July Product Updates: Faster Conformer Searches, Protein-Ligand Preparation, F-SAPT Enhancements, & More

We are announcing several powerful new features in Promethium. These updates are designed to enhance your workflow efficiency and applicability, improve data visualization, and streamline your overall user experience.

What’s New:

1. Faster Conformer Searches: Optimization of the semi-empirical (ANI) filtering stage resulting in speedups of up to 10x
2. Protein-ligand Cutout and Preparation: Create a cutout of the protein binding site with the bound ligand for use in any Promethium workflow
3. F-SAPT Enhancements: Visualize F-SAPT order-2 pairwise interactions and view numerical order-2 data in a table
4. Memory Estimation for Additional Workflows: Estimate the required GPU memory for Geometry Optimization and F-SAPT workflows via the API
5. Download Data from Result Tables and Plots in an Excel spreadsheet: Easily download data directly in an excel spreadsheet format
6. Design and Functionality Enhancements: Redesigned navigation bar, newly added workflow input form navigation, and ability to delete submitted workflows via the GUI

1. Faster Conformer Searches

Our latest update to the Conformer Search workflow delivers significant optimizations, resulting in up to a 10x speedup for the semi-empirical (ANI) filtering stage. This enhancement allows users to conduct conformer searches more efficiently, significantly reducing computational time while maintaining accuracy.

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An internal benchmark using pharmaceutical small molecules demonstrates that the semi-empirical filtering stage now completes in a fraction of the time—showing improvements ranging from 2.5x to 10x faster, depending on the molecule.

Don’t just take our word for it—try the new and improved Conformer Search workflow for yourself!

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2. Protein-ligand Cutout and Preparation

Our new Protein-ligand Cutout and Preparation tool allows you to easily create a cutout of the protein binding site with the bound ligand, based either on distance from the ligand or a target number of atoms in the prepared system. The tool can be found under the "Tools" header in the top navigation bar.

The prepared cutout can be seamlessly integrated into any relevant Promethium workflow. Whether you want to use a constrained Geometry Optimization workflow to relax a cutout of the protein-ligand complex or simulate a reaction using the Reactant-Product Transition State Optimization, this tool ensures that you start with the right input structure(s).

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3. F-SAPT Enhancements

We have significantly enhanced the functional group symmetry-adapted perturbation theory (F-SAPT) workflow. You can now visualize order-2 pairwise interactions and see the interaction energy value for each fragment by hovering over any atom in the fragment, providing deeper insights into intermolecular interactions. Additionally, energy totals for the selected fragments are displayed above each visualization and all numerical order-2 data can be viewed in a table format, allowing for easier analysis and interpretation of interaction energies. These enhancements will enable more detailed and accurate studies of molecular interactions.

4. Memory Estimation for Additional Workflows

We have extended our memory estimation capabilities via the API to include the Geometry Optimization and F-SAPT workflows. This feature allows you to predict the memory requirements of your computations prior to workflow submission, ensuring that your configuration does not exceed the available GPU memory—avoiding unexpected workflow failures.

To read more, see the Memory Estimation endpoint in our API documentation: https://app.promethium.qcware.com/docs/api/#tag/Workflows/operation/estimate_workflow_memory 

5. Download Data From Result Tables and Plots in an Excel Spreadsheet

We understand the importance of data accessibility and flexibility. With our new download feature, you can now download data from a result table and the underlying data in a plot directly in an Excel spreadsheet format. This functionality allows you to easily share your findings, perform further analysis, and integrate Promethium data with other tools and workflows.

6. Design and Functionality Enhancements

We have made several improvements to the design and functionality of the Promethium interface:

• Redesigned Navigation Bar: A more intuitive and user-friendly navigation bar to help you find what you need faster.
• New Workflow Input Form Navigation: Enhanced navigation within workflow input forms to streamline the setup process.
• Ability to Delete Submitted Workflows via GUI: You can now delete submitted workflows directly from the Graphical User Interface (GUI), giving you more control over your workflow management.

These updates represent our ongoing commitment to providing you with the best tools for your research. We believe these new features will enhance your productivity.

We look forward to hearing about your experiences with these new features and how they are helping you achieve your research goals.

Happy computing!