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SABIO-RK--database for biochemical reaction kinetics.

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually … extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.

Authors: U. Wittig, R. Kania, M. Golebiewski, M. Rey, L. Shi, L. Jong, E. Algaa, A. Weidemann, H. Sauer-Danzwith, S. Mir, O. Krebs, M. Bittkowski, E. Wetsch, I. Rojas, W. Muller

Date Published: 22nd Nov 2011

Publication Type: Journal

Das biomolekulare Erkennungspuzzle

Abstract

Not specified

Author: Rebecca C. Wade

Date Published: 18th Nov 2011

Publication Type: Journal

The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations

Abstract

Not specified

Authors: Outi M. H. Salo-Ahen, Rebecca C. Wade

Date Published: 1st Oct 2011

Publication Type: Journal

The Use of Spin Traps for the Kinetic Investigation of Elementary Events of Pseudoliving Radical Reversible Addition-Fragmentation Chain-Transfer Polymerization

Abstract (Expand)

The spin-trapping technique is used for the first time to study the kinetics and mechanism of addition and fragmentation elementary events in reversible addition-fragmentation chain-transfer pseudoliving … radical polymerization. As shown by the example of the spin-trap-reversible addition-fragmentation chaintransfer agent model system, the constants of addition (substitution) of the model tert-butyl radical to polymeric reversible addition-fragmentation chain-transfer agents (poly(styrene dithiobenzoate), poly(n-butyl acrylate) dithiobenzoate, etc.) are one to two orders of magnitude higher than the constants of addition reactions involving low-molecular-mass reversible addition-fragmentation chain-transfer agents (tert-butyl dithiobenzoate, benzyl dithiobenzoate, di-tert-butyl trithiocarbonate, and dibenzyl trithiocarbonate). This circumstance makes it possible to significantly widen the synthetic possibilities of reversible addition-fragmentation chain-transfer polymerization. Rate constants of the fragmentation reaction for a number of intermediates are estimated, and the relationship between their structure and stability is ascertained. For the model reaction of the interaction (addition and fragmentation) of the tert-butyl radical with low-molecular-mass reversible addition-fragmentation chain-transfer agents, equilibrium constants are calculated via the methods of computational chemistry.

Authors: V. B. Golubev, A. N. Filippov, E. V. Chernikova, M. L. Coote, C. Y. Lin, G. Gryn’ova

Date Published: 1st Sep 2011

Publication Type: Journal

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

Abstract

Not specified

Authors: D. Cardinale, G. Guaitoli, D. Tondi, R. Luciani, S. Henrich, O. M. H. Salo-Ahen, S. Ferrari, G. Marverti, D. Guerrieri, A. Ligabue, C. Frassineti, C. Pozzi, S. Mangani, D. Fessas, R. Guerrini, G. Ponterini, R. C. Wade, M. P. Costi

Date Published: 23rd Aug 2011

Publication Type: Journal

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9

Abstract

Not specified

Authors: Vlad Cojocaru, Kia Balali-Mood, Mark S. P. Sansom, Rebecca C. Wade

Date Published: 11th Aug 2011

Publication Type: Journal

On the structure and dynamics of the complex of the nucleosome and the linker histone

Abstract

Not specified

Authors: Georgi V. Pachov, Razif R. Gabdoulline, Rebecca C. Wade

Date Published: 1st Jul 2011

Publication Type: Journal

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