About this event

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.



Tuesday, 21st December

9:00-10:00 Structural Biology - Introduction

Irina Moreira

10:00-11:00 Protocol 1: Molecular Visualization - PyMOL

Salete Baptista 

11:00-11:15 Break           

11:15-12:00 Protocol 2: Homology Modeling - Modeller

Carlos Barreto

12:00-13:00 Protocol 3: Ligand-protein Docking

                Rita Melo

13:00- 14:30 Lunch Break

14:30-16:00 Protocol 4: Autodock4 and Autodock Vina - Part I

               Bruno Victor

16:00-16:15 Break

16:15-18:00 Protocol 4: Autodock4 and Autodock Vina - Part II

                Bruno Victor


Wednesday, 22nd December

09:00-10:00 Introduction to MD Simulations

Miguel Machuqueiro

10:00-10:15 Break

10:15-12:30 Protocol 5: MD Simulations

                           Miguel Machuqueiro/Tomás Silva

12:30- 14:30 Lunch Break

14:30-15:30 Coarse-grain MD Simulations using Martini

                           Manuel N. Melo

15:30-15:45 Break

15:45-18::00 Protocol 6: Coarse-grain MD Simulations using Martini 3

                            Manuel N. Melo/Luís Borges-Araújo


Requirements for the lectures

-    Basic knowledge of biophysics.


Requirements for the tutorials

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 tutorial.



- 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 Sciences and Technology of University of Coimbra




Sofia Oliveira

Rua da Quinta Grande, 6
2780-156 Oeiras

Event Type
Workshops and courses