Items where Author is "Hayward, Steven"

Published

Hayward, Steven (2024) Protein folding, protein dynamics and the topology of self-motions. Royal Society Open Science, 11 (9). ISSN 2054-5703

Hayward, Steven (2023) A retrospective on the development of methods for the analysis of protein conformational ensembles. The Protein Journal, 42 (3). pp. 181-191. ISSN 1572-3887

Iakovou, Georgios, Laycock, Stephen D. and Hayward, Steven (2022) Interactive flexible-receptor molecular docking in VR using DockIT. Journal of Chemical Information and Modeling, 62 (23). 5855–5861. ISSN 1549-9596

Hayward, Steven and Kitao, Akio (2021) The role of the half-turn in determining structures of Alzheimer’s Aβ wild-type and mutants. Journal of Structural Biology, 213 (4). ISSN 1047-8477

Hayward, Steven (2021) Characterizing protein regions with different flexibility properties and their link to sequence and functional annotations - Speaker. In: ELIXIR 3D-BioInfo Community in Structural Bioinformatics, AGM, 2021-11-02 - 2021-11-04, Online.

Iakovou, Georgios, Laycock, Stephen and Hayward, Steven (2021) Software Introduction: Methodological advances for interacting with biomolecules using haptics. Ensemble, 23 (4). pp. 283-289. ISSN 1884-6750

Hayward, Steven and Milner-White, E. James (2021) Determination of amino acids that favour the αL region using Ramachandran propensity plots. Implications for α-sheet as the possible amyloid intermediate. Journal of Structural Biology, 213 (2). ISSN 1047-8477

Iakovou, Georgios, Alhazzazi, Mousa, Hayward, Steven and Laycock, Stephen D. (2020) DockIT: A tool for interactive molecular docking and molecular complex construction. Bioinformatics, 36 (24). 5698–5700. ISSN 1367-4803

Veevers, Ruth, Cawley, Gavin and Hayward, Steven (2020) Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression. BMC Bioinformatics, 21. ISSN 1471-2105

Alhazzazi, Mousa, Hayward, Steven and Laycock, Stephen D. (2020) GPU-Accelerated Generation of the Molecular Surface. In: Eurographics Conference. UNSPECIFIED.

Veevers, Ruth and Hayward, Steven (2019) Methodological improvements for the analysis of domain movements in large biomolecular complexes. Biophysics and Physicobiology, 16. pp. 328-336. ISSN 2189-4779

Matthews, Nick, Kitao, Akio, Laycock, Stephen and Hayward, Steven (2019) Haptic-assisted interactive molecular docking incorporating receptor flexibility. Journal of Chemical Information and Modeling, 59 (6). pp. 2900-2912. ISSN 1549-9596

Hayward, Steven and Kitao, Akio (2019) Multi-strand β-sheet of Alzheimer Aβ(1-40) folds to β-strip helix: Implication for protofilament formation. Journal of Biomolecular Structure and Dynamics, 37 (8). pp. 2143-2153. ISSN 1538-0254

Roccatano, Danilo and Hayward, Steven (2019) Free energy profile of domain movement in ligand-free citrate synthase. Journal of Physical Chemistry B, 123 (9). 1998–2004. ISSN 1520-6106

Veevers, Ruth and Hayward, Steven (2018) Morphing and docking visualisation of biomolecular structures using multi-dimensional scaling. Journal of Molecular Graphics and Modelling, 82. pp. 108-116. ISSN 1093-3263

Matthews, Nick, Easdon, Robert, Kitao, Akio, Hayward, Steven and Laycock, Stephen (2017) High quality rendering of protein dynamics in space filling mode. Journal of Molecular Graphics and Modelling, 78. pp. 158-167. ISSN 1093-3263

Hayward, Steven and Milner-White, E. James (2017) Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments. Proteins: Structure, Function, and Bioinformatics, 85 (10). 1866–1881. ISSN 0887-3585

Hayward, Steven and Milner-White, E.J. (2017) Cover Image, Volume 85, Issue 10 (page C1). Wiley, Proteins: Structure, Function and Bioinformatics.

