4th Beilstein ESCEC Symposium 2009

13 – 16 September 2009

Hotel Jagdschloss Niederwald, Rüdesheim, Germany

Scientific program: Carsten Kettner and Martin G. Hicks


Proceedings of this Beilstein ESCEC Symposium.


The post-”omic” era can be characterized by investigations of dynamic processes within and between cells, tissues and organs. Such investigations are carried out using a combination of interdisciplinary procedures at both the theoretical and experimental level. One aspect of intracellular dynamics is the determination of complex metabolic networks and their high dynamic behavior, and their associated mechanistic pathways. Continuous technical and methodological advances and improvements have meant that biochemical pathway analysis can now be carried out in much greater depth and with increased efficiency and accuracy.

Unfortunately, such progress has led to a confusing and highly undesirable situation with respect to trying to make the maximum use of the experimental data derived from the functional characterizations of enzymes since a variety of experimental designs and analytical methods have been employed. The result is that there is a lack of systematic collections of comparable functional enzyme data. The pre-requisite for both comparability and reliability of such data is the provision of minimum information about experimental design and experimental results as well as standardization of the conditions and procedures involved in the experiments.

However, the current position is not encouraging: the quality of reported experimental data of enzymes is insufficient for the needs of systems level investigations and thus is, in point of fact, neither applicable for modeling and simulation nor for the functional characterization of the individual cellular components.

Consequently, a high quality level balance between experimental in-put data and modeled out-put data needs to be created.

The STRENDA Commission (Standards for Reporting Enzyme Data), founded in 2003, is concerned with the improvement of the quality of reporting functional enzyme data to support, inter alia, enzyme kinetics for application in the in silico investigation of biological systems. The Commission has developed a set of guidelines for the reporting of data in publications. These guidelines along with the recommendations of a number of other groups that are also concerned with the standardization of reporting and experimental procedures are intended to pave the way to Good Publication Practice to ensure data quality and data identification.

This 4th Beilstein ESCEC Symposium, organized by the Beilstein-Institut together with the STRENDA Commission, provides a platform to discuss the checklists, to consider further suggestions and to improve existing recommendations. This symposium is also intended to interconnect the diverse standardization initiatives by giving the opportunity to representatives from journals and funding agencies as well as experimentalists and theoreticians to discuss such topics as, e.g. 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 should be measured, what kind of data constitute the minimum required information, and which experimental conditions should be recommended.

Scientific Program

Structure and Function of Enzymes in the Vicinal Oxygen Chelate Superfamily as Revealed by in vitro Homologous Recombination
Richard N. Armstrong, Vanderbilt University, Nashville, TN, USA

Functional Annotation for Members of the Amidohydrolase Superfamily
Frank M. Raushel, Texas A&M University, College Station, TX, USA

Understanding Enzymes as Reporters or Targets in Assays Using Quantitative High-throughput Screening (qHTS)
Douglas S. Auld, NIH - National Human Genome Research Institute, Rockville, MD, USA

How Streptococcus Makes Isoprenoids
Scott T. Lefurgy, The Albert Einstein College of Medicine, Bronx, NY, USA

Information Transfer - How Far Will it Go?
Thomas S. Leyh, The Albert Einstein College of Medicine, Bronx, NY, USA

Evolution of New Specificities in a Superfamily of Phosphatases
Karen N. Allen, Boston University, MA, USA

Suggestions for a Protein Species Nomenclature
Hartmut Schlüter, University Medicine Hamburg-Eppendorf, Germany

Standard Formats for Presentation of Spectroscopic Data on Enzymes
Richard Cammack, King's College London, UK

Integrated Modelling of Protein Structure, Interaction and Evolution
Yu (Brandon) Xia, Boston University, MA, USA

Different Contributions of the Various Isoenzymes tot heflux  in the Aspartate-derived Amino Acid Pathway in Arabidopsis
Marìa Luz Càrdenas, CNRS-BIP, Marseille, France

Design Principles Regulating Information Processing through Signalling Networks
Ursula Klingmüller, German Cancer Research Center (DKFZ), Heidelberg, Germany

Parameterization of Large-scale Autonomous Network Models From Time-series Metabolite Data
Klaus Mauch, Insilico Biotechnology AG, Stuttgart, Germany

Interferon Gamma Stimulated STAT1 Signalling in Pancreatic Stellate Cells: From Experimental Data to Mathematical Models
Katja Rateitschak, University of Rostock, Germany

Using Generalized Supply-demand Analysis to Identify Regulatory Metabolites
Johann Rohwer, University of Stellenbosch, South Africa

Standards for Experimentation and Modelling in International Collaboration
Edda Klipp, Humboldt University Berlin, Germany

Comparative Metabolomics Approaches for Bioefficacy Validation and Quality Control of Herbal Medicines
Lie-Fen Shyur, Academie Sinica, Taipei, Taiwan

Measuring Enzyme Activities under Standardized in vivo-like Conditions for Systems Biology
Karen van Eunen, Chalmers University of Technology, Gothenburg, Sweden

Re-evaluation of the EC Number System from a Genomic Perspective
Minoru Kanehisa, Kyoto University, Japan

Promoting Coherent Minimum Reporting GUidelines for Biological and Biomedical Investigations: the MIBBI Project
Christopher F. Taylor, European Bioinformatics Institute, Cambridge, UK

Guidelines for Reporting Biocatalytic Reactions
Lucia Gardossi, Università degli Studi de Trieste, Italy

Reaction Progress Curves and Kinetic Parameters
Keith F. Tipton, Trinity College, Dublin, Ireland

Enzymes in Modelling & Disease - Contributions from the BRENDA Database
Dietmar Schomburg, Technical University Braunschweig, Germany

Standardized Enzyme Kinetics for Systems Biology
Pedro Mendes, The University of Manchester, UK

SABIO-RK: Kinetic Data for Reaction Mechanism Steps
Ulrike Wittig, EML Research gGmbH, Heidelberg, Germany

Moving Towards Comprehensive Tables of Standard Formation Properties of Biochemical Substances
Robert N. Goldberg, National Institute of Standards and Technology, Gaithersburg, MD, USA