organised by

Carsten Baldauf (link), Structural Bioinformatics Group, TU Dresden

Daniel Merkle (link), Parallel and Complex Systems Group, University of Leipzig

hosted by

Maria Teresa Pisabarro (link), Structural Bioinformatics Group, TU Dresden

contact

mdoc07(at)biotec.tu-dresden.de

This satellite conference of the ECCS 2007 is partially funded by the Klaus Tschira Foundation gGmbH (link)

The preliminary program of MDCO-2007 can be found here

Overview

The molecular docking problem is to find the best orientation of two molecules to each other. The interaction can be modeled by a scoring function that includes terms describing the inter- and intramolecular energies. The number of degrees of freedom strongly depends on the complexity of the docking approach. The resulting fitness landscape is highly irregular. Due to this complexity sophisticated optimization algorithms are needed. Bio-inspired methods are known to be valuable tools to successfully explore such search spaces.

In order to gain a deeper insight to biochemical processes and to support the finding of potent drugs, these methods are of great importance in academic and industrial research.

Unfortunately, there is a lack of communication between the communities from computer and life sciences involved in these topics. This event is intended to overcome this and to serve as a platform for exchange of knowledge and for discussion. The focus is not limited on original work but also on introductory talks from the different fields of research.

Topics

1) Modeling of molecular interaction

The fitness function describes the energetical contributions of molecular interaction and internal energy of the involved molecules. The modeling can be performed with knowledge based or empirical force fields, grid based energy functions or shape-based methods. The increase of computational power now allows the modeling with higher accuracy and the introduction of receptor flexibility.

2) High throughput screening and clustering

In drug discovery and pharmaceutical research molecular docking approaches are often utilized to screen large libraries of compounds with millions of entries. To lower the computational costs efficient computation of energy values and effective and fast optimization methods are necessary. Even massively parallel approaches are of interest.

3) Protein-Protein Docking

The interactions of proteins with each other play a key-role in signalling pathways and the self assembly of complex protein aggregates. The availability of a large number of protein structures offers the possibility to study these interactions with computational methods. But due to the size of proteins and the nature of their interactions special approaches and approximations are needed.

4) Bio-inspired optimization

The most successful approaches for molecular docking are based on bio-inspired methods. A profound understanding of the underlying problem is necessary to chose the best optimization algorithm and its components. Recently, it was shown that particle swarm optimization and ant algorithms outperform well known approaches based on genetic algorithms.

5) Fitness landscapes

For related optimization problems like protein folding a systematical analysis of the energy fitness landscape leads to a better understanding of real biological processes. For molecular docking there is still a lack of a thorough analysis of the highly irregular fitness landscapes, which usually has a large number of local minima.

6) Multi-objective approaches

Usually in molecular docking the fitness of a conformation is defined by the binding free energy of two molecules. An approach which has already shown to be very successful is to design a multi-objective algorithm based on the different components of the scoring function. Furthermore, optimization functions that could not be expressed with energy terms (e.g. the solvent accessible surface of a molecule) would most likely improve a docking approach.

Invited speakers:

• Vigneshwaran Namasivayam, Robert Günther, Institute of Biochemistry, University of Leipzig (link), Leipzig, Germany (Talk on Bio-Algorithms in Molecular Docking)
• Martin Middendorf, University of Leipzig (link), Leipzig, Germany (Talk on Swarm Intelligence)
• Michael Thormann, Origenis AG (link), Munich, Germany
• Peter Stadler, IZBI Leipzig (link), Leipzig, Germany (Talk on Fitness landscapes)
• Rebecca Wade, EML Heidelberg (link), Heidelberg, Germany (Protein-protein docking by simulating the process of association subject to biochemical constraints)
• Wolfgang Wenzel, FZ Karlsruhe (link), Karlsruhe, Germany
• Eckart Zitzler, ETH Zürich (link), Zürich, Switzerland (Talk on Mulitobjective Optimization)
• Angel R. Ortiz, Universidad Autonónoma de Madrid (link), Madrid, Spain (Talk on Solvent Models for Protein-Ligand Docking)
• Oliver Korb, University of Konstanz (link), Konstanz, Germany (Application of Ant Colony Optimization to Structure-Based Drug Design)
• El-Ghazali Talbi, University of Lille (link), Lille, France (Evolutionary Molecular Docking on Large Networks)

Registration

There is no additional participation fee for this satellite workshop (but it is necessary to pay the fee for the main conference). You will have to register from the the main conference web site espressing your wish to take part to this satellite meeting.

Submission, Deadlines, and Publication

If you want to give an oral presentation at our satellite conference or if you want to present a poster, please submit a 1-page abstract till 01. July 2007 to both of the organizers.