Iakovou, Georgios, Hayward, Steven and Laycock, Stephen (2017) Virtual environment for studying the docking interactions of rigid biomolecules with haptics. Journal of Chemical Information and Modeling, 57 (5). 1142–1152. ISSN 1549-9596

Iakovou, Georgios, Laycock, Stephen and Hayward, Steven (2016) Determination of locked interfaces in biomolecular complexes using Haptimol_RD. Biophysics and Physicobiology, 13. pp. 97-103. ISSN 2189-4779

Girdlestone, Christopher and Hayward, Steven (2015) The DynDom3D webserver for the analysis of domain movements in multimeric proteins. Journal of Computational Biology, 23 (1). pp. 21-26. ISSN 1557-8666

Iakovou, Georgios, Hayward, Steven and Laycock, Stephen D. (2015) Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics. Journal of Molecular Graphics and Modelling, 61. pp. 1-12. ISSN 1093-3263

Hayward, Steven and Kitao, Akio (2015) Monte Carlo sampling with linear inverse kinematics for simulation of protein flexible regions. Journal of Chemical Theory and Computation, 11 (8). 3895–3905. ISSN 1549-9626

Taylor, D., Cawley, G. and Hayward, S. (2014) Quantitative method for the assignment of hinge and shear mechanism in protein domain movements. Bioinformatics, 30 (22). pp. 3189-3196. ISSN 1367-4803

Iakovou, Georgios, Hayward, Steven and Laycock, Stephen (2014) A real-time proximity querying algorithm for haptic-based molecular docking. Faraday Discussions, 169. pp. 359-377. ISSN 1359-6640

Hayward, Steven, Leader, David P., Al-Shubailly, Fawzia and Milner-White, E. James (2014) Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides. Proteins: Structure Function and Bioinformatics, 82 (2). pp. 230-239. ISSN 0887-3585

Taylor, Daniel, Cawley, Gavin and Hayward, Steven (2013) Classification of protein domain movements using Dynamic Contact Graphs. PLoS One, 8 (11). ISSN 1932-6203

Hayward, Steven and Milner-White, E. James (2011) Simulation of the β- to α-sheet transition results in a twisted sheet for antiparallel and an α-nanotube for parallel strands: Implications for amyloid formation. Proteins: Structure, Function, and Bioinformatics. pp. 3193-3207. ISSN 1097-0134

Stocks, Matthew, Laycock, Stephen and Hayward, Steven (2011) Applying forces to elastic network models of large biomolecules using a haptic feedback device. Journal of Computer-Aided Molecular Design, 25 (3). pp. 203-211. ISSN 1573-4951

Hayward, Steven and Kitao, Akio (2010) Effect of end constraints on protein loop kinematics. Biophysical Journal, 98 (9). pp. 1976-1985.

Laycock, S. D., Stocks, M. B. and Hayward, S. (2010) Navigation and exploration of large data-sets using a haptic feedback device. In: ACM Siggraph: Posters, 2010-01-01.

Stocks, Matthew B., Hayward, Steven and Laycock, Stephen D. (2009) Interacting with the biomolecular solvent accessible surface via a haptic feedback device. BMC Structural Biology, 9. ISSN 1472-6807

Poornam, Guru Prasad, Matsumoto, Atsushi, Ishida, Hisashi and Hayward, Steven (2009) A method for the analysis of domain movements in large biomolecular complexes. Proteins: Structure, Function, and Bioinformatics, 76 (1). pp. 201-212. ISSN 0887-3585

Qi, Guoying and Hayward, Steven (2009) Database of ligand-induced domain movements in enzymes. BMC Structural Biology, 9. ISSN 1472-6807

Nishima, Wataru, Qi, Guoying, Hayward, Steven and Kitao, Akio (2009) DTA: Dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Bioinformatics, 25 (5). pp. 628-635. ISSN 1460-2059

Yura, Kei and Hayward, Steven (2009) The interwinding nature of protein-protein interfaces and its implication for protein complex formation. Bioinformatics, 25 (23). pp. 3108-3113. ISSN 1367-4803

Ishida, Hisashi and Hayward, Steven (2008) Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome. Biophysical Journal, 95 (12). pp. 5962-5973.

Hayward, Steven and Milner-White, E. James (2008) The geometry of alpha-sheet: Implications for its possible function as amyloid precursor in proteins. Proteins: Structure, Function, and Bioinformatics, 71 (1). 415 - 425. ISSN 0887-3585

Hayward, Steven and de Groot, Bert L. (2008) Normal Modes and Essential Dynamics. In: Molecular Modeling of Proteins. Methods in Molecular Biology, 443 . The Humana Press Inc, USA, pp. 89-106. ISBN 978-1-59745-177-2

Snow, Catherine, Qi, Guoying and Hayward, Steven (2007) Essential dynamics sampling study of adenylate kinase: Comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions. Proteins: Structure Function and Bioinformatics, 67 (2). pp. 325-337. ISSN 0887-3585

Hayward, Steven and Kitao, Akio (2006) Molecular dynamics simulations of NAD(+)-induced domain closure in horse liver alcohol dehydrogenase. Biophysical Journal, 91 (5). pp. 1823-1831.

