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1-12 of 12
Keywords: modelling
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Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2017) 45 (3): 785–791.
Published: 15 June 2017
... test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages...
Articles
Heteromeric amino acid transporters. In search of the molecular bases of transport cycle mechanisms
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (3): 745–752.
Published: 09 June 2016
... and to evaluate the functional relevance of heavy and light subunit interactions for the amino acid transport cycle. amino acid transporters heterodimer heteromeric amino acid transporter (HAT) modelling structure transport mechanism 1 In memory of Steve Baldwin, who put us on the right...
Articles
Using the fragment molecular orbital method to investigate agonist–orexin-2 receptor interactions
Open AccessAlexander Heifetz, Matteo Aldeghi, Ewa I. Chudyk, Dmitri G. Fedorov, Mike J. Bodkin, Philip C. Biggin
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (2): 574–581.
Published: 11 April 2016
... modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX 2 R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small...
Articles
A multi-scale, multi-disciplinary approach for assessing the technological, economic and environmental performance of bio-based chemicals
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2015) 43 (6): 1151–1156.
Published: 27 November 2015
... chemicals, particularly during the early research phase. Recently, the Multi-scale framework for Sustainable Industrial Chemicals (MuSIC) was introduced to address this issue by integrating modelling approaches at different scales ranging from cellular to ecological scales. This framework can be further...
Articles
Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2015) 43 (5): 1023–1032.
Published: 09 October 2015
... and [email protected] ) 1 6 2015 © 2015 Authors; published by Portland Press Limited 2015 EPR MD simulations ABCB1 MsbA DEER PELDOR modelling protein dynamics Knowledge of the molecular structure of membrane proteins is essential to understand their function. Most...
Articles
G-Protein-Coupled Receptors: from Structural Insights to Functional Mechanisms
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (1): 135–136.
Published: 29 January 2013
... of relating observations on isolated receptors or receptors expressed in model systems to receptor function in vivo . 1 To whom correspondence should be addressed (email [email protected] ). 20 11 2012 © The Authors Journal compilation © 2013 Biochemical Society 2013 β...
Articles
Computational optimization and biological evolution
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2010) 38 (5): 1206–1209.
Published: 24 September 2010
...Igor Goryanin Modelling and optimization principles become a key concept in many biological areas, especially in biochemistry. Definitions of objective function, fitness and co-evolution, although they differ between biology and mathematics, are similar in a general sense. Although successful...
Articles
Modelling the effects of inhibitors of guanine nucleotide synthesis: implications for studies of cellular differentiation pathways
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2010) 38 (5): 1314–1318.
Published: 24 September 2010
... these observations with the known actions of mizoribine I have adapted an existing model of human purine metabolism composed as an S-system familiar from Biochemical Systems Theory. Mizoribine's actions were then simulated and compared with experimental data. 1 To whom correspondence should be addressed...
Articles
Modelling and simulation for metabolomics data analysis
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2005) 33 (6): 1427–1429.
Published: 26 October 2005
... producing synthetic data sets by simulation of realistic biochemical network models with the purpose of comparing data analysis methods. Because we have full knowledge of the underlying ‘biochemistry’ of these models, we are better able to judge how well the analyses reflect true knowledge about the system...
Articles
Systems biology: will it work?
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2005) 33 (3): 503–506.
Published: 01 June 2005
...M.P. Williamson Systems biology describes the collection of a set of measurements on a system, integrated with a mathematical model of that system. The model and the measurements must be made together and refined iteratively, requiring close collaboration between biologists and modellers...
Articles
Structural elements involved in activation of the γ-aminobutyric acid type A (GABAA) receptor
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2004) 32 (3): 540–546.
Published: 01 June 2004
... in Ligand-Gated Ion Channel Function: a Biochemical Society Focused Meeting held at Merck Shape & Dohme, Harlow, 29 January 2004 25 February 2003 © 2004 Biochemical Society 2004 γ-aminobutyric acid (GABA) ligand-gated ion channel (LGIC) LGIC activation LGIC structure modelling...
Articles
Petri Net representations in systems biology
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Journal:
Biochemical Society Transactions
Biochem Soc Trans (2003) 31 (6): 1513–1515.
Published: 01 December 2003
... of and other relationships, which allows its users to classify a gene, protein, compound or pathway within a knowledge base. (ii) Database models, which define the way biological information is stored in a database [2]. A database model may be derived from an ontology, in which case it shares the same logical...