Allison Group - Publications

2016

1. A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe.
   T. Pichugina, T. Sugawara, A. Kaykov, W. Schierding, K. Masuda, J. Uewaki, R.S. Grand, J.R. Allison, R.A. Martienssen, P. Nurse, M. Ueno and J.M. O'Sullivan, Sci. Rep. 6, 18757 (2016)
   
   
2. Positive selection or free to vary? Assessing the functional significance of sequence change using molecular dynamics.
   J.R. Allison, M. Lechner, M.P. Hoeppner and A.M. Poole PLoS One 11, e0147619 (2016)
   
   
3. Let the powers combine.
   J.R. Allison, Structure 24, 5-6 (2016)
   
   

2015

4. Comment on "A tensor-free method for the structural and dynamic refinement of proteins using residual dipolar couplings"
   L.N. Wirz and J.R. Allison, J. Phys. Chem. B 119, 8223-8224 (2015)
   
   
5. Deciphering β-lactoglobulin interactions at an oil-water interface: a molecular dynamics study
   D. Zare, K.M. McGrath, and J.R. Allison, Biomacromolecules 16, 1855-1861 (2015)
   
   
6. Fitting alignment tensor components to experimental RDCs, CSAs and RQCs
   L.N. Wirz and J.R. Allison, J. Biomol. NMR 62, 25-29 (2015)
   
   

2014

7. A relationship between the transient structure in the monomeric state and the aggregation propensities of α-synuclein and β-synuclein.
   J.R. Allison, R. Rivers, J.C. Christodoulou, M. Vendruscolo and C.M. Dobson, Biochemistry 53, 7170-7183 (2014)
   
   
8. Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure.
   R.S. Grand, T. Pichugina, L.R. Gehlen, M.B. Jones, P. Tsai, J.R. Allison, R. Martienssen and J.M. O'Sullivan, Nucl. Acids Res. 42, 12585-12599 (2014)
   
   

2013

1. Molecular dynamics simulations of barley and maize lipid transfer proteins show ligand binding preferences in agreement with experimental data
   L.J. Smith, Y. Roby, J.R. Allison and W.F. van Gunsteren, Biochemistry 52, 5029-5038 (2013)
   
   
2. Relative free enthalpies for point mutations in two proteins with highly similar sequences but difference folds
   N. Hansen, J.R. Allison, F.H. Hodel and W.F. van Gunsteren, Biochemistry 52, 4962-4970 (2013)
   
   
3. Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12
   L.J. Smith, W.F. van Gunsteren and J.R. Allison, Prot. Sci. 22, 56-64 (2013)
   
   
4. Directed evolution of a model primordial enzyme provides insights into the development of the genetic code.
   M.M. Müller, J.R. Allison, M. Hongdilokkul, L. Gaillon, P. Kast, W.F. van Gunsteren, P. Marlière and D. Hilvert, PLoS 9, e1003187 (2013)
   
   

2012

1. Implicit solvation parameters derived from explicit water forces in large-scale molecular dynamics simulations
   J. Kleinjung, W. Scott, J.R. Allison, W.F. van Gunsteren, F. Fraternali, J. Chem. Theory Comput. 8, 2391-2403 (2012)
   
   
2. Probing the structure and dynamics of proteins by combining molecular dynamics simulations and experimental NMR data
   J.R. Allison, S. Hertig, J.H. Missimer, L.J. Smith, M.O. Steinmetz and J. Dolenc, J. Chem. Theory Comput. 8, 3430-3444 (2012)
   
   
3. Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data
   J.R. Allison Biophys. Rev. (in press) 4, 189-203 (2012)
   
   
4. On developing coarse-grained models for biomolecular simulation: a review
   S. Riniker, J.R. Allison and W.F. van Gunsteren, Phys. Chem. Chem. Phys. 14, 12423-12430 (2012)
   
   
5. On the calculation of 3Jαβ-coupling constants for side chains in proteins
   D., Steiner, J.R. Allison, A.P. Eichenberger and W.F. van Gunsteren, J. Biomol. NMR 53, 223-246 (2012)
   
   
6. Implicit solvation parameters derived from explicit water forces in large-scale molecular dynamic simulations
   J. Kleinjung, W.R.P. Scott, J.R. Allison, W.F. van Gunsteren, and F. Fraternali, J. Chem. Theory Comput. 8, 2391-2403 (2012)
   
   
7. New functionalities in the GROMOS biomolecular simulation software
   A.-P.E. Kunz, J.R. Allison, D.P. Geerke, B.A.C. Horta, P.H. Hünenberger, S. Riniker, N. Schmid, and W.F. van Gunsteren, J. Comput. Chem. 33, 340-353 (2012)
   
   
8. Coarse-grained models for the solvents dimethyl sulfoxide, chloroform and methanol
   J.R. Allison, S. Riniker, and W.F. van Gunsteren, J. Chem. Phys. 136, 054505 (2012)
   
   

2011

1. Current Computer Modeling Cannot Explain Why Two Highly Similar Sequences Fold into Different Structures
   J.R. Allison, M. Bergeler, N. Hansen, and W.F. van Gunsteren, Biochemistry 50, 10965-10973 (2011)
   
   
2. The GROMOS++ software for the analysis of biomolecular simulation trajectories
   A.P. Eichenberger, J.R. Allison, J. Dolenc, D.P. Geerke, B.A.C. Horta, K. Meier, C. Oostenbrink, N. Schmid, D. Steiner, D. Wang, and W.F. van Gunsteren, J. Chem. Theory Comput. 7, 3379-3390 (2011)
   
   
3. Biomolecular structure refinement using the GROMOS simulation software
   N. Schmid, J.R. Allison, J. Dolenc, A.P. Eichenberger, A.-P.E. Kunz, and W.F. van Gunsteren, J. Biomol. NMR 51, 265-281 (2011)
   
   
4. A refined, efficient mean solvation force model that includes the interior volume contribution
   J.R. Allison, K. Boguslawska, F. Fraternali, and W.F. van Gunsteren, J. Phys. Chem. B 115, 4547-4557 (2011)
   
   

2010

1. Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation
   J.R. Allison, G.-P. Moll, and W.F. van Gunsteren, Biochemistry 49, 6916-6927 (2010)
   
   
2. Comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stabilities
   J.R. Allison, M. Müller, and W.F. van Gunsteren, Prot. Sci. 19, 2186-2195 (2010)
   
   

2009

1. Determination of the free energy landscape of α-synuclein using spin-label nuclear magnetic resonance measurements
   J.R. Allison, P. Varnai, C.M. Dobson, and M. Vendruscolo, J. Am. Chem. Soc. 131, 18314-18326 (2009)
   
   
2. A method to explore protein side chain conformational variability using experimental data
   J.R. Allison and W.F. van Gunsteren, ChemPhysChem 10, 3213-3228 (2009)