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Keywords: simulation
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Biochem Soc Trans (2020) 48 (1): 25–37.
Published: 24 December 2019
... and unbiased simulation methods. In particular, we focus on interactions of integral membrane proteins with cholesterol, and with anionic lipids such as phosphatidylinositol 4,5-bis-phosphate and cardiolipin. Peripheral membrane proteins are exemplified via interactions of PH domains with phosphoinositide...
Biochem Soc Trans (2015) 43 (5): 952–958.
Published: 09 October 2015
... selected and finally illustrate how MD simulations can be used as a means to give more confidence about models that have been generated via this approach. 1 To whom correspondence should be addressed (email philip.biggin@bioch.ox.ac.uk ) . One of the main goals or aims of homology modelling...
Includes: Supplementary data
Biochem Soc Trans (2015) 43 (2): 162–167.
Published: 07 April 2015
...Syma Khalid; Nils A. Berglund; Daniel A. Holdbrook; Yuk M. Leung; Jamie Parkin Molecular modelling and simulations have been employed to study the membranes of Gram-negative bacteria for over 20 years. Proteins native to these membranes, as well as antimicrobial peptides and drug molecules have...
Biochem Soc Trans (2013) 41 (2): 554–558.
Published: 21 March 2013
... of the Stokes equation to a Fourier space: in the standard notation of stochastic differential equations, one obtains (4) As an example of results that can be obtained using the GIB method, in the present article, we report on simulations of the supercoiling of a 600 bp DNA minicircle that has...
Biochem Soc Trans (2012) 40 (2): 438–443.
Published: 21 March 2012
... and functional properties of the various domains of full-length kinesin-1 molecules are summarized and a computer model is presented that uses this information to simulate the motion of a bead carried by a kinesin molecule along a microtubule, with and without a weak optical trap present. A video sequence made...
Includes: Multimedia, Supplementary data
Biochem Soc Trans (2008) 36 (1): 22–26.
Published: 22 January 2008
...Adrian J. Mulholland Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight...
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...
Biochem Soc Trans (2003) 31 (6): 1513–1515.
Published: 01 December 2003
... biochemical network modelling Petri Net simulation systems biology Unravelling Nature s Networks 1513 Petri Net representations in systems biology J.W. Pinney1, D.R. Westhead and G.A. McConkey Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K. Abstract The mathematical structures...
Biochem Soc Trans (2003) 31 (6): 1472–1473.
Published: 01 December 2003
... held at University of Sheffield, 21 July 2003 16 June 2003 © 2003 Biochemical Society 2003 collaboration language model network simulation standard Abbreviation used: SBML, systems biology markup language. 1472 Biochemical Society Transactions (2003) Volume 31...