfolio serving multiple industries.
- Revvity Signals: Life sciences informatics and software division of Revvity (formerly PerkinElmer), offering Signals platforms for chemistry, biology, and translational R&D. Broad incumbent with overlapping cheminformatics and drug discovery software offerings.
Emerging players
- XtalPi: AI-driven drug discovery company combining physics-based modeling with AI and a synthesis-aware compound space (VAST). Both partner and adjacent competitor to Molsoft in computational drug discovery and ultra-large library screening.
Market position
Strengths5 records
Weaknesses5 records
Competitive moat5 records
Key risks6 records
Key highlights7 records
Customer concentration
Molsoft social profiles
Digital presenceMolsoft financial estimates
Financial estimateRevenue estimate
Valuation estimate
Molsoft leadership team
Management profileNumber of profiles
Profiles3 records
Molsoft funding detail
Funding detailFunding overview
Funding rounds
Investors
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
Molsoft 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 Molsoft
What does Molsoft do?
Molsoft develops and licenses the ICM (Internal Coordinate Mechanics) software platform for computational drug discovery, offering tools for molecular modeling, flexible docking, virtual ligand screening, protein homology modeling, and cheminformatics. The platform is sold as ICM-Pro with add-on modules (VLS, Homology, GINGER, RIDGE, RIDE, CombiRIDGE, V-SYNTHES, MolScreen) and standalone cheminformatics products (ICM-Chemist, MolCart, ICM-Scarab), plus contract research and consulting services for pharmaceutical, biotech, academic, and government customers.
Is Molsoft a public or private company?
Molsoft is a private company. It is classified as founder individual operated bootstrapped and is currently operating.
When was Molsoft founded?
Molsoft was founded in 1994. It employs 11 to 50 people.
Where is Molsoft based?
Molsoft is headquartered in San Diego, United States, in the North America region.
How does Molsoft make money?
Four revenue lines are on record. Software Licensing is the primary driver. The others are GPU License Add-ons, contract Research Services and cloud Computing Services.
Who are Molsoft's main competitors?
Direct peers on record are Optibrium, Cresset, Chemical Computing Group (CCG), ChemAxon, Schrödinger and OpenEye Scientific (Cadence Design Systems). Broad incumbents are Dotmatics, BIOVIA (Dassault Systèmes) and Revvity Signals. XtalPi is listed as an emerging player.
Does Molsoft have an API?
No public API is recorded for Molsoft.
What industry is Molsoft in?
Molsoft's product category is Computational 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 5132 and its SIC code is 8731.