Introduction to the SAMSON platform

Here’s the outline of what we’ll be doing today. The documentation links below are provided in case you would like to learn more about a specific topic, but everything will be explained during the lecture.

Part I – Introduction to modeling

Getting around, importing, selecting and inspecting

Visualizing and animating

Gaming Tournament! Find Lennard-Jones clusters!

Sign into your account, visit the Lennard-Jones model extension, click Add, then do the same for the Cluster Game extension. Then, restart your SAMSON. The two extensions will be automatically installed.

Building molecules, patterns, and more

Part II – GenAI and advanced modeling

Tutorial: Docking ligands into proteins

Try to complete the Docking Tutorial until the part “Visualizing results” (included).

Predicting biomolecular structures and sharing jobs

We will use Boltz-2, an open source equivalent of AlphaFold 3, to predict structures of protein-ligand complexes and binding affinities.

1. Single protein

Add one protein chain (A):
QLEDSEVEAVAKGLEEMYANGVTEDNFKNYVKNNFAQQEISSVEEELNVNISDSCVANKIKDEFFAMISISAIVKAAQKKAWKELAVTVLRFAKANGLKTNAIIVAGQLALWAVQCG

2. Protein and ligands

Add two protein chains (A, B):
MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ

Add two ligands from their CCD code (C, D): SAH

Add two ligands from their SMILES code (E, F): N[C@@H](Cc1ccc(O)cc1)C(=O)O

3. Predicting binding affinities

Add one protein sequence (A): MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ

Add one ligand from its SMILES code (B): N[C@@H](Cc1ccc(O)cc1)C(=O)O

Request affinity calculations for B.

Tutorial: Molecular dynamics simulations

Try to complete the GROMACS Wizard Tutorial until the part “Step 3: NVT equilibration” (included).

Creating and sharing apps

Download the Embedded App Demo document into SAMSON.

Resources