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Domain Movement Classification: 'Hinge and Shear'
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Domain Movement Classification using Dynamic Contact Graphs
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Domain Movement in large biomolecular complexes
DynDom3D

Domain Movement in large biomolecular complexes
DynDom3D

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  References

Click on underlined title for abstract or full paper

Databases

Daniel Taylor, Gavin Cawley, Steven Hayward, "Quantitative Method for the Assignment of Hinge and Shear Mechanism in Protein Domain Movements" Bioinformatics, 2014.

Daniel Taylor, Gavin Cawley, Steven Hayward, "Classification of Domain Movements in Proteins Using Dynamic Contact Graphs" PLOS ONE, 8(11), 2013.

Guoying Qi, Steven Hayward, "A database of ligand-induced domain movements in enzymes" BMC Structural Biology, 9(13), 2009.

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

R. A. Lee, M. Razaz, S. Hayward, "The DynDom database of protein domain motions" Bioinformatics, 19, 10, 2003.

Methods

C.Girdlestone, S.Hayward, "The DynDom3D webserver for the analysis of domain movements in multimeric proteins" Journal of Computational Biology, 23(1), 21-26, 2016.

G.Poornam, A. Matsumoto, H.Ishida, S.Hayward, "A method for the analysis of domain movements in large biomolecular complexes" Proteins, 76, 201-21, 2009.

S. Hayward, R. A. Lee, "Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50" J Mol Graph Model, Dec, 21(3), 181-3, 2002.


DynDom main reference:

S. Hayward, H. J. C. Berendsen, "Systematic Analysis of Domain Motions in Proteins from Conformational Change; New Results on Citrate Synthase and T4 Lysozyme" Proteins, Structure, Function and Genetics, 30, 144, 1998.


S. Hayward, A. Kitao, H. J. C. Berendsen, "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 Genetics, 27, 425, 1997.

Applications

S. Hayward, A. Kitao, "Molecular Dynamics Simulations of NAD+-Induced Domain Closure in Horse Liver Alcohol Dehydrogenase" Biophysical Journal, 91:1823-1831, 2006.

I. Daidone, D. Roccatano, S. Hayward, "Investigating the accessibility of the closed domain conformation of citrate synthase using essential dynamics sampling" J. Mol. Biol. , 339, 515, 2004.

S. Hayward, "Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements" J. Mol. Biol. , 339, 1001, 2004.

D. Roccatano, A. E. Mark, S. Hayward, "Investigation of the Mechanism of Domain Closure in Citrate Synthase by Molecular Dynamics Simulation" J. Mol. Biol. , 310, 1039, 2001.

S. Hayward, "Structural Principles Governing Domain Motions in Proteins " Proteins, Structure, Function and Genetics, 36, 425, 1999.

B. L. de Groot, S. Hayward, D. van Aalten, A. Amadei, H. J. C. Berendsen, "Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between Molecular Dynamics and Crystallographic Data" Proteins, Structure, Function and Genetics, 31, 116, 1998.

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