exascreen Archives - Pharmacelera | Pushing the limits of computational chemistry

VAST Novel Chemical Space Integrated with exaScreen® to Leverage 3D Ultra-Large Chemical Spaces

Enric Herrero — Mon, 27 Apr 2026 12:59:23 +0000

Barcelona, Spain, and Cambridge, United States – April 28^th – Pharmacelera, the leading provider of advanced computational tools for drug discovery, and XtalPi, a pioneering Drug Discovery powered by AI and Automation, today announced the launch of a powerful new joint solution that integrates the XtalPi’s VAST^TMlibrary with Pharmacelera’s flagship virtual screening platform, exaScreen^®. This launch will provide researchers with unprecedented access to synthetically tractable chemical space combined with cutting-edge 3D computational methods for hit and lead discovery.

As the pharmaceutical industry increasingly turns to ultra-large libraries to identify novel hits, the challenge lies in navigating chemical diversity accurately while ensuring synthetic feasibility. The new joint solution directly addresses this challenge by combining Pharmacelera’s advanced Quantum-Mechanics-based tools with the XtalPi VAST^TM chemical space, a curated collection of chemically diverse and highly synthesizable compounds.

With this launch, researchers can:

Conduct accurate and efficient virtual screening across the VAST^TM library either through the licensing of the technology or through service projects
Rapidly source and synthesize compounds for experimental validation.
Expand opportunities to generate novel Intellectual Property (IP) through VAST^TM chemical space and custom follow-up synthesis
Streamline the path from virtual prediction to real-world testing.

“The integration of the VAST chemical space into exaScreen® represents a major step forward for researchers. Together with Pharmacelera, we are enabling scientists to move seamlessly from computational insights to physical compounds with unmatched efficiency.”

Peiyu Zhang, Chief Science Officer of XtalPi

“This launch is fully aligned with Pharmacelera’s mission to push the boundaries of computational drug discovery.”

Rémy Hoffmann, Chief Business Development Officer at Pharmacelera

“We are thrilled to collaborate with XtalPi to apply our accurate QM- and ML-based algorithms to the VAST chemical Space, giving researchers access to a truly tractable and innovative chemical space.”

Enric Gibert, CEO of Pharmacelera

About XtalPi

XtalPi is an innovative technology platform company powered by artificial intelligence (Al) and robotics. Founded in 2015 on the MIT campus, XtalPi is dedicated to driving intelligent and digital transformation in the Life Sciences and new materials industries. With tightly interwoven quantum physics, Al, cloud computing, and large-scale clusters of robotic workstations, XtalPi offers a range of technology solutions, services, and products to accelerate and empower innovation for biopharmaceutical and new materials companies worldwide.

About Pharmacelera

Pharmacelera is a deep-tech science-first company founded by experienced drug hunters, high-performance computing engineers, and leading academic researchers. The company has developed a proprietary in-silico platform that integrates accurate 3D Quantum-Mechanics (QM) models with advanced Artificial Intelligence (AI) algorithms to design novel, diverse, and high-quality molecules from ultra-large and previously untapped chemical spaces. Pharmacelera solutions provide access to its cutting-edge technology for HitID, H2L and LO. Founded in 2015 and with offices in Barcelona and Boston, Pharmacelera collaborates with leading pharmaceutical and biotech organizations across Europe and the United States.

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New JCIM paper about ultralarge chemical space exploration

Enric Herrero — Wed, 11 Jun 2025 12:37:30 +0000

Enric Herrero

Chief Technology Officer

In our latest paper published in the Journal of Chemical Information and Modeling (JCIM) by the American Chemical Society, we introduce two innovative methods for exploring ultra-large chemical libraries using accurate 3D quantum mechanics-based descriptors.

The rapid expansion of ultra-large chemical libraries has revolutionized drug discovery, providing access to billions of compounds. However, this growth poses relevant challenges for traditional virtual screening (VS) methods. To address these limitations, synthon-based approaches have emerged as scalable alternatives, exploiting combinatorial chemistry principles to prioritize building blocks over enumerated molecules.

With current library sizes, synthon-based approaches have 100k times lower computational cost than brute force methods. Since chemical spaces are growing rapidly and synthon-based methods scale better, this gap will continuously grow.

