All Outputs (65)

Molecular dynamics simulations using graphics processing units (2011)
Journal Article
Baker, J., & Hirst, J. (2011). Molecular dynamics simulations using graphics processing units. Molecular Informatics, 30(6-7), https://doi.org/10.1002/minf.201100042

It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In t... Read More about Molecular dynamics simulations using graphics processing units.

First principles predictions of thermophysical properties of refrigerant mixtures (2011)
Journal Article
Oakley, M. T., Hainam, D., Hirst, J., & Wheatley, R. J. (2011). First principles predictions of thermophysical properties of refrigerant mixtures. Journal of Chemical Physics, 134, https://doi.org/10.1063/1.3567308

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures wit... Read More about First principles predictions of thermophysical properties of refrigerant mixtures.

Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures (2010)
Journal Article
Kountouris, P., & Hirst, J. D. (2010). Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11, Article 407. https://doi.org/10.1186/1471-2105-11-407

Background

β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains.

Results

We have developed a novel method... Read More about Predicting beta-turns and their types using predicted backbone dihedral angles and secondary structures.

Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures (2010)
Journal Article
Kountouris, P., & Hirst, J. (2010). Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures. BMC Bioinformatics, 11,

Background: β-turns are secondary structure elements usually classified as coil. Their prediction is important, because of their role in protein folding and their frequent occurrence in protein chains.

Results: We have developed a novel method tha... Read More about Predicting β-turns and their types using predicted backbone dihedral angles and secondary structures.

Exploring protein structural dissimilarity to facilitate structure classification (2009)
Journal Article
Jain, P., & Hirst, J. (2009). Exploring protein structural dissimilarity to facilitate structure classification. BMC Structural Biology, 9, https://doi.org/10.1186/1472-6807-9-60

Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classi... Read More about Exploring protein structural dissimilarity to facilitate structure classification.