Milner-White, James E., Watson, James D., Qi, Guoying and Hayward, Steven (2006) Amyloid formation may involve α- to β sheet interconversion via peptide plane flipping. Structure, 14 (9). pp. 1369-1376. ISSN 0969-2126

Qi, Guoying, Lee, Richard and Hayward, Steven (2005) A comprehensive and non-redundant database of protein domain movements. Bioinformatics, 21 (12). pp. 2832-2838. ISSN 1460-2059

Hayward, Steven (2004) Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements. Journal of Molecular Biology, 339 (4). pp. 1001-1021. ISSN 0022-2836

Daidone, Isabella, Roccatano, Danilo and Hayward, Steven (2004) Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling. Journal of Molecular Biology, 339 (3). pp. 515-525. ISSN 0022-2836

Lee, Richard A., Razaz, Moe and Hayward, Steven (2003) The DynDom database of protein domain motions. Bioinformatics, 19 (10). pp. 1290-1291. ISSN 1367-4803

Hayward, Steven and Lee, Richard A. (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. Journal of Molecular Graphics and Modelling, 21 (3). pp. 181-183. ISSN 1093-3263

Hayward, Steven (2001) Peptide-plane flipping in proteins. Protein Science, 10 (11). pp. 2219-2227. ISSN 1469-896X

Roccatano, Danilo, Mark, Alan E. and Hayward, Steven J. (2001) Investigation of the mechanism of domain closure in citrate synthase by molecular dynamics simulation. Journal of Molecular Biology, 301 (5). pp. 1039-1053. ISSN 0022-2836

Hayward, Steven (2001) Normal Mode Analysis of Biological Molecules. In: Computational Biochemistry and Biophysics. Marcel Dekker, New York, pp. 153-168. ISBN 978-0824704551

Berendsen, Herman J. C. and Hayward, Steven (2000) Collective protein dynamics in relation to function. Current Opinion in Structural Biology, 10 (2). pp. 165-169. ISSN 0959-440X

Hayward, S. (1999) Structural principles governing domain motions in proteins. Proteins, Structure, Function and Genetics, 36 (4). pp. 425-435.

Kitao, Akio, Hayward, Steven and Go, Nobuhiro (1998) Energy landscape of a native protein: Jumping-among-minima model. Proteins, Structure, Function and Genetics, 33 (4). pp. 496-517.

Hayward, Steven and Berendsen, Herman J. C. (1998) Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme. Proteins, Structure, Function and Genetics, 30 (2). pp. 144-154.

de Groot, B. L., Hayward, S., van Aalten, D. M. F., Amadei, A. and Berendsen, H. J. C. (1998) Domain motions in bacteriophage T4 lysozyme; a comparison between molecular dynamics and crystallographic data. Proteins, Structure, Function and Genetics, 31 (2). pp. 116-127.

Hayward, Steven, Kitao, Akio and Berendsen, Herman J. C. (1997) Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme. Proteins: Structure, Function, and Bioinformatics, 27 (3). pp. 425-437. ISSN 0887-3585

van der Spoel, David, de Groot, Bert L., Hayward, Steven, Berendsen, Herman J. C. and Vogel, Hans J. (1996) Bending of the calmodulin central helix: A theoretical study. Protein Science, 5 (10). pp. 2044-2053.

Hayward, Steven and Gō, Nobuhiro (1995) Collective variable description of native protein dynamics. Annual Review in Physical Chemistry, 46. pp. 223-250.

Hayward, Steven, Kitao, Akio and Gō, Nobuhiro (1995) Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and Principal Component Analysis. Proteins, Structure, Function and Genetics, 23 (2). pp. 177-186.

Kitao, Akio, Hayward, Steven and Go, Nobuhiro (1994) Comparison of normal mode analysis on a small globular protein in dihedral angle space and Cartesian coordinate space. Biophysical Chemistry, 52 (2). pp. 107-114. ISSN 0301-4622

Hayward, Steven, Kitao, Akio and Gō, Nobuhiro (1994) Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis. Protein Science, 3 (6). pp. 936-943. ISSN 1469-896X

Hayward, S., Kitao, Akio, Hirata, Fumio and Gō, Nobuhiro (1993) Effect of solvent on the collective motions in globular protein. Journal of Molecular Biology, 234 (4). pp. 1207-1217. ISSN 1089-8638

Hayward, S., Kitao, A., Hirata, F. and Go, N. (1993) The Effect of Water on the Low Frequency Motions in BPTI. In: Computer Aided Innovation of New Materials II. Elsevier.

Hayward, S. and Collins, J. F. (1992) Limits on alpha-helix prediction with neural network models. Proteins: Structure, Function, and Bioinformatics, 14 (3). pp. 372-381. ISSN 0887-3585

Hayward, S., Heermann, Dieter W. and Binder, K. (1987) Dynamic percolation transition induced by phase separation: A Monte Carlo analysis. Journal of Statistical Physics, 49 (5-6). pp. 1053-1081. ISSN 0022-4715