Molecular Docking, Complexity, and Optimization
TU Dresden, Germany

 An ECCS 2007 Satellite Conference, Dresden 4th or 5th October 2007

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)
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 speaker

    * Robert Gnther, Institute of Biochemistry, University of Leipzig 
      Leipzig, Germany
    * 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
    * Wolfgang Wenzel, FZ Karlsruhe (link), Karlsruhe, Germany
    * Eckart Zitzler, ETH Zrich (link), Zrich, Switzerland 
      (Talk on Mulitobjective Optimization)

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.

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