This cloud-native, SaaS-based platform breaks down traditional barriers in drug discovery by uniting all disciplines—biology, chemistry, and computational sciences—in a single, integrated workspace. It empowers cross-functional teams to ideate, design, analyse, and optimise drug candidates faster and with greater precision than ever before.

By streamlining the entire early-stage pipeline, from de novo molecule generation, through lead optimisation, to advanced molecular dynamics simulations on the optimised molecules, Molecule GEN enables a more intelligent, collaborative, and agile approach to drug discovery, redefining how discovery teams across the globe collaborate and innovate.

Breaking Silos: Unified Collaboration Across Disciplines

Drug discovery has long suffered from fragmented workflows. Molecule GEN is engineered to bring together domain experts in biology, medicinal chemistry, and AI into one seamless digital environment. No more tool-hopping, data handovers, or version conflicts. Teams collaborate in real-time, reviewing the same molecule, sharing annotations, and running analysis workflows, all without switching platforms.

• Biologists can upload targets, annotate biological pathways, and explore binding sites visually using intuitive structural overlays. Their biological hypotheses can be directly integrated into downstream chemistry and AI design steps, reducing ambiguity and accelerating feedback loops.
  
  
• Medicinal Chemists can draw, refine, and manipulate molecular structures using smart chemistry-aware editors like MolBench. They can also receive suggestions from CoPilot to rapidly iterate on leads, helping translate biological insights into chemically viable compounds.
  
  
• AI Researchers can generate novel compounds, test hypotheses using machine learning models, and seamlessly integrate their outputs with experimental workflows, making the traditionally abstract world of algorithms more actionable for the entire team.

• Computational Chemists can perform molecular dynamics simulations and binding free energy calculations for in silico validation of AI-generated and expert-designed molecules, ensuring a higher probability of success in subsequent in vitro and in vivo tests. 

This unified design ensures that insights flow instantly between disciplines, enabling rapid iteration, richer candidate profiling, and more informed decision-making. Alignment between teams now takes minutes instead of days.

Integrated Workflows: From Idea to Optimised Lead

Molecule GEN offers an end-to-end discovery pipeline that guides users from concept to candidate, utilising tightly integrated workflows. Each module is purpose-built and interoperable, ensuring seamless transitions from one phase to the next. No data reformatting, no exports, just uninterrupted scientific progression.

De Novo Design with (MAIMol)

At the heart of Molecule GEN lies MAIMol, a proprietary generative AI engine that creates entirely new molecular structures tuned to specific biological targets. MAIMol is trained on vast datasets of chemical structures, bioactivity profiles, and synthetic accessibility data. It enables researchers to generate molecules with:

• High binding potential to user-defined targets
  
  
• Favourable drug-likeness scores (QED)
  
  
• Low synthetic complexity (SA)
  
  

This allows researchers to intelligently explore chemical space and generate candidates with a balance of novelty, feasibility, and relevance. Unlike traditional hit identification, where discovery often relies on brute-force screening, MAIMol helps you start closer to the finish line.

Virtual Screening with (Ranker)

Once molecules are generated, Ranker steps in. This GPU-accelerated engine performs:

• High-throughput docking simulations to assess how molecules bind to their targets
  
  
• ADMET filtering to flag liabilities related to toxicity, permeability, or metabolic instability
  
  
• Non-covalent interaction (NCI) analysis to understand critical binding interactions
  
  

Ranker helps shrink the chemical universe down to a few meaningful options. It provides scoring, sorting, and annotation tools to help users quickly prioritise leads for further refinement. For many teams, this phase previously required multiple weeks of manual work across platforms. Now it’s embedded and instant.

ADMET Profiling with (ADMET Pro)

ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling remains a cornerstone of drug development. ADMET Pro brings this evaluation earlier into the pipeline using AI-based predictions of:

• Oral absorption and bioavailability
  
  
• Tissue distribution (including BBB penetration)
  
  
• Drug-drug interaction risks (e.g., CYP inhibition)
  
  
• Toxicological red flags such as hepatotoxicity, cardiotoxicity, and mutagenicity
  
  

With easy-to-navigate visual dashboards and benchmarking against known drug profiles, teams can make confident early decisions. This reduces the likelihood of investing in candidates that will later fail due to poor pharmacokinetics or safety issues.

Lead Optimisation: Tools for Systematic Refinement

Molecule GEN’s lead optimisation suite provides the tools to transition from a hit to a clinical candidate, all within one environment.

• SubstituteR automates R-group substitutions, helping explore structure-activity relationships (SAR) rapidly and systematically.
  