In this work, we present exaScreen and exaDock, two novel synthon-based methodologies designed for ligand-based and structure-based VS, respectively.

exaScreen: Our 3D ligand-based tool for virtual screening exploits atomic descriptors to select the optimal synthons through similarity measurements of the 3D molecular fields generated by the synthons and the reference fragment. For the set of reference compounds considered, the overall accuracy of exaScreen compares with the results obtained with brute force, as noted in the similar recovery of actives and the significant degree of identity between the actives selected by the two methods but at a significantly lower computational cost. exaScreen explores 70 billion compounds in less than 7 hours in a single workstation and requires less than 6 GB of disk storage.

exaDock: Our new structure-based method for ultra-large libraries exploits a restrained docking to explore hybrid compounds (fragment reference + synthon) recurrently for the distinct reference fragments, which ultimately leads to the selection of the optimal synthon-based compounds built from the best ranked synthons identified for the reference fragments. The exaDock methodology can perform a search of EnamineREAL with a 50K lower computational cost than brute force.

We evaluated both approaches across 11 diverse biological targets, including kinases and GPCRs. We show that exaScreen and exaDock achieve recovery rates comparable to brute-force screening strategies, offering computationally efficient strategies for VS in ultra-large chemical spaces using accurate 3D descriptors.

One particularly interesting observation is the difference in scaffold overlap between our proposed methods and brute-force methods. In ligand-based, there is a significant overlap among the recovered active scaffolds while, in structure-based, the overlap is lower. This difference is explained by the influence of the geometrical and physicochemical properties of the binding site, particularly to the compactness of the pocket and to the solvent exposure of the reference fragments.

Join our webinar

If you are interested in knowing more, register to our joint webinar with Enamine on June 19th at 4PM CET, 10AM ET!

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New release out – 2025.01

Enric Herrero — Mon, 10 Feb 2025 10:40:07 +0000

We’re excited to announce the release of Pharmacelera’s 2025.01 software update!

What’s New in 2025.01?

🔹 Custom Ultra-Large Library Generation – The new exaScreen®-intra add-on allows you to generate exaScreen®-compatible libraries from your own internal Building Blocks and chemical reactions.

🔹 Advanced Filtering Options – PharmScreen® now supports enhanced substructure pattern matching, enabling more precise compound searches.

🔹 Boosted Performance & Scalability – Both PharmScreen® and exaScreen® now support processors with hundreds of threads, delivering significantly faster results.

🔹 Updated Screening Libraries – Our latest screening libraries now include:

Enamine Screening Collection
Molport
Enamine REAL Space (now featuring 70 billion compounds, screenable in under 7 hours, using less than 6 GB of storage).

🔹 Expanded File Format Support – Molecular field projections and QSAR model coefficients can now be exported in DX and GRD formats, ensuring compatibility with a wider range of visualizers.

🔹 PharmQSAR® Integration in MolXplore – You can now visualize PharmQSAR® models directly in MolXplore, making SAR analysis of QSAR coefficients more intuitive.

Request your license

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Hit identification for CCR2 using ultra-large virtual screening and FEP

Fernando Martín — Wed, 26 Jun 2024 13:18:21 +0000

Barcelona, Leiden and Uppsala, July 2nd 2024 – Pharmacelera, the leading provider of computational tools for hit discovery, the Leiden Academic Center for Drug Research (LACDR) at Leiden University and MODSIM Pharma AB, the leading provider of physics-based biomolecular simulations tools, have announce the collaboration on a common project for the identification of new bio-active chemical entities for the C-C chemokine type 2 receptor (CCR2).

The project implies the combination of Computer-Aided Drug Design software with experimental validation and is performed in a sequential manner. The first stage consists in the identification of novel and diverse hits using exaScreen®, Pharmacelera proprietary technology, to perform a virtual screening of the Enamine REAL Space (48 billion compounds) based on 3D interaction fields derived from Quantum-Mechanics (QM) calculations. Selected candidates will be experimentally validated at the LACDR in a radioligand binding assay. Using this information, MODSIM Pharma will apply its proprietary Free Energy Perturbation (FEP) technology to optimize, prioritize and propose novel compounds that will be experimentally validated.

The research is part of the master’s project of Donald van Pinxteren, who will carry out the execution and analysis of the results obtained in the screening and FEP methods.

