pharmqsar 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.

Request your license

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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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Mid 2021 Summary

Fernando Martín — Tue, 20 Jul 2021 06:31:59 +0000

The summer season has already started and, we would like to share with you what happened in Pharmacelera during the first half of 2021: new customers and collaborations, new team members, PharmWebinars series, technology updates, …

Let’s have a look!

Business News

We successfully finalized services projects with customers located in the US, UK, Germany, Spain, Italy, and Switzerland among others.
The incorporation of Bill Wiersma as Sales Director in North America will strengthen the interactions with US customers. Bill has 30+ years of experience in the scientific software market.
The commercial team is also reinforced by Greta Canovas as CFO. Greta has consolidated experience working with different start-ups.

A whitepaper with Labiotech, gave more detail on our technology and the success stories with two clients located in the UK.
Our PharmWebinars continued with two new sessions:
- For “New Frontiers in CNS”, we were joined by Marco Devivo (IIT), Maria Laura Bolognesi (University of Bologna), and Steve Penrose (Anima Biotech). The webinar was complemented by a Case Study Session presented by Giorgia Zaetta (Pharmacelera).
- “New Approaches in GPCR Drug Design” saw a collaboration between Thijs Beuming (Lantham Biopharm Group), Zara Sands (Confo Therapeutics), and Javier Vazquez (Pharmacelera).

Technology News

PharmScreen 2021.06 release is available! This update includes a faster virtual screening (up to 20%) with multithreaded machines, new modes of alignment, and new features in the SaaS GUI. Have a look to the video and request a trial today!

Three master students joined to Pharmacelera to implement new functionalities and performance improvements in PharmScreen.
New release of PharmQSAR tool with new functionalities like the generation of predictive models and preparation of molecular libraries in a single tool.
Iktos will apply Pharmacelera’s accurate Quantum-Mechanics (QM) hydrophobic molecular 3D descriptors via the software package PharmQSAR to develop Machine Learning (ML) predictors for key molecular properties in de-novo drug discovery.
We have developed an Application Program Interface (API) for PharmScreen and PharmQSAR. This interface will help with the integration of our tools with third-party solutions. This API will be available soon for our clients.

Join us and stay tuned for a the second half of 2021 by following us in LinkedIn!

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