Computational Structural Biology Tools

BioData.pt | ELIXIR Portugal

A showcase of a robust  pipeline of in silico protein-ligand characterization methods to address one of today's biggest biological problems

Universidade de Coimbra

<h2>About this event</h2>SARS-COV-2 triggered a worldwide pandemic disease, COVID-19, for which an effective treatment has not yet been settled. Among the most promising targets to fight this disease is SARS-CoV-2 main protease (Mpro), which has been extensively studied in the last few months. There is an urgency for developing effective computational protocols that can help us tackle these key viral proteins. Hence, we have put together a robust and thorough pipeline of in silico protein-ligand characterization methods to address one of the biggest biological problems currently plaguing our world. These methodologies were showcased to characterize the interaction of SARS-CoV-2 Mpro with an α-ketoamide inhibitor and include details on:Protocol 1 - How to upload, visualize and manage the three-dimensional structure of the complex and acquire high-quality figures for scientific publications using PyMOL;Protocol 2 - Perform homology modeling with MODELLER;Protocol 3 - Perform protein-ligand docking calculations using HADDOCK;Protocol 4 - Run a virtual screening protocol of a small compound database of SARS-COV-2 candidate inhibitors with AutoDock 4 and AutoDock Vina;Protocol 5 - Atomistic conformational sampling (MD simulations using GROMACS) and free energy calculations (MM-PBSA) of the interaction between SARS-CoV-2 Mpro and a α-ketoamide inhibitor;Protocol 6 - Coarse-grain modeling of the interaction between SARS-CoV-2 Mpro and a α-ketoamide inhibitor, using the Martini 3 force field.Guidelines for careful data analysis and interpretation are also provided for each Protocol. <h2>Programme</h2><h3>Tuesday, 21st December </h3>9:00-10:00 Structural Biology - Introduction Irina Moreira10:00-11:00 Protocol 1: Molecular Visualization - PyMOL Salete Baptista 11:00-11:15 Break 	 11:15-12:00 Protocol 2: Homology Modeling - Modeller Carlos Barreto12:00-13:00 Protocol 3: Ligand-protein Docking Rita Melo13:00- 14:30 Lunch Break14:30-16:00 Protocol 4: Autodock4 and Autodock Vina - Part I 	 Bruno Victor16:00-16:15 Break16:15-18:00 Protocol 4: Autodock4 and Autodock Vina - Part II Bruno Victor<h3>Wednesday, 22nd December </h3>09:00-10:00 Introduction to MD Simulations Miguel Machuqueiro10:00-10:15 Break10:15-12:30 Protocol 5: MD Simulations Miguel Machuqueiro/Tomás Silva12:30- 14:30 Lunch Break14:30-15:30 Coarse-grain MD Simulations using Martini Manuel N. Melo15:30-15:45 Break15:45-18::00 Protocol 6: Coarse-grain MD Simulations using Martini 3 Manuel N. Melo/Luís Borges-Araújo

<h2>Requirements for the lectures</h2>- Basic knowledge of biophysics. <h2>Requirements for the tutorials</h2>To be able to follow the tutorials you need to have a basic knowledge of:- 	Linux command line.If you do not have prior experience with this, or if you would like a refresher, please look through this<a href="https://swcarpentry.github.io/shell-novice/" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer"> tutorial</a>. <h2>Registration</h2>- Free with access to all talks and networking.- Maximum number of participants: 25.- Registration will be on a first come, first serve basis.The conference will be provided in person. Adress: Room 1.1, Department of Life Sciences, Faculty of Science and Technology of University of Coimbra<h2>Organization</h2>University of Coimbra

<h3>Code of Conduct</h3>The <a href="https://biodata.pt/sites/default/files/2021-02/BioData.pt%20Code%20of%20Conduct%20for%20Events.pdf" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">BioData.pt Code of Conduct</a> has been adapted from ELIXIR Hub Code of Conduct for Events so all participants at BioData.pt events can interact with each other in a respectful and safe environment safeguarding their personal integrity in case they believe there has been a breach to this Code of Conduct.Please note that the event will be recorded.

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