molxplore Archives - Pharmacelera | Pushing the limits of computational chemistry

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.

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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!

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