Ligand-protein docking, and computer-aided drug design

Overview

This workshop aims to present basics on protein structure, visualization and several computer-aided drug design tools developed at SIB. Several examples are taken from different therapeutic fields.

Participants will use powerful, yet simple, professional tools, commonly used in molecular modelling, drug design and drug-target analysis. Some of these tools are based on original and unique technologies and databases developed by the SIB, like the SwissBioisostere database. The lectures and workshops will be given by the developers of the methods, who will be available to answer questions regarding the participants' own research and needs.

Learning objectives

At the end of the tutorial, participants are expected to be able to:

• use Swiss-PdbViewer to superpose and compare proteins
• use UCSF chimera to display molecules in 3D and analyse protein-ligand complexes
• submit docking calculations in via UCSF Chimera and analyse results, use atelier-drug-design.ch to link docking and lead optimisation
• use SwissBioisostere for lead optimization
• use SwissADME for estimation of pharmacokinetic and pharmacodynamic properties, synthetic accessibility, druglikeness, etc...
• use SwissTargetPrediction to predict primary and secondary targets of small molecules and predict drug repurposing
• use SwissSimilarity to perform ligand-based screening

Prerequisites

Competencies

• Basic knowledge in biology
• Very basic knowledge in chemistry.

Technical

• Laptop with a mouse, and with two software installed: Swiss-PdbViewer, UCSF Chimera and a web browser (recent version of Firefox, Chrome or Safari). Please, install UCSF Chimera version 1.11 for which you can find a Mac OS X version here (32 bits version here) and a Windows version here (32 bits version here).
• To verify that Swiss-PdbViewer is compatible with your hardware / graphic card, unzip the package and drag the 1crn.ent file onto the Swiss-PdbViewer application. A structure should appear in the main window.
  Known incompatible hardware: SurfacePro.

Application

The application fees for academics are 100 CHF. The fees include course material and coffee breaks. Participants from non-academic institutions should contact us.

Deadline for registration and free-of-charge cancellation is set to March 6. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available at https://www.sib.swiss/training/terms-and-conditions.

You will be informed by email of your registration confirmation.

Location

University of Lausanne, Genopode building, classroom 2020 (Metro M1 line, Sorge station)

Additional information

Coordination: SIB Training Group

You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.