2Nd Beilstein ESCEC Symposium 2006

19 – 23 September 2006

Hotel Jagdschloss Niederwald, Rüdesheim, Germany

Scientific program: Carsten Kettner and Martin G. Hicks


Proceedings of this Beilstein ESCEC Symposium.


The post-genomic era is significantly characterized by a high integration and interdisciplinary of research resources from such diverse fields as computational biology, bioinformatics, functional genomics, structural biology, and proteomics. In this perspective, established biological systems can be comprehensivley investigated in terms of interactions of individual or groups of proteins and enzymes as well as the behaviour of collective networks of such interactions. On the other hand, these systems can be re-examined in the light of new results that suggest novel associations between otherwise unrelated pathways and individual proteins.

Modern experimental technologies are providing seemingly endless opportunities to generate massive amounts of sequence, expression and functional data. Continuous advances and improvements have enabled proteome analyses to proceed with increased depth and efficiency. To capitalize on this enormous pool of information and in order to understand fundamental biological phenomena it is essential to collect, organize, categorize, analyze, and share data and results.

However, whilst the large international genome sequencing projects elicited considerable public attention with the creation of huge sequence databases, it has become increasingly apparent that functional data for the gene products, in particular for enzymes, has either limited accessibility or is unavailable. Additionally, although enzyme structural information has been rapidly accumulated in databases, little effort has been invested toward systematic characterization of enzyme functions.

The problem is twofold; deriving data from experimental work is expensive and very time consuming and it is inherently very difficult to collect, interpret and standardize published data since they are widely distributed among journals covering a number of fields, and the data itself is often dependent on the experimental conditions.

For these reasons a systematic and standardized collection of functional enzyme data is essential for the interpretation of the genome information.

The first ESCEC meeting in 2003 resulted in a general agreement that standardization of experiments and methods for enzyme characterization is definitely necessary and in the formation of the STRENDA commission.

STRENDA stands for Standards for Reporting Enzyme Data and the commission accompanies the upcoming series of ESCEC symposia.

This forthcoming symposium provides a platform to discuss a number of checklists worked out and presented by the STRENDA commission. These lists are intended to support the improvement of reporting enzyme data. The result of these discussions may lead to the adoption of the presented and discussed lists and to an agreement on their recommending character for future publications which can be presented to the scientific community by ways of a publication. Further aims are to collect ideas on organism-related definitions of experimental conditions as well as to discuss the demands of systems biology on the quality of data to be considered for the preparation of further checklists by the commission. And finally, this symposium provides the occasion to share STRENDA's experiences with other standardization initiatives with the medium-term aim of creating a joint standardization movement.

Scientific Program

Enzyme Data Standardization – The Way Forward
Carsten Kettner, Beilstein-Institut, Frankfurt am Main, Germany

Standardized Reporting of Data is not Much Use if the Data Themselves are Lousy
Keith F. Tipton, Trinity College, Dublin, Ireland

Thermodynamics of Enzyme-catalyzed Reactions
Robert A. Alberty, Massachusetts Institute of Technology, Cambridge, USA

The Current Status of the IUBMB Recommendations (1981) on Symbolism and Terminology in Enzyme Kinetics
Athel Cornish-Bowden, CNRS-BIP, Marseille, France

A Universal Rate Equation for Systems Biology
Johann Rohwer, University of Stellenbosch, South Africa

Assaying Enzymes from Hyperthermophiles
Wilfred R. Hagen, Delft University of Technology, The Netherlands

Assay of Enzymes with Difficult or Unknown Substrates: The “99” Oxidoreductases as an Example
Richard Cammack, King's College London, UK

Investigations of Proteases – Suggestions
Hartmut Schlüter, University Medical Center Hamburg-Eppendorf, Germany

Leveraging the Structure-Function Relationships of Mechanistically Diverse Enzyme Superfamily
Scott Pegg, University of California, San Francisco, USA

Kinetic Characterization of Alcohol Dehydrogenases and Matrix Metalloproteinases: A Reflection on Standardization of Assay Conditions
Jan-Olof Winberg, University of Tromsø, Norway

Does Enzymology Need its own Ontology?
Kirill Degtyarenko, European Bioinformatics Institute, Cambridge, UK

The Systems Biology Ontology
Nicolas LeNovere, European Bioinformatics Institute, Cambridge, UK

Molecular Simulations of Enzyme Catalysis
Martin Field, Laboratoire de Dynamique Moleculaire, Institut de Biologie Structurale, Grenoble, France

Standards for Reporting Experimental Procedures – Example of a Synergistic Approach
Susanna A. Sansone, European Bioinformatics Institute, Cambridge, UK

Analysis of High-Throughput Data on the Basis of Metabolic Network Models
Hermann-Georg Holzhütter, Charité – Humboldt University Berlin, Germany

Functional Implications of Changes in Gene Expression
Jildau Bouwman, Vrije Universiteit Amsterdam, The Netherlands

Investigations with Global Constraint-based Metabolic Models
Vincent Schachter, Genoscope, Centre national de séquençage, Evry, France

Strategy to Develop Large-Scale Kinetic Models on the Basis of Enzyme Structural and Functional Information: Progress and Problems
Oleg Demin, Moscow State University, Russia

Systems Biology of Signal Transduction and Cancer
Ursula Klingmüller, German Cancer Research Center (DKFZ), Heidelberg, Germany

SABIO-RK (System for the Analysis of Biochemical Pathways – Reaction Kinetics)
Isabel Rojas-Muijca, EML Research gGmbH, Heidelberg, Germany

Discrepancy and Discovery – The Need for Accurate, Inadequate Models of Biology
Thomas S. Leyh, The Albert Einstein College of Medicine, Bronx, New York, USA

Beyond Flat Files: Data Modelling, Editing, Archival and Interchange
Steffen Neumann, Leipniz Institute for Plant Biochemistry, Halle/Saale, Germany

New Developments at the BRENDA Enzyme Information System Host
Dietmar Schomburg, University of Cologne, Germany

Simulation and Parameter Estimation on the Basis of Experimental Enzymatic Data
Ursula Kummer, EML Research gGmbH, Heidelberg, Germany

Integrating Structural and Kinetic Enzymatic Information in Systems Biology
Matthias Stein, EML Research gGmbH, Heidelberg, Germany

Project CyberCell: Calibrating Biophysical Data to the Complexity of the Intracellular Environment
Michael J. Ellison, University of Alberta, Edmonton, Canada

Discovering Novel Enzymes and Pathways by Comparative Genomics
Valérie de Crécy-Lagard, University of Florida, Gainesville, USA

JWS Online; a Web-based Tool for Curation, Review, Storage and Analyses of Kinetic Models
Jacky L. Snoep, University of Stellenbosch, South Africa