Lorentz Center - Optimizing Drug Design from 20 Jul 2009 through 23 Jul 2009
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    Optimizing Drug Design
    from 20 Jul 2009 through 23 Jul 2009




Lectures take place in Room 201 of the Huygens building.

(click here for pdf format)



Monday 20 July 2009



09:00 –  10:00 uur        Registration and coffee

10:00 –  10:30 uur        Welcome by Lorentz Center and Organizers

10:30 –  11:30 uur        Keynote Presentation

                                       Christos Nicolaou: Focusing Multi-Objective Optimization

                                       Search: Knowledge-Driven De Novo Drug Design


12:00 –  14:00 uur        Lunch Break in the Huygens restaurant



14:00 –  15:00 uur        Keynote Presentation

                                       Nathan Brown: Multiobjective Optimisation in Drug

                                       Discovery: Where Are We Now?


15:15 – 16:15 uur         Brainstorming: What is the goal (and what are the problems!)

                                       of optimization in drug design? Summary of results


16:30 – 17:30 uur         Session: Tools in Multiobjective Drug Design

                                       John Holliday: Recent Studies for Optimising Similarity-

                                       based Virtual Screening

                                       Pascal Bonnet: An Efficient Conformational Search Tool for

                                       Drug Design  


17:30 – 19:00 uur         Wine & Cheese party in the Common Room



Tuesday 21 July 2009



09:00 – 10:00 uur         Keynote Presentation

                                       Carlo Poloni and Danilo Di Stefano: Multiobjective Robust

                                       Design Optimization of Docked Ligands

10:00 – 10:30 uur         Coffee/Tea Break

10:30 – 12:00 uur         Session: Selection for Diversity and Robustness (1)

                                       Thorsten Meinl: Multiobjective Diversity Selection for High

                                       Throughput Screening

                                       Willem van Hoorn: Fast multi-objective design of

                                       combinatorial libraries using Pareto ranking

                                       Alexander Aleman: Enhancing Search Space Diversity in

                                       Evolutionary Multiobjective Optimization of Molecules using



12:00 – 13:30 uur         Lunch Break in the Huygens Restaurant



13:30 – 15:00 uur         Session: Selection for Diversity and Robustness (2)          

                                       Eckart Zitzler: Integrating the Issue of Solution Robustness

                                       Into Hypervolume-based Multiobjective Search

                                       Heike Trautmann: Multiobjective Optimization with

                                       Desirability Functions and Desirability Indices

                                       Johannes Kruisselbrink: Desirability Indexes in Drug



15:00 – 16:00               Breakout Session: How to formulate Search Objectives,

                                       (Diversity-based) Selection Criteria and Constraints?

16:00 – 16:30 uur         Coffee / Tea Break

16:30 – 17:00 uur         Presentation of Results from Breakout Session

17:30 – 18:30 uur         Poster and software demo session


19:30 uur                       Informal social event/dinner at the ‘van der Werff’ cafι

                                       Steenstraat 2, Leiden; close to the Central Station)




Wednesday 22 July 2009




09:00 - 10:00 uur          Session: New Algorithmic Ideas

                                       Ofer M. Shir: Experimental Optimization in Quantum Control

                                       Amiram Goldblum: Forming focused libraries and

                                       discovering active molecules with Iterative Stochastic

                                       Elimination algorithm

10:00 - 10:30 uur          Coffee/Tea Break

10:30 - 12:30 uur          Session: Interactive Approaches to Drug Design

                                       Keynote Presentation

                                       Ian Parmee: Evolutionary and Agent-based Search and

                                       Exploration in Combinatorial Chemical Library Design and in

                                       the De Novo Design of Novel Molecules

                                       Keynote Presentation

                                       Matthew Segall: Enabling Interactive Multi-Objective

                                       Optimization for Drug Discovery Scientists    


12:30 - 14:00 uur          Lunch break in the Huygens Restaurant

                                       Discussion, Poster Session


14:00 - 15:30 uur          Breakout session; Tentative Topic: Automatic Optimization

                                       vs. Interactive Exploration and Learning: The role of the

                                       human expert in optimizing drug design


15:30 - 16:00 uur          Coffee/Tea Break

16:00 - 17:00 uur          Presentation of Breakout session results


17:30 - 22:00 uur          Bus to dinner on the boat; back at the hotel at 22:30hrs.

                                       The bus will leave at the side of the building 17:45hrs at the

                                       latest and leave for the Zijldijk where the boat is harboured.

                                       The trip on the Kaag Lakes, Old Rhijn etc. is 4 hours (we

                                       leave at 18:00hrs) and on board we will serve dinner (buffet).

                                       The boat has 3 decks,    2 inside and 1 on top of the boat.

                                       The boat returns at 22:00hrs to the Zijldijk where the bus is

                                       waiting. The bus will bring you to the     hotel or at request to

                                       the Lorentz Center and Leiden Central Station.




Thursday 23 July 2009




09:00 - 09:40 uur          Session: Case Studies and Applications

                                       Lisa Michielan: Investigating Potency and Selectivity of

                                       Human Adenosine Receptor Antagonists   

                                       Eelke v. der Horst: Multi-Objective Evolutionary Design

                                       of Selective Adenosine receptor ligands

09:50 - 10:30 uur          Hernando Sanchez Faddeev: Computer aided design

                                       of a ligand specific to 14-3-3 gamma isoform, danio rerio

                                       Rameshwar Kadam: Virtual Fragment Based Lead Design

                                       Approach: Experimental and Informatics Challenges -

                                       Resolutions and Applications


10:30 – 11:00 uur         Coffee/tea break

11:00 - 12:00 uur          Discussion: Conclusions and Outlook; What are the lessons

                                       learned and important future topics to address? 

12:00 - 14:00 uur          Lunch break in the Huygens Restaurant

                                       Concluding discussion



=== end of workshop ===



List of Posters


Michael Emmerich and Viktoria Li: Landscape Analysis in Optimizing Molecular Drug Design

Eric Faddiev: Multi-Objective Design of Gamma-Isoform Specific Ligands of the 14-3-3 Protein

Matteo Floris: MMsINC, a free web-oriented database of commercially-available compounds for virtual screening and chemoinformatic applications

Divita Garg: Thymidylate Synthase protein-mRNA interactions

Heike Trautmann, Boris Naujoks: Online Convergence Detection in Evolutionary Multiobjective Algorithms

Rui Li, Jeroen Eggermont, Michael Emmerich: Gaussian Process Models for Metamodeling and Optimization in Mixed-Integer Spaces