July 2025

This is the third issue of our new monthly newsletter, designed to keep you up to date on the latest SAMSON developments, new features, collaborations, and upcoming events.

Learn Boltz-2 in under five minutes

Boltz-2 is now available in SAMSON, and a new video tutorial explains how to use it, how to share job results with colleagues, and how to generate protein-ligand interaction diagrams - all in under five minutes.

Extensions updates

Enhanced Features

Many SAMSON extensions were updated this month:

• Biomolecular Structure Prediction: besides now supporting the Boltz-2 model, the different services feature enhanced input validation (including CCD codes via RCSB), and easy chain selection.

  

• Interaction designer: View protein segments for residues in binding sites, enhancing clarity and analysis.

  

• Batch Protein Prepare: Now supports entire folders of structural files (PDB, PDBx/mmCIF, MMTF, MOL2).

• Martinize: Integrated vermouth-martinize updated to v0.14.0.
• OpenMM Wizard: Updated to OpenMM v8.3.1, including CHARMM36 2024 and new water models.
• Adenita: New CanDo format exporter and standardized nucleic acid residue naming.
• ARAP Interpolator: Enhanced exporting, now includes the entire interpolation path in a single PDB file.
• Fetch / Protein Structure Downloader: Supports extended PDB codes and offers a streamlined user interface.
• 3D-SNFG visualization for glycans: Consistent shape sizing improvements.
• Default visual preset enhancements: Quick-access node groups for ligands, water, ions, DNA, RNA, lipids, and glycans are now created automatically, with improved glycan visualization.

Bug Fixes

We've resolved issues across several extensions including Python Scripting, AutoDock Vina Extended, Adenita, SMILES Manager, and ARAP Interpolator ensuring smoother performance.

Documentation Updates

Updated tutorials available:

• Protein alignment
• Generate a transition path between protein structures with ARAP interpolation
• Create molecular boxes with Molecular Box Builder
• Build custom polymers with Polymer Builder

Explore more on our Tutorials Page.

Webinar Recording

Missed our Summer webinar introducing SAMSON 2025 R1 and R2? Watch it on YouTube .

Upcoming events

Stephane Redon, CEO of OneAngstrom, will be present at the ACS Fall Meeting in Washington, DC (August 17-21, 2025). To discuss how SAMSON can help you integrate all your resources and streamline your molecular design workflows, you can schedule a chat with him.

Coming Soon: SAMSON 2025 R3

We're preparing SAMSON 2025 R3! Your feedback is vital - let us know your feature requests.

Thank you for being part of our growing community!