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

 
Program

Program

 

Lectures take place in Room 201 of the Huygens building.

(click here for pdf format)

 

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Monday 20 July 2009

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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

                                       Discussion

 

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

 

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Tuesday 21 July 2009

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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

                                       Niching

 

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

                                       Discussion

 

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

                                       Design

 

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)

 

 

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Wednesday 22 July 2009

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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.

 

 

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Thursday 23 July 2009

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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



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