Ligand-protein docking, and computer-aided drug design

Overview

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

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

Learning objectives

At the end of the tutorial, participants will be able to:

• use UCSF chimera to display molecules in 3D and analyse protein-ligand complexes
• submit docking calculations through UCSF Chimera and analyse results at atomic scale
• use SwissSimilarity to perform ligand-based screening
• use SwissTargetPrediction to predict the most probable protein targets of bioactive small molecules in the context of secondary effect, drug repurposing or deconvolution of phenotypic screen
• use SwissADME to estimate ADME, physicochemical, pharmacokinetic, druglikeness and related properties
• use SwissBioisostere for for selecting molecular replacements in the context of lead optimization or scaffold hopping.
• use WebMO to investigate electronic properties of small molecules

Prerequisites

Competencies

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

Technical

• Laptop with two software installed: UCSF Chimera and a web browser (recent version of Firefox, Chrome or Safari). Please, install UCSF Chimera version 1.13 for which you can find a Mac OS X version here and a Windows version here.

Application

Registration fees for academics are 120 CHF and 600 CHF for for-profit companies. The fees include course material and coffee breaks.

Deadline for registration and free-of-charge cancellation is set to 1 November. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available here.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Venue and time

University of Basel, precise location on due time.

Additional information

Coordination: Grégoire Rossier, 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.