Covalent and non-covalent protein-ligand docking with the Fitted Suite by Molecular Forecaster

In this tutorial, you will learn how to perform covalent and non-covalent protein-ligand docking with the FITTED Suite SAMSON Extension. The FITTED Suite SAMSON Extension was done in partnership with Molecular Forecaster and wraps their Fitted Docking software. FITTED stands for Flexibility Induced Through Targeted Evolutionary Description. This fully automated docking software is unique in that it considers the flexibility of macromolecules, the presence of bridging “displaceable” water molecules, covalent functional groups, and proton shifts upon metal coordination. FITTED is…

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Protein docking with Hex

In this tutorial, you will see how to perform protein docking with Hex SAMSON Extension. The Hex SAMSON Extension wraps the protein docking program Hex developed by Dave Ritchie (Protein Docking Using Case-Based Reasoning. A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). Proteins: Structure, Function, Bioinformatics) Content Requirements First steps Validation of the system Preparation of the system Setup of the system Hex parameters Setup of the search domain Running the docking and more Results Performing further analysis Requirements…

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Docking ligands and libraries of ligands with AutoDock Vina Extended

In this tutorial, you will see how to dock ligands or libraries of ligands into proteins with AutoDock Vina Extended SAMSON Extension and how to visualize and analyze the results. The AutoDock Vina Extended SAMSON Extension wraps the popular protein-ligand docking program AutoDock Vina (O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461) and extends its functionality by providing…

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What’s new in SAMSON 2020 R2

The new SAMSON 2020 R2 release brings further improvements throughout the core of SAMSON: Custom color palettes Cumulative updates since SAMSON 2020 R1, including quick minimization, a new displacer editor, etc. Support for a new type of nodes, meshes, i.e. textured triangular surfaces. A variety of new features and fixes of reported issues. For developers: new functionality in the SAMSON API and a new module that allows you to view the functionality exposed by SAMSON Elements, which you can use in…

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Export atoms trajectories along paths

In this tutorial, we will show how to export atoms positions (for all atoms in the system or for a selection of atoms) along paths in PDB files thanks to the Export Along Paths app. This could be useful for example if you want to generate reaction coordinates for free energy calculations.   Requirements SAMSON version 0.7.0 or higher Export Along Paths Element Before starting the tutorial, please download the 1pv7_ligand_complex_with_paths (~13 MB) which contains files for this tutorial. Tutorial…

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Optimize transition paths with the Parallel Nudged Elastic Band (P-NEB) method

The Nudged Elastic Band (NEB) method allows for finding saddle points and minimum energy paths between known conformations. The method optimizes a number of intermediate images along the path by finding the lowest possible energy for each image while maintaining equal spacing between neighboring images. This constrained optimization is done by adding spring forces. The NEB method can be used, for example, to determine transition paths between already obtained structures corresponding to local energy minima (obtained using, e.g., the FIRE…

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Protein Path Finder

In this post, we will show how to use the Protein Path Finder app for finding possible paths between two conformations of a protein. Content Requirements Tutorial Loading the input model Launching the Protein Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths…

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Ligand Path Finder

In this post, we will show how to use the Ligand Path Finder app for finding possible ligand unbinding pathways from a protein. Content Requirements Tutorial Loading the input model Launching the Ligand Path Finder app Setting up the interaction model and the state updater for energy evaluation Setting up the system Defining the sampling box Defining the parameters Running, pausing, or stopping the planner Results Next steps Creating pathlines Improving paths with P-NEB Exporting atoms trajectories along paths Requirements…

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Pathlines

In this post, we will show you how to create pathlines thanks to the Pathlines visual model. Pathlines are visual models which represent the trajectory of the center of mass of selected atoms along selected Paths. Pathlines may be used to understand the motion of a single atom, or a group of atoms, along a Path. Before starting the tutorial, please, download this archive: Pathlines (~13MB). It contains a file (1pv7_ligand_complex_with_paths.sam) from the Ligand unbinding pathway search tutorial with already…

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Building a SAMSON Element on Linux

Please, refer to the updated version: Developer guide: Building a SAMSON Element on Linux. This tutorial shows how to build SAMSON Elements on Linux using QtCreator. For other IDE, please, check the Main steps to configure a project for your SAMSON Element. This tutorial was done with QtCreator v.4.4.1 and Qt 5.9.3. For an older version, please, check SAMSON School 2017: Introduction and installation of the SAMSON SDK. If you experience any problems with building your SAMSON Element, please let…

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