Working synergistically on this project reinforces the collaboration between Pharmacelera and MODSIM, and clearly highlight that integrated resources, expertise, and capabilities are key for speeding up drug discovery projects.

About Pharmacelera

Pharmacelera develops advanced computational tools for the discovery of novel hits using accurate Quantum-Mechanics (QM), Artificial Intelligence (AI), and High-Performance Computing (HPC). The company’s products PharmScreen®, exaScreen® and PharmQSAR® use 3D molecular descriptors derived from Quantum-Mechanics (QM) calculations to mine an unexplored chemical space and to identify hits uncovered by traditional algorithms. Pharmacelera is a private company founded in 2015 and based in Barcelona, Spain. The company works with several big pharma and biotech organizations across Europe and the United States.

About MODSIM Pharma AB

MODSIM Pharma develops computational software and pipelines to increase the performance of structure-based drug discovery. The company has developed highly computationally efficient Free Energy Perturbation simulations protocols adapted for high-performance computing (HPC). The QresFEP module allows for systematic in-silico mutagenesis applicable to assess site-directed mutagenesis experiments or protein stability studies. With QligFEP, MODSIM Pharma can perform ligand optimization, scaffold hopping, linker length adjustment or postscoring pose ranking, based on accurate and systematic FEP simulations of ligand series. Initially focused on G protein-coupled receptors (GPCRs), the company has recently evolved the GPCR-Modsim web server, a one-stop shop for the 3D modeling and molecular dynamics (MD) simulations of GPCRs, into a generic membrane protein modeling and simulation package optimized for HPC.

MODSIM Pharma is a private company founded in 2018 and based in Uppsala, Sweden. The company offers the optimized combination of either module to address problems related to target characterization of structure-based ligand optimization and has agreements or contracts with different biotech and pharma companies.

About LACDR

The Leiden Academic Centre for Drug Research (LACDR) is a centre of excellence for multidisciplinary research on drug discovery and development. Despite major advances in medicine- research, many common diseases such as cancers, neurological or cardiovascular diseases, or auto-immune diseases, still lack effective treatment, or are still often found incurable. That is why our work to develop new and more effective drugs is essential. At the LACDR we work at the leading edge of drug-design and fundamental research of new drugs, optimization of existing drugs, and personalised medicine.

Media Contacts

Pharmacelera

Rémy Hoffmann, CBDO (remy.hoffmann@pharmacelera.com)

MODSIM Pharma

Hugo Gutiérrez de Terán, CEO (hugo@modsim-pharma.com)

University of Leiden

Willem Jespers, Assistant Professor (w.jespers@lacdr.leidenuniv.nl)

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Pharmacelera extends the current partnership with Enamine for the screening of ultra-large chemical libraries

Fernando Martín — Tue, 07 May 2024 08:06:19 +0000

Barcelona, Spain, and Kyiv, Ukraine, 07 May 2024. Pharmacelera, the leading provider of computational tools for hit discovery, and Enamine, the developer of the world’s largest and most reputable virtual space: REAL, have announced the extension of their current partnership to explore an extraordinary magnitude of compounds, that has been extended by a 10 fold factor – when compared to the early version -. Ultra-large chemical libraries constitute a key paradigm to tap into new and still unexplored chemical spaces, increasing the probability for the researcher to find new and chemically diverse potent hits for Discovery Programs. Efficient handling of the ultra-large compound libraries still remains the main challenge.

In 2022, Pharmacelera and Enamine started their collaboration with the plug-in of Enamine Real Database – over 165 well-validated parallel synthesis protocols applied to over 138,000 qualified reagents and building blocks at this stage- to the new version of Pharmacelera’s virtual screening flagship tool. The resulting software product was named exaScreen® . exaScreen® is harnessing the power of Artificial Intelligence (AI) and Quantum-Mechanics (QM) algorithms. The success of this initial phase prompted both partners to create an efficient approach to give their customers an access to more REAL Compounds to find new diverse starting points for drug discovery by allowing the screening of Enamine’s REAL Space consisting today of 48 billion compounds. The resulting hits can be synthesized by Enamine within only a 3-4 weeks period with an 80% success rate. More analogues for hit follow-up activities are accessible for Pharmacelera’s customers,with Enamine offering an access to several trillions of REAL Compounds, and an even of make-on-demand (“MADE”) Building Blocks.

