Items where Author is "Hayward, Steven"

Article

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2024) Protein folding, protein dynamics and the topology of self-motions. Royal Society Open Science, 11 (9). ISSN 2054-5703

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 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

Iakovou, Georgios, Laycock, Stephen and Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2021) Software Introduction: Methodological advances for interacting with biomolecules using haptics. Ensemble, 23 (4). pp. 283-289. ISSN 1884-6750

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-7451-2509, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0002-4118-9095 and Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2020) Investigation of sequence features of hinge-bending regions in proteins with domain movements using kernel logistic regression. BMC Bioinformatics, 21. ISSN 1471-2105

Veevers, Ruth and Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 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

Iakovou, Georgios, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 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. ORCID: https://orcid.org/0000-0002-4118-9095 and Hayward, S. ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604, 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 ORCID: https://orcid.org/0000-0002-4118-9095 and Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2013) Classification of protein domain movements using Dynamic Contact Graphs. PLoS One, 8 (11). ISSN 1932-6203

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 and Kitao, Akio (2010) Effect of end constraints on protein loop kinematics. Biophysical Journal, 98 (9). pp. 1976-1985.

Stocks, Matthew B., Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (2009) Database of ligand-induced domain movements in enzymes. BMC Structural Biology, 9. ISSN 1472-6807

Nishima, Wataru, Qi, Guoying, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (2008) Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome. Biophysical Journal, 95 (12). pp. 5962-5973.

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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

Snow, Catherine, Qi, Guoying and Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (2005) A comprehensive and non-redundant database of protein domain movements. Bioinformatics, 21 (12). pp. 2832-2838. ISSN 1460-2059

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (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 ORCID: https://orcid.org/0000-0001-6959-2604 (2003) The DynDom database of protein domain motions. Bioinformatics, 19 (10). pp. 1290-1291. ISSN 1367-4803

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 (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. ORCID: https://orcid.org/0000-0001-6959-2604 (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

Berendsen, Herman J. C. and Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2000) Collective protein dynamics in relation to function. Current Opinion in Structural Biology, 10 (2). pp. 165-169. ISSN 0959-440X

Hayward, S. ORCID: https://orcid.org/0000-0001-6959-2604 (1999) Structural principles governing domain motions in proteins. Proteins, Structure, Function and Genetics, 36 (4). pp. 425-435.

Kitao, Akio, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604 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. ORCID: https://orcid.org/0000-0001-6959-2604, 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 ORCID: https://orcid.org/0000-0001-6959-2604, 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 ORCID: https://orcid.org/0000-0001-6959-2604, 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 ORCID: https://orcid.org/0000-0001-6959-2604 and Gō, Nobuhiro (1995) Collective variable description of native protein dynamics. Annual Review in Physical Chemistry, 46. pp. 223-250.

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604, 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 ORCID: https://orcid.org/0000-0001-6959-2604 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 ORCID: https://orcid.org/0000-0001-6959-2604, 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. ORCID: https://orcid.org/0000-0001-6959-2604, 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. ORCID: https://orcid.org/0000-0001-6959-2604 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. ORCID: https://orcid.org/0000-0001-6959-2604, 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

Book Section

Alhazzazi, Mousa ORCID: https://orcid.org/0000-0001-7451-2509, Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Laycock, Stephen D. (2020) GPU-Accelerated Generation of the Molecular Surface. In: Eurographics Conference. UNSPECIFIED.

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 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

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2001) Normal Mode Analysis of Biological Molecules. In: Computational Biochemistry and Biophysics. Marcel Dekker, New York, pp. 153-168. ISBN 978-0824704551

Hayward, S. ORCID: https://orcid.org/0000-0001-6959-2604, 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.

Conference or Workshop Item

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (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.

Laycock, S. D., Stocks, M. B. and Hayward, S. ORCID: https://orcid.org/0000-0001-6959-2604 (2010) Navigation and exploration of large data-sets using a haptic feedback device. In: ACM Siggraph: Posters, 2010-01-01.

Other

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 and Milner-White, E.J. (2017) Cover Image, Volume 85, Issue 10 (page C1). Wiley, Proteins: Structure, Function and Bioinformatics.