LigandScout XT Next Generation
All new, yet familiar
Redefining Drug Discovery with AI, Scale & Dynamics
Next Generation Molecular Design
LigandScout XT expands our gold-standard award winning LigandScout 4.5 platform with revolutionary new modalities — from billion-compound virtual screening and covalent inhibitor profiling to AI-driven molecule generation and full molecular dynamics integration.
Building on our award winning 3D-pharmacophore technology LigandScout XT, simulations are done with high precision and unprecedented speed enabling scientists to tackle modern and challenging new approaches in drug discovery with confidence and high efficiency.
.
Ultra-Large VS - Covalent Screening - AI Generative Builder - MD Simulations - Water Thermodynamics
All of that with extreme high performance.
We call that our Next Generation!
Features Overview
LigandScout XT expands the gold standard with project-based workflows, new next generation alignments, next generation clustering, next generation high performance VS for ultra large libraries, next generation MD analysis and water mapping, next generation pharmacophores for PPIs, allosteric apo sites, next generation conformation generation tools for macrocycles.
Extreme high performance.
No need for docking because the ultra fast feature rich pharmacophore partial matching approach can replace slow docking.
This ‘ultra luxury’ platform is for the modeling professional who needs reliability, fast execution for exploratory research (e.g., MD and water mapping to meaningful med chem decisions) to achieve meaningful results rapidly and efficiently for addressing modern modalities.
10⁹
Compounds screened
Ultra-Large Scale Virtual Screening
Screen up to one billion compounds against pharmacophore models. Seamless integration with ultra-large chemical libraries for unprecedented hit-finding power.
GIGASCALE
AI
De novo design
AI Generative Molecule Builder
De novo molecule generation conditioned on pharmacophore models. AI proposes novel scaffolds fitting your 3D feature requirements and ADMET constraints.
AI · DE NOVO
360°
Covalent discovery
Covalent Ligand Virtual Screening
Model warhead reactivity and covalent binding modes. Identify irreversible inhibitor candidates within our pharmacophore screening workflows.
COVALENT
MD Simulations
Dynamics
Easy-to-Set-Up
Launch GPU-accelerated molecular dynamics from LigandScout. Automated force-field assignment and trajectory analysis — one seamless workflow.
MD · GPU
MD+H₂O
MD simulations with water thermodynamics
Water Thermodynamic Mapping
Identify displaceable vs. conserved water sites from MD trajectories using free-energy scores to guide ligand design decisions.
ΔGSOLV
Plus all Features from LigandScout 4.5 Expert
.
AI Generative Molecule Design
LigandScout features and AI Generative Molecule Builder that revolutionizes de novo design by seamlessly integrating the powerful REINVENT reinforcement learning framework with our world-class 3D-pharmacophore technology. By using precise pharmacophoric features as structural checkpoints alongside multi-parameter ADMET constraints, the generative engine intelligently navigates chemical space to output optimized, novel chemotypes.
Molecular Dynamics (MD)
LigandScout XT seamlessly integrated Molecular Dynamics (MD) simulations takes structural biology and molecular design to the next dimension, by breaking down the barriers of setting up complex computational physics and furthermore integrating analysis tools geared for molecular design and virtual screening.
No Technical Barriers - Intuitive and Easy MD Set-up
Powered by the industry-leading, GPU-accelerated OpenMM engine, LigandScout XT transforms what is typically a daunting, command-line-heavy process into a highly intuitive, visual workflow.
With just a few straightforward clicks, users can seamlessly prepare protein-ligand complexes, automatically assign robust force-field parameters, define custom solvation boxes, and deploy high-performance OpenMM simulations without ever writing a single line of code.
Traditionally, setting up rigorous MD simulations required navigating convoluted command-line interfaces, piecing together intricate parameter scripts, and manually defining complex system topologies — a daunting bottleneck that often slowed down rapid drug discovery efforts.
LigandScout XT completely removes this technical barrier by offering an incredibly intuitive, fully GUI-driven experience that democratizes dynamic simulations for medicinal chemists and computational scientists alike.
Integrated Tools and Ultra Fast Simulations
This deeply integrated, user-friendly workflow means that evaluating the temporal stability of a target compound, uncovering cryptic sub-pockets, or observing the dynamic evolution of critical pharmacophore interactions over time is no longer an arduous technical chore and it is ultra fast.
