Biomedical subjects

Ralf Hofestaedt

Publications and source records attributed to Ralf Hofestaedt.

3 recordsLinked to original sources

PubMed2005

An algorithm for linear metabolic pathway alignment.

Metabolic pathway alignment represents one of the most powerful tools for comparative analysis of metabolism. It involves recognition of metabolites common to a set of functionally-related metabolic pathways, interpretation of biological evolution processes and determination of alternative metabolic pathways. Moreover, it is of assistance in function prediction and metabolism modeling. Although research on genomic sequence alignment is extensive, the problem of aligning metabolic pathways has received less attention. We are motivated to develop an algorithm of metabolic pathway alignment to reveal the similarities between metabolic pathways. A new definition of the metabolic pathway is introduced. The algorithm has been implemented into the PathAligner system; its web-based interface is available at http://bibiserv.techfak.uni-bielefeld.de/pathaligner/.

Algorithms↗

PubMed2004

STCDB: Signal Transduction Classification Database.

The Signal Transduction Classification Database (STCDB) is a database of information relative to the classification of signal transduction. It is based primarily on a proposed classification of signal transduction and it describes each type of characterized signal transduction for which a unique ST number has been provided. This document presents, in its first version, the classification of signal transduction in eukaryotic cells. Approved classifications are available for web browsing at http://www.techfak.uni-bielefeld.de/~ mchen/STCDB.

Animals↗

PubMed2003

iUDB: an object-oriented system for modelling, integration and analysis of gene controlled metabolic networks.

The rate constant of an enzyme-catalysed reaction is one of the major target properties to understand protein function. Atomic-detail computer simulations can in principle be used to estimate rate constants from the energy profile along the reaction coordinate. For such simulations, molecular mechanics is combined with a quantum description of the reaction process. In molecular mechanics calculations, the electrostatic field is represented by the Coulomb potential of partial atomic charges which have been parametrised for small building blocks in vacuum and transferred to the macromolecule. In aqueous solution, however, the electrostatic interactions are affected by the solvent polarization. While this can be described by numerically solving the Poisson-Boltzmann equation, it is computationally expensive. A simple approximation to this is to optimally reproduce the electrostatic potential in solution by reparametrising the partial atomic charges in such a way that a simple Coulomb potential can still be used. Such a procedure would allow to perform fast calculations of reaction processes in proteins while accounting for the solvent screening effect. Here, this method is tested on myosin, a motor protein that is both an enzyme and exists in very different conformations.

Citric Acid Cycle↗