Coronavirus: computing the opening motion of the SARS-CoV-2 spike

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In this small article, we provide a brief introduction about the way the SARS coronavirus 2 (SARS-CoV-2) operates, and we provide results of our computations of the motion of its spike from its closed state to its open, receptor-binding state. Introduction The SARS coronavirus 2 (SARS-CoV-2) – the virus that causes the COVID-19 disease – has transmembrane spikes (S proteins on the image below) attached to its lipid membrane. It is because of these spikes – their relatively large number –…

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User guide update

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We know SAMSON’s new open approach to molecular modeling, with its apps, editors, interactive simulation, inspectors, etc. can sometimes be daunting for new users. If you’re feeling this too, you’ll be happy to learn about the user guide update that was released a few days ago. Check it out to learn about inspecting molecules, and so much more, at https://documentation.samson-connect.net/users/latest. Don’t hesitate to share the link! And if you need help, please join us on the forum.

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Analyzing molecular trajectories with MDAnalysis in SAMSON

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MDAnalysis is a well-known Python library for analyzing molecular dynamics trajectories. In this tutorial, we demonstrate how it can be used to analyze trajectories saved in Path nodes in SAMSON and superimpose structures. Analyzing trajectories Let us, for example, compute the radius of gyration and the RMSD for a protein with trajectories saved in Path in SAMSON. To use the functionality of MDAnalysis, we need to export trajectories we would like to analyze from SAMSON into a format supported by…

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SMILES Manager

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Hello everyone, In this post I will present you the new version of the SMILES Manager module that I integrated in the SAMSON platform. It is based on RDKit, an open source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules SMILES strings to a 2D and 3D structures. The module interface presents two tabulations: Manage SMILES and Replace fragments. I will present these two sections one by one as they…

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Building nanotubes models with SAMSON

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In this quick tutorial, you will learn how to easily generate nanotube models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Element that you can find on SAMSON Connect: If you need help with installing new SAMSON Elements to your SAMSON installation, please visit this page. If you need help with installing SAMSON itself, please visit this page. Note: you can check whether you have this SAMSON Element in at least three different ways: In…

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SAMSON 0.7.0 is available on Windows, Linux and Mac!

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We are proud to announce that SAMSON 0.7.0 is now available on Windows, Linux and Mac! SAMSON 0.7.0 has tons of new features and improvements, both in its core and through SAMSON Elements, so here’s an overview. Python scripting Here it is: Python scripting is now available! Most of the SAMSON API is exposed in Python, and a Jupyter console embedded in SAMSON allows you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from…

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Normal Modes Advanced

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Hello all, Welcome to this tutorial, I will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Element. This SAMSON Element computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021 / acs.jctc.7b00197.). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the NMAL module…

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What’s coming up next

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As SAMSON 0.7.0 is approaching, we would like to highlight a few upcoming features that we feel are bringing us a little closer to our vision of a federating platform for computational nanoscience. Python scripting Python scripting is coming to SAMSON 0.7.0, and we are (very) excited about it. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts.…

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