As part of this extended partnership, Enamine will receive a license to use exaScreen® for their internal library research work.

“Screening of ultra-large virtual chemical libraries has shown to be a powerful approach that can give a quick access to potent IP-free hits for a wide variety of targets. We are really delighted to count on Pharmacelera among our armada of talented deep -tech partners, and to extend our current collaboration with Pharmacelera to use their exaScreen® technology to extract the needles from our exciting expandable 3D space environment, but also being glad to use it in-house for our own screening library development work.», said Michael Bossert, Head of Strategic Alliances at Enamine.

“This agreement is fully aligned with Pharmacelera’s strategy to work with leading institutions in the field of Drug Discovery that have complementary technology and expertise”, says Rémy Hoffmann, Chief Business Development Officer at Pharmacelera. “We are thrilled to expand the current collaboration started on December 2022 with Enamine, the prominent compound provider, to apply our accurate Quantum-Mechanics (QM) and Machine Learning (ML) algorithms to mine the Enamine’s REAL Space and deliver synthesizable compounds that can be further evaluated in biological assays”, said Enric Gibert, Pharmacelera’s CEO.

About Enamine

Enamine is a scientifically driven integrated discovery Contract Research Organisation with unique partnering opportunities in exploring new chemical space. The company combines access to the inhouse produced screening compounds (4.2M in stock) and building blocks (300K in stock) with a comprehensive platform of integrated discovery services to advance and accelerate the efforts in Drug Discovery. For more information visit: https://enamine.net

About Enamine REAL Space

Enamine REAL Space contains 48 billion make-on-demand molecules that can be synthesized at Enamine extremely fast (3-4 weeks), with high feasibility (over 80%), and inexpensive. The REAL compounds are created by parallel chemistry through the compilation of 424,490 building blocks via more than 164 well-validated parallel synthesis protocols, underlying Enamine’s approach to design make-on-demand compounds to maximize synthesis success rate.

About Pharmacelera

Pharmacelera develops advanced computational tools for the discovery of novel hits using accurate Quantum-Mechanics (QM), Artificial Intelligence (AI), and High-Performance Computing (HPC). The company’s products PharmScreen®, exaScreen® and PharmQSAR® use 3D molecular descriptors derived from Quantum-Mechanics (QM) calculations to mine an unexplored chemical space and to identify diverse hits uncovered by traditional algorithms. Pharmacelera is a private company founded in 2015 and based in Barcelona, Spain. The company works with several big pharma and biotech organizations across Europe and the United States.

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Access to Pharmacelera technologies

Fernando Martín — Wed, 07 Feb 2024 12:24:05 +0000

Fernando Martin

Pre & Post Sales Manager

The technology behind a software is important, but so is how to access it. The user interface (UI) allows users to effectively interact with the software and take advantage of the technology behind it. That’s why it’s important to provide users with user-friendly, powerful and intuitive UIs.

Each user is unique and has different needs, both in terms of preferences and the resources available to them. It is therefore important to offer different methods to suit those needs. In this article we will discuss the different ways to access Pharmacelera technologies.

Command-line Interface (CLI)

The CLI is probably one of the most widespread ways to interact with PharmScreen, exaScreen and PharmQSAR. This is the preferred option when using Linux operating systems through terminal applications, having access to all software functionalities. For other operating systems, you can take advantage of the Application Programming Interface (see below). Some of the features of the CLI are:I

It is a versatile way to interact PharmScreen, exaScreen and PharmQSAR with the system environment, having good control over the execution process.
You can leverage programming languages such as Bash or Python to automate certain processes (e.g., running several virtual screening campaigns at once).
You need fewer hardware resources: Graphical environments require more hardware resources for molecular visualization.
It allows you to connect to external resources such as other workstations, high performance computing (HPC) clusters, where there are usually no graphical interfaces.
You can run graphical applications, such as MolXplore, to analyze screening results.

Application Programming Interface (API)

The API is another way to interact with our software. The API will allow you to run our tools on any OS, thanks to its integration with Docker. Some of the API features are:

The ability to run Pharmacelera technologies on any operating system.
To use simple configuration files to run your screening campaigns.
To run your computations on external workstations, HPC clusters or cloud services, such as Amazon Web Services (AWS).