  
• BioSwap allows fragment replacement guided by bioisosteric principles. This helps maintain activity while improving physicochemical properties or IP space.
  
  
• Hopper enables scaffold hopping to explore new backbones with similar biological profiles, opening new chemical series and reducing risks related to resistance or patentability.
  
  
• Leader applies structural refinements aimed at boosting metrics like solubility, permeability, and synthetic feasibility.
  
  

Together, these tools ensure that every lead has been shaped by science, guided by data, and refined for success.

Built for Experts and Newcomers Alike

A major strength of Molecule GEN is its usability. Whether you’re a seasoned computational chemist or a bench scientist exploring AI-powered design for the first time, the platform adapts to your comfort level and expertise.

MolBench: Chemistry Made Simple

MolBench allows users to:

• Sketch molecules with built-in chemical intelligence
  
  
• Convert between formats like SMILES, InChI, and 3D coordinate files
  
  
• Receive real-time feedback on docking scores, QED, and SA
  
  
• Overlay molecules on binding sites for context-rich design
  
  
• Track and compare multiple versions of a molecule through the workflow
  
  

It reduces time spent jumping between tools and empowers chemists to make decisions within a single environment.

CoPilot: AI-Powered Design for Everyone

CoPilot lets anyone design better molecules using natural language. Just type your objective, like “reduce toxicity,” “increase BBB penetration,” or “enhance potency for kinase inhibition”, and CoPilot returns multiple improved variants.

Each suggestion comes with:

• Rationale for the structural changes
  
  
• Visual comparisons of key parameters
  
  
• Downloadable reports for team review or documentation
  
  
• Options to forward suggestions directly to optimisation or screening
  
  

By lowering the technical barrier, CoPilot allows more diverse team members to contribute meaningfully to molecular design decisions.

Molecular Dynamics for Everyone: LodeStar

Molecular dynamics (MD) simulations have long been confined to experts with advanced computational skills. LodeStar changes that.

With its intuitive UI and GPU-powered backend, LodeStar lets researchers run high-fidelity MD simulations, calculate binding free energies (MM-GBSA / MM-PBSA), and analyse detailed ligand interactions—no scripting required. This democratisation of MD enables routine use in hit validation and lead refinement, helping teams make better, earlier decisions.

Don’t be fooled by the simplicity and accessibility of LodeStar—this is not just another box to check in your molecular dynamics (MD) toolkit. Beneath its user-friendly interface lies a powerful engine capable of executing Relative Binding Free Energy (RBFE) protocols—one of the most advanced and accurate methods for predicting ligand binding affinities in drug discovery today.

Thus, LodeStar is truly a trailblazing platform that brings state-of-the-art computational chemistry within reach of both experts and newcomers alike, accelerating insights without compromising scientific rigour.  

SaaS Simplicity, Enterprise-Grade Power

Molecule GEN is cloud-native, meaning no installation or local infrastructure is required. It’s accessible from anywhere, scales automatically with your needs, and delivers robust enterprise security.

Key benefits include:

• Zero setup time: Start immediately from any browser
  
  
• Elastic compute: GPU-heavy tasks run in parallel and scale with demand
  
  
• Secure architecture: End-to-end encryption, audit trails, and role-based access
  
  
• Global collaboration: Invite collaborators, annotate in real-time, and work asynchronously or together
  
  

Whether you're a growing biotech or a multinational pharmaceutical company, Molecule GEN offers a flexible, compliant, and efficient way to empower your discovery teams.

Why It Matters

Traditional drug discovery is a funnel: thousands of compounds are filtered down over years of experimentation, and most fail. This process is long, expensive, and full of uncertainty.

Molecule GEN turns that model on its head.

Instead of mass-screening blindly, it enables:

• Smart generation of candidate molecules using AI
  
  
• Continuous filtering with predictive modelling
  
  
• Instant iteration through embedded design tools
  
  
• Collaborative workflows that reduce back-and-forth
  
  

With Molecule GEN, teams move from hypothesis to hit in a matter of days, not months, while reducing costs and increasing confidence at every stage.

The Bottom Line

Molecule GEN isn’t just a tool; it’s a transformation in how discovery happens.

By enabling seamless collaboration between biology, chemistry, and AI, integrating every phase of the early discovery process, and eliminating infrastructure headaches through a SaaS-first approach, Molecule GEN helps organisations accelerate and improve their path from concept to clinic.

As discovery timelines shrink and therapeutic targets become more complex, platforms like Molecule GEN are essential to staying competitive. It empowers your team to design smarter, move faster, and work together more effectively—paving the way for tomorrow’s breakthroughs in medicine.