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Keywords: molecular dynamics
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Articles
Biochem Soc Trans (2023) 51 (1): 275–285.
Published: 16 January 2023
... histocompatibility complex molecular dynamics peptide loading complex Activation of the T-cell mediated adaptive arm of the immune system relies upon transport of potential antigens within our cells to the cell surface. It is a longstanding challenge of the field to generate predictive models...
Articles
Biochem Soc Trans (2022) 50 (1): 569–581.
Published: 25 February 2022
...John W. Vant; Daipayan Sarkar; Jonathan Nguyen; Alexander T. Baker; Josh V. Vermaas; Abhishek Singharoy Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology...
Articles
Biochem Soc Trans (2022) 50 (1): 541–554.
Published: 07 February 2022
... future directions for research in the field. e-mail: lindorff@bio.ku.dk 10 12 2021 13 1 2022 17 1 2022 © 2022 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2022 conformational ensemble molecular dynamics protein structure...
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Biochem Soc Trans (2021) 49 (6): 2527–2537.
Published: 16 November 2021
...Alzbeta Tuerkova; Peter M. Kasson The protein–membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become...
Includes: Supplementary data
Articles
Biochem Soc Trans (2021) 49 (1): 415–429.
Published: 05 February 2021
... such as statistical coupling analysis [ 40 ] can identify residues that are involved in allosteric signal propagation. Structural analyses such as normal mode analysis may reveal intrinsic dynamic motions encoded in the protein structures [ 41 ]. Classical molecular dynamics (MD) simulations can uncover changes...
Articles
Biochem Soc Trans (2020) 48 (4): 1447–1461.
Published: 14 August 2020
... all-atom molecular dynamics to mean-field theories. We discuss the advantage and limit of each modeling technique, and summarize the theoretical insights that, despite certain controversy, deepened our understanding of the hairy pore. Correspondence: Igal Szleifer ( igalsz@northwestern.edu...
Articles
Biochem Soc Trans (2020) 48 (4): 1707–1724.
Published: 05 August 2020
... simulation techniques such as molecular dynamics simulations allow characterisation of the metastable conformational states and the transitions between them, and thus free energy landscapes, to be characterised, the barriers between states can be high, precluding efficient sampling without substantial...
Articles
Biochem Soc Trans (2020) 48 (1): 25–37.
Published: 24 December 2019
... access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . free energy lipid membrane protein molecular dynamics simulation Biological membranes are formed from a bilayer...
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Articles
Biochem Soc Trans (2015) 43 (5): 952–958.
Published: 09 October 2015
...-binding domains by the linker, using molecular dynamics Mol. Inform. 2013 32 529 540 10.1002/minf.201200175 18 Moradi M. Tajkhorshid E. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution Proc. Natl. Acad. Sci. U.S.A. 2013 110 18916...
Includes: Supplementary data
Articles
Biochem Soc Trans (2015) 43 (2): 151–156.
Published: 07 April 2015
... drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand–protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events...
Articles
Biochem Soc Trans (2015) 43 (2): 269–274.
Published: 07 April 2015
... conducted using phospho–Ser 65 (pSer 65 ) and Ser 65 to study the motion of the auto-inhibited structure that leads to an active conformation of the E3 enzyme. The molecular motion required for release of the auto-inhibitory structure was furthered using accelerated molecular dynamics and sampling...
Articles
Biochem Soc Trans (2013) 41 (2): 620–624.
Published: 21 March 2013
..., I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations...
Articles
Biochem Soc Trans (2013) 41 (1): 205–212.
Published: 29 January 2013
..., accomplished through the use of MD (molecular dynamics) simulations. Our pipeline for the MD simulations of GPCRs, implemented in the web service http://gpcr.usc.es , is updated in the present paper and illustrated by recent applications. Special emphasis is put on the A 2A adenosine receptor, one...
Articles
Biochem Soc Trans (2011) 39 (1): 31–35.
Published: 19 January 2011
... C (bridge–helix C-terminal hinge) cause a substantial increase in specific activity (‘superactivity’). Fully atomistic molecular dynamics simulations show that kinking of the BH-H C appears to be driven by cation–π interactions and involve amino acid side chains that are exceptionally highly...
Articles
Biochem Soc Trans (2008) 36 (1): 55–58.
Published: 22 January 2008
... Molecular Dynamics molecular recognition protein flexibility quantitative structure–activity relationship structure-based drug design GSK3 (glycogen synthase kinase 3), also known as TPK I (tau protein kinase I), is a serine/threonine protein kinase encoded by two isoforms in humans, termed...
Articles
Biochem Soc Trans (2008) 36 (1): 27–32.
Published: 22 January 2008
... bilayer based on coarse-grained Molecular Dynamics simulations is described. This method has been used to develop a database of CG simulations (coarse-grained simulations) of membrane proteins ( http://sbcb.bioch.ox.ac.uk/cgdb ). Comparison of CG simulations and AT simulations (atomistic simulations...
Articles
Biochem Soc Trans (2008) 36 (1): 11–15.
Published: 22 January 2008
... Studies: A Biochemical Society Focused Meeting in conjunction with the Molecular Graphics and Modelling Society held at Manchester Interdisciplinary Biocentre, Manchester, U.K., 10–11 September 2007. Organized and Edited by Mike Sutcliffe (Manchester, U.K.). MD Molecular Dynamics...
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Biochem Soc Trans (2007) 35 (6): 1551–1557.
Published: 23 November 2007
... (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp 62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly...
Articles
Biochem Soc Trans (2005) 33 (5): 1012–1015.
Published: 26 October 2005
.... 1 To whom correspondence should be addressed (email gunnar@dbb.su.se ). 21 7 2005 hydrophobicity scale membrane protein molecular dynamics protein–lipid interactions transmembrane The exposed surface of integral membrane proteins generally seems to reflect quite...
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Articles
Biochem Soc Trans (2004) 32 (1): 28–32.
Published: 01 February 2004
... active than the parent peptide. We will also report on our progress towards understanding the dynamic character of compstatin using molecular dynamics simulations. The identification of an ensemble of interconverting conformers of compstatin with variable populations is a first step towards...