3rd Beilstein ESCEC Symposium 2007

23 – 26 September 2007

Hotel Jagdschloss Niederwald, Rüdesheim, Germany

Scientific program: Carsten Kettner and Martin G. Hicks


Proceedings of this Beilstein ESCEC Symposium.


The almost complete sequencing of the genomes from numerous organisms paved the way for the development and application of new experimental and instrumental techniques which contribute to the understanding of complex biological pathways and networks by providing apparently endless opportunities to generate massive amounts of data. Cell machinery is currently envisaged as an inter-relationship of enzymes, proteins and chemical compounds. However, both a large number of metabolic pathways and enzymes even in well-described pathways still remain unknown. It is therefore necessary to develop further experimental and mathematical methods to reconstruct unknown parts of the networks, to identify genes for missing enzymes and to characterize the kinetic behaviour of those enzymes that have been identified.

The post-genomic era is also characterized by the concept of systems biology. This has gained significant momentum and metabolic research is now being conducted on an integrated and cross-disciplinary platform pulling together its resources from diverse fields such as mathematics, computational biology, bioinformatics, functional genomics and proteomics, and structural biology. The enormous growth in the computation speed and data storage capability has fuelled new opportunities for both the accumulation of massive amounts of sequence, expression and functional data and the characterization, analysis and comparison of larger biological systems. However, as long as the data quality of the in-put and the resulting modelling data cannot be improved, the chances of success for this young discipline to escape from the verbally overused –omics-sciences are poor.

Systems level investigation of genomic and proteomic scale information requires incomparably higher demands for data quality than in previous decades. Truly integrated databases that deal with heterogeneous data need to be developed to be able to retrieve properties of genes, for kinetics of enzymes, for behaviour of complex networks and for the analysis and modelling of complex biological processes. One perspective of the output can be the investigation of cellular pathways involved in disease biology and targeted by newer molecular therapeutics. The understanding of these processes will assist the development of early diagnosis, prognosis and the prediction of response to individual therapies.

Despite the fast paced global efforts in biological systems research, the current analyses are limited by the lack of available systematic collections of comparable functional enzyme data. Besides its reliability, these data have to provide defined minimum experimental information, they must be available from the literature along with their accepted enzyme names, and must be as comprehensive as possible.

The STRENDA commission, founded on the 1st ESCEC meeting in 2003, has worked out a number of checklists which are intended to improve the quality of reporting enzyme data and thus to support the comparability of inter alia enzyme kinetics. The commission has also spent much time and effort in the creation of an electronic data submission system which allows authors to deposit their data and to provide an interaction record accession number that can be quoted in publications.

This forthcoming 3rd ESCEC symposium, organized by the Beilstein-Institut together with the STRENDA commission, provides a platform to discuss the checklists, to collect further suggestions regarding them, the submission system and organism-related definitions of experimental data. Further questions such as how to organize and store these massive data sets in standard and easily accessible forms, which new experimental tools have to be developed to gather and configure such data into interactive models, which parameters are to be measured, and which experimental conditions appropriate to be recommended will also be discussed. Finally, this symposium is intended to be a connector for the diverse standardization initiatives already existing.

Scientific Program

Functional Genomics in Escherichia coli: Experimental Approaches for the Assignment of Enzyme Function
Richard N. Armstrong, Vanderbilt University, Nashville, TN, USA

Cholesterol Oxidase: Modulating Catalysis at the Membrane
Nicole S. Sampson, Stony Brook University, USA

An Approach to Acquire Quantitative Data for Systems Biology
Jildau Bouwman, Vrije Universiteit Amsterdam, The Netherlands

Building Blocks for Metabolomics: Computer-assisted Structure Elucidation of Biological Metabolites
Christoph Steinbeck, University of Tübingen, Germany

Teaching Enzyme Kinetics and Metabolism in the 21st Century
Athel Cornish-Bowden, CNRS-BIP, Marseille, France

From Data Integration to System Modelling: Establishing Systems Biology Data and Process Standards for White, Green and Red Biotechnology Applications
Hans-Peter Fischer, Genedata AG, Basel, Switzerland

How to Improve Standardization of Procedures for Catalytic Concentration Measurement of Enzymes?
Gerhard Schumann, Medical School Hannover, Hannover, Germany

Developing Common Reporting Standards for the Proteomics Community
Sandra Orchard, European Bioinformatics Institute, Cambridge, UK

Towards Publication Standards in Proteomics Research
Hans-Joachim Kraus, PROTEOMICS Managing Editor, Wiley-VCH, Weinheim, Germany

BRENDA, AMENDA, FRENDA, and STRENDA, a Smooth Relationship?
Dietmar Schomburg, TU Braunschweig, Germany

ESCEC Perspectives: Round-table Discussion, chaired by Keith Tipton

Thermodynamic Studies of Enzyme-Catalyzed Reactions
Robert N. Goldberg, National Institute of Standards and Technology, Gaithersburg, USA

Effects of pH in Biochemical Thermodynamics and Enzyme Kinetics
Robert A. Alberty, Massachusetts Institute of Technology, Cambridge, USA

Development of an Extensible System for the Data Capture and Storage of Enzyme Kinetics Experimental Data
Neil Swainston, Manchester Centre for Integrative Systems Biology, University of Manchester, UK

Integration and Annotation of Kinetic Data of Biochemical Reactions in SABIO-RK
Ulrike Wittig, Heidelberg Institute for THeoretical Studies (HITS), Germany

The MetaCyc Database and the BioCyc Collection of Pathway/Genome Databases
Ron Caspi, Bioinformatics Research Group, CA, USA

From Protein Structures via Molecular Interaction Fields to Enzyme Kinetic Parameters
Matthias Stein, EML Research gGmbH, Heidelberg, Germany

The Inorganic Dimension – Metal Ions in Enzyme Activity
Richard Cammack, King's College London, UK

Rebirth of the Integrated Rate Equation and its Misuse
Keith F. Tipton, Trinity College, Dublin, Ireland

Capillary-electrophoresis Coupled Mass Spectrometry of Urinary Polypeptides for Clinical Applications
Harald Mischak, mosaiques diagnostics & therapeutics AG, Hannover, Germany

Protein Species - the Future Challenge for Enzymology
Hartmut Schlüter, University Medical Center Hamburg-Eppendorf, Germany

Symbolic Control Analysis of Cellular Systems
Johann Rohwer, University of Stellenbosch, South Africa

JWS Online: a Web-accessible Model Database and Simulator
Jacky Snoep, University of Stellenbosch, South Africa

Integrated Modelling in Computational Proteomics
Yu (Brandon) Xia, Boston University, USA

Validity Tests and Merging of Biochemical Models
Wolfram Liebermeister, Max Planck Institute for Molecular Genetics, Berlin, Germany

Refining Metabolic Models with Large-scale Mutant Phenotype Assays
Vincent Schächter, Genoscope Institut de Génomique, Evry, France