MolXplore

MolXplore is our GUI for analyzing the results obtained by our technologies. This tool, compatible with any operating system or accessible via web browser, provides a modern and intuitive environment to have a deeper understanding of your screening results, helping you to select the right compounds for later phases.

You can find the features and options of MolXplore in this post.

Knime nodes

The Knime platform is a graphical solution to build workflows that can help you analyze your data. The Pharmacelera extension (PharmScreen and exaScreen nodes) can easily connect to chemoinformatics nodes to run and analyze your virtual screening campaigns, connecting the results to other nodes for further analysis.

Some of the features of the Pharmacelera nodes developed for Knime are:

An intuitive graphical user interface for setting up and running a virtual screening campaign using PharmScreen or exaScreen.
The nodes use the Pharmacelera API, which means you can use Knime nodes on any operating system and run your screenings locally or on a remote cluster.
You can reuse existing workflows created by Pharmacelera or the Knime community, making it easier to analyze your data.

Want to learn more?

If you would like to evaluate how our software can help you in your drug discovery projects or are looking for more customized services, please do not hesitate to contact us. We will provide you with personalized assistance so that you can find the best solution for your research.

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New Graphical User Interface: MolXplore

Fernando Martín — Thu, 11 Jan 2024 10:15:03 +0000

Fernando Martin

Pre & Post Sales Manager

For some computational and medicinal chemists, a good graphical user interface (GUI) is essential. It makes it easier to analyze, understand and draw conclusions from results. And that is what MolXplore is: a novel and modern GUI that helps scientists visualize the potential compound candidates of a virtual screening campaign, analyze the results using the different options available, and draw the right conclusions about which compounds should be prioritized for further analysis, such as performing a docking campaign or directly purchasing the molecules for in vitro assays.

In this first version of MolXplore, scientists will be able to analyse the results of PharmScreen, our 3D ligand-based virtual screening software, by loading the results and analysing them according to different options, such as evaluating the similarity of the candidates with respect to the reference molecule, superimposing the molecular fields and the chemical structures, or filtering the compounds according to different physicochemical properties, …

Many ways to analyze your data

There are many ways to interact with your results in MolXplore:

Molecular viewer: Here you can evaluate different properties of your compounds, such as the molecular fields for 7 different properties, different physicochemical descriptors, the 2D representation of the molecule or overlay your compounds on the reference molecule. You will find different ways to represent your compounds, such as line, sticks or ball & stick.

Data table: This feature allows you to select, sort and filter the screened compounds based on various physicochemical properties. The table is synchronized with the molecular viewer to help you to make better decisions when selecting a compound as a candidate. The table also allows you also to group your compounds and download them in a single file.

Property plot: The plot feature will help you to gain a deeper understanding of your compounds, plotting two different properties at the same time, helping to understand, for example, how your compounds may cluster based on two different selected properties. The plot feature is synchronized with the data table as well as the viewer, completing the list of tools for extracting conclusions from your screening.

The GUI is compatible with Linux and Windows, so you can analyze the results from any computer. MolXplore is included in your PharmScreen license. Request your license now!

Request your license

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New Pharmacelera nodes for KNIME

Fernando Martín — Wed, 13 Dec 2023 13:58:39 +0000

Fernando Martin

Pre & Post Sales Manager

We are pleased to announce a new update of our Pharmacelera KNIME nodes. Access to our tools is enhanced with the update of our nodes, making them easier to use for scientists who are familiar with KNIME and for first-time users. Not only have we adapted our tools to the latest versions of KNIME, but we have also provided them with new functionalities compared to previous versions.

What's new?

Let’s take a look at some of the new features:

The nodes have been configured so they can always use the latest version of PharmScreen and exaScreen.
The exaScreen node is now available! Our latest technology for huge chemical library screening is now available in KNIME, which mean that you can know mine efficiently billions of compounds, obtaining a list of synthesizable and purchasable compounds that can be further analyzed with your preferred cheminformatics workflow.

