Topic outline

  • General

    Ligand-protein docking and computer-aided drug design

    Lausanne, 2-3 November 2015

    Trainers: Nicolas Guex, Vital-IT group
    Vincent Zoete, Ute Roehrig and Antoine Daina, Molecular Modelling group
    Venue: University of Lausanne, Genopode Building
    ECTS: 0.5 (given a passed exam)
    Fee: 100 CHF for academics. Others, please contact us
    Application deadline: 25 October 2015
    Application status: Closed

    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 therapeutical 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.

    Audience

    The workshop is intended for a wide audience covering master students to PostDocs in Biology, Chemistry and Pharmacology, up to senior researchers from Universities or private companies.

    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 October 25. 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 http://www.isb-sib.ch/training/training-general-conditions.html.

    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: Diana Marek

    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@isb-sib.ch.

    • Programme

      Monday 2 November (9h-17h)

      Morning

      • Short introduction on protein structure
      • Practical utilization of Swiss-PdbViewer
      • In particular, you will learn how to 
        - look at a structure, both globally (as a fold) or in detail (e.g. an active site)
        - compare several structures to identify differences
        - identify residues participating in protein-protein interactions
        - understand the limits of energy minimization
        - make a crude model to visualize the result of genetic mutations onto a protein structure.

      Afternoon

      • Short introduction to computer-aided drug design
      • Short introduction to molecular recognition and docking
      • Practical utilization of UCSF Chimera to analyse ligand-protein complexes and perform small molecule docking
      • Pratical introduction to docking and lead optimisation with atelier-drug-design.ch

      Tuesday 3 November (9h-17h)

      Morning

      • Short introduction to virtual screening and reverse screening
      • Practical utilisation of SwissSimilarity to perform high-throuput ligand-based screening
      • Practical utilisation of SwissTargetPrediction to predict possible targets of bioactive small molecules

      Afternoon

      • Short introduction to ADME properties estimation and lead optimisation
      • Practical utilisation of SwissBioisostere to perform lead optimisation
      • Practical utilisation of SwissADME to estimate logP, pharmacokinetic and pharmacodynamic properties, synthetic accessibility, drug-likeness, etc...