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Analysis and comparison of metabolic pathway databases.

Abstract (Expand)

Enormous amounts of data result from genome sequencing projects and new experimental methods. Within this tremendous amount of genomic data 30-40 per cent of the genes being identified in an organism … remain unknown in terms of their biological function. As a consequence of this lack of information the overall schema of all the biological functions occurring in a specific organism cannot be properly represented. To understand the functional properties of the genomic data more experimental data must be collected. A pathway database is an effort to handle the current knowledge of biochemical pathways and in addition can be used for interpretation of sequence data. Some of the existing pathway databases can be interpreted as detailed functional annotations of genomes because they are tightly integrated with genomic information. However, experimental data are often lacking in these databases. This paper summarises a list of pathway databases and some of their corresponding biological databases, and also focuses on information about the content and the structure of these databases, the organisation of the data and the reliability of stored information from a biological point of view. Moreover, information about the representation of the pathway data and tools to work with the data are given. Advantages and disadvantages of the analysed databases are pointed out, and an overview to biological scientists on how to use these pathway databases is given.

Authors: U. Wittig, A. De Beuckelaer

Date Published: 24th Jul 2001

Publication Type: Journal

Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F

Abstract

Not specified

Authors: Francesca De Rienzo, Razif R. Gabdoulline, M. Cristina Menziani, Pier G. De Benedetti, Rebecca C. Wade

Date Published: 2001

Publication Type: Journal

Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter Autotrophicus GJ10

Abstract

Not specified

Authors: Jan Kmuníček, Santos Luengo, Federico Gago, Angel Ramirez Ortiz, Rebecca C. Wade, Jiří Damborský

Date Published: 2001

Publication Type: Journal

Comparative Binding Energy (COMBINE) analysis of Influenza Neuraminidase-Inhibitor Complexes

Abstract

Not specified

Authors: Ting Wang, Rebecca C. Wade

Date Published: 2001

Publication Type: Journal

Protein-protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations

Abstract

Not specified

Authors: Razif R. Gabdoulline, Rebecca C. Wade

Date Published: 2001

Publication Type: Journal

Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms

Abstract

Not specified

Authors: S.K. Luedemann, R.R. Gabdoulline, V. Lounnas, R.C. Wade

Date Published: 2001

Publication Type: Journal

Protein Interaction Property Similarity Analysis

Abstract

Not specified

Authors: R. C. Wade, R. R. Gabdoulline, F. De Rienzo

Date Published: 2001

Publication Type: Journal

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