The nodes are now compatible with the Pharmacelera API. This option allows you to run your calculations in your own computer, no matter if it is running Linux, Windows or Mac.
Need more computer power? An additional feature that comes with the Pharmacelera API is the possibility to run your calculations on an external computer (workstation or cluster), adding the possibility to access to HPC resources.
New design for node configuration. KNIME is changing its interface to Modern UI. And our nodes too. This new interface allows to group the configuration elements, so you can easily identify the different options of the node.

Compatibility with the latest version of KNIME: The latest version is 5.2, so we have made our nodes compatible with it. However, we understand that many users may be using 4.7, so we will maintain compatibility with this version, although we encourage migration.
The nodes are accompanied by new components that facilitate the configuration of the input data, like the exaScreen configuration, helping you to load your files and select where to cut your reference molecule.

Third party nodes are evolving constantly, so we have reviewed our previous workflows and updated them, including new ones.

Try them now!

Want to try the new Pharmacelera nodes? Write us to contact@pharmacelera.com or fill in the form and ask for your license!

KNIME is an open-source platform built to productionize data science from day 1 by a team with a strong scientific background. Today it has a strong user community of 300,000+ across all industries and in over 60 countries.

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General Inception and Pharmacelera Partner to Advance Drug Discovery with Exponential Screening Capabilities

Fernando Martín — Tue, 09 May 2023 14:27:06 +0000

3D quantum-mechanics, molecular descriptors, and artificial intelligence provide unique capabilities in the chemical space to identify and qualify novel hits

PALO ALTO, Calif and BARCELONA, Spain: General Inception (GI), a global company Igniter, and Pharmacelera, a Barcelona-based deep-tech company, announced its partnership to use exaScreen® for novel drug discovery. The platform technology, developed by Pharmacelera, enables exponential screening capabilities of in-silico compound libraries, increasing the exploration of chemical space to identify hits. Traditional technologies can only mine about 10 million diverse molecules versus exaScreen®’s over 30 billion. The collaboration will focus on the application of exaScreen®’s state-of-the-art virtual screening technology for General Inception’s therapeutics companies looking for novel, diverse and synthesizable hits. exaScreen® uses accurate 3D Quantum-Mechanics (QM) molecular descriptors and Artificial Intelligence (AI) to mine efficiently a humongous chemical space and potentially boost the Intellectual Property (IP) of drug discovery projects.

“This is a step forward in our aim to retrieve and discover new chemical matter, which is a fundamental pillar in early drug discovery,” said Dr. Venkat Reddy, Chief Scientific Officer of General Inception. “Pharmacelera has already demonstrated that their proprietary technology is able to identify novel yet feasible scaffolds that are totally missed by traditional screening methodologies. We look forward to applying this technology and believe it will provide a meaning benefit to the drug discovery efforts of our companies.”

“We are very excited to establish this collaboration with General Inception, a fast-growing company Igniter in the United States and Europe,” said Dr. Enric Gibert, Pharmacelera’s CEO. “We appreciate getting in on the ground-floor of collaborations to best leverage the power of exaScreen®. GI’s business model enables us to reach a diverse group of innovative companies at the start of their journey and collaborate with pharma executives to resolve key challenges in drug discovery.”

ABOUT GENERAL INCEPTION

General Inception is pioneering company creation as an Igniter company. General Inception partners with extraordinary scientific founders at the inception of their journey to efficiently translate their groundbreaking innovations into transformational companies that address humanity’s grand challenges. As a business co-founder, GI brings together domain and functional expertise, executive talent, infrastructure and development resources, and capital to ignite, nurture and scale the company journey.

For more information, please visit www.generalinception.com

ABOUT PHARMACELERA

Pharmacelera develops advanced computational tools for the discovery of novel hits using accurate Quantum-Mechanics (QM), Artificial Intelligence (AI) and High-Performance Computing (HPC). The company’s products use 3D molecular descriptors to mine an unexplored chemical space and to identify hits uncovered by traditional algorithms. Pharmacelera is a private company founded in 2015 and based in Barcelona, Spain. The company works with several big pharma and biotech organizations across Europe and the United States.

For more information, please visit www.pharmacelera.com and www.pharmacelera.com/exascreen/

CONTACTS:

General Inception

Rebecca Galler – rebecca.galler@generalinception.com

Pharmacelera

Rémy Hoffmann – remy.hoffmann@pharmacelera.com

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