Dynamic Pharmacophores
Beyond simply generating simulations, LigandScout XT revolutionizes how you interpret complex MD trajectory data through its innovative dynamic pharmacophore tools. Analyzing the massive amounts of data generated during an MD run can be overwhelming, but our software streamlines this by automatically extracting and tracking key 3D-pharmacophore interaction features across the entire simulation enabling visualization of buried information such as
- the stability of critical ligand-receptor interactions
- transient but crucial binding events that static crystal structures might miss, and intuitively frequency of interaction patterns.
By bridging the gap between rigorous MD and intuitive advance dynamic pharmacophores LigandScout XT provides actionable, deep-level insights into target flexibility and compound efficacy.
By effortlessly transforming static structural snapshots into fluid, time-resolved dynamic models directly from the interface, LigandScout XT empowers discovery teams to rapidly validate binding modes, refine their in silico SAR, and rigorously de-risk lead candidates prior to synthesis.
LigandScout XT Remote
LigandScout XT Remote unlocks the full power of high-performance computing (HPC) speed integrated in LigandScout XT platform and cloud resources directly from the desktop. Designed to bridge the gap between advanced computational chemistry and user-friendly accessibility, LigandScout Remote seamlessly integrates remote cluster execution into the familiar LigandScout graphical interface. Whether you are screening massive compound databases or performing rapid 3D conformer generation, LigandScout XT Remote transparently handles all data conversion, network communication, and job scheduling behind the scenes. By eliminating the need for command-line expertise and tedious manual file transfers, LigandScout XT Remote empowers researchers to combine the intuitive, day-to-day usability of a local desktop application with the immense processing capabilities of modern HPC environments.
Publications
By now more than 4000 publications have used or cited LigandScout technology in different areas of computer-aided molecular design, starting from hit identification, to hit to lead, and lead optimization up to fragment-based discovery, drug repurposing and target predicton.
For an up-to-date list of publications involving LigandScout, check Google Scholar.
LigandScout XT
Recent Application Publications with LigandScout XT.
- Doijen J, Xie J, Marsili S, Bains T, Mann MK, Abeywickrema P, Van den Broeck N, Permann C, Langer T, Ibis G, Mattelaer CA, Harvey J, van Raalte S, Fino R, Pande V, Peeters D, Patrick A, Van Damme E, van Vlijmen H, Van Loock M, Jacoby E. A New Fragment-Based Pharmacophore Virtual Screening Workflow Identifies Potent Inhibitors of SARS-CoV-2 NSP13 Helicase. J Comput Chem. 2025; 5;46(23): e70201. DOI: 10.1002/jcc.70201.
- Kalaba, P, Perisic Böhm, M, D̵ikić, F, Tomašević, N, Drdla-Schutting, R, Hasinger, S, Ines, DM, Wolf, A, Belil-Catalina, M, Bryant, SD, Spetea, M, Gruber, CW, Muttenthaler, NM and Keimpema, E. Development and Biological Characterization of Fluorescent Dynorphins for the Visualization of Kappa Opioid Receptors. J. Med. Chem. 2026. DOI: 10.1021/acs.jmedchem.5c03072
LigandScout Primary Technology Articles
Inte:Ligand received the Innovation prize for its unique structure-based pharmacophore technology. The following articles describe the methodology and algorithms of Inte:Ligand's structure-based pharmacophore creation tool LigandScout:
- Wolber, G.; Langer, T.; LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters J. Chem. Inf. Model; 2005; 45(1); 160-169. DOI: 10.1021/ci049885e
- Wolber, G.; Dornhofer, A. A.; Langer, T.; Efficient overlay of small organic molecules using 3D pharmacophores J. Comput. Aided Mol. Des.; 2007; 20(12); 773-788. DOI: 10.1007/s10822-006-9078-7
- Kainrad T., Hunold S., Seidel T., Langer T.; LigandScout Remote: A New User-Friendly Interface for HPC and Cloud Resources J. Chem. Inf. Model; 2018. DOI: 10.1021/acs.jcim.8b00716
- Seidel, T., Bryant, S.D., Ibis, G., Poli, G. and Langer, T. (2017). 3D Pharmacophore Modeling Techniques in Computer-Aided Molecular Design Using LigandScout. In Tutorials in Chemoinformatics, A. Varnek (Ed.). DOI: 10.1002/9781119161110.ch20on