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Publications

[27] D. J. Cole, M. Janecek, J. E. Stokes, M. Rossmann, J. C. Faver, G. J. McKenzie, A. R. Venkitaraman, M. Hyvonen, D. R. Spring, D. J. Huggins, W. L. Jorgensen
Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction
Chemical Communications, 53, 9372 (2017) Full text

[26] A. S. Fokas, D. J. Cole, N. D. M. Hine, S. A. Wells, M. C. Payne, A. W. Chin
Evidence of correlated static disorder in the Fenna-Matthews-Olson complex
Journal of Physical Chemistry Letters, 8, 2350 (2017) Full text

[25] S. E. Morgan, D. J. Cole, A. W. Chin
Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex
Scientific Reports, 6, 36703 (2016) Full text

[24] D. J. Cole, N. D. M. Hine
Applications of Large-Scale Density Functional Theory in Biology
Journal of Physics: Condensed Matter, 28, 393001 (2016) Full text

[23] A. S. Fokas, D. J. Cole, S. E. Ahnert, A. W. Chin
Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis
Scientific Reports, 6, 33213 (2016) Full text

[22] D. J. Cole, J. Z. Vilseck, J. Tirado-Rives, M. C. Payne, W. L. Jorgensen
Biomolecular Force Field Parameterization via Atoms in Molecule Electron Density Partitioning
Journal of Chemical Theory and Computation, 12, 2312 (2016) Full text

[21] D. J. Cole, J. Tirado-Rives, W. L. Jorgensen
Molecular Dynamics and Monte Carlo Simulations for Protein-Ligand Binding and Inhibitor Design
Biochimica et Biophysica Acta (BBA) - General Subjects, 1850, 966 (2015) Full text

[20] L. P. Lee, N. Gabaldon Limas, D. J. Cole, M. C. Payne, C.-K. Skylaris, T. A. Manz
Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms
Journal of Chemical Theory and Computation, 10, 5377 (2014) Full text

[19] G. Lever, D. J. Cole, R. Lonsdale, K. E. Ranaghan, D. J. Wales, A. J. Mulholland, C.-K. Skylaris, M. C. Payne
Large-Scale Density Functional Theory Transition State Searching in Enzymes
Journal of Physical Chemistry Letters, 5, 3614 (2014) Full text

[18] A. S. Fokas, D. J. Cole, A. W. Chin
Constrained Geometric Simulation of the Fenna-Matthews-Olson Complex: The Role of Correlated Motion in Reducing Uncertainty in Excitation Energy Transfer
Photosynthesis Research, 122, 275 (2014) Full text

[17] C. Weber, D. J. Cole, D. D. O'Regan, M. C. Payne
Renormalization of Myoglobin-Ligand Binding Energetics by Quantum Many-Body Effects
Proc. Natl. Acad. Sci. U.S.A., 111, 5790 (2014) Full text

[16] W. J. Belfield, D. J. Cole, I. L. Martin, M. C. Payne, P.-L. Chau
Constrained Geometric Simulation of the Nicotinic Acetylcholine Receptor
Journal of Molecular Graphics and Modelling, 52, 1-10 (2014) Full text

[15] D. J. Cole, J. Tirado-Rives, W. L. Jorgensen
Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering
Journal of Chemical Theory and Computation, 10, 565 (2014) Abstract Full text

[14] J. L. Kozuska, I. M. Paulsen, W. J. Belfield, I. L. Martin, D. J. Cole, A. Holt, S. M. J. Dunn
Impact of Intracellular Domain Flexibility upon Properties of Activated Human 5-HT3 Receptors
British Journal of Pharmacology, 171, 1617 (2014) Full text Commentary

[13] D. J. Cole, A. W. Chin, N. D. M. Hine, P. D. Haynes, M. C. Payne
Toward ab initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex
Journal of Physical Chemistry Letters, 4, 4206 (2013) Abstract Full text

[12] L. P. Lee, D. J. Cole, C.-K. Skylaris, W. L. Jorgensen, M. C. Payne
Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning
Journal of Chemical Theory and Computation, 9, 2981 (2013) Abstract Full text

[11] G. Lever, D. J. Cole, N. D. M. Hine, P. D. Haynes, M. C. Payne
Electrostatic Considerations Affecting the Calculated HOMO-LUMO Gap in Protein Molecules
Journal of Physics: Condensed Matter (Fast Track Communications), 25, 152101 (2013) Abstract Full text

[10] L. P. Lee, D. J. Cole, M. C. Payne, C.-K. Skylaris
Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems
Journal of Computational Chemistry, 34, 429 (2013) Abstract Full text

[9] D. J. Cole, D. D. O'Regan, M. C. Payne
Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U
Journal of Physical Chemistry Letters, 3, 1448 (2012) Abstract Full text

[8] D. J. Cole, P. K. Ang, K. P. Loh
Ion Adsorption at the Graphene/Electrolyte Interface
Journal of Physical Chemistry Letters, 2, 1799 (2011) Abstract Full text

[7] D. J. Cole, E. Rajendra, M. Roberts-Thomson, B. Hardwick, G. J. McKenzie, M. C. Payne, A. R. Venkitaraman, C. -K. Skylaris
Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity
PLoS Computational Biology, 7, e1002096 (2011) Abstract Full text

[6] D. J. Cole, C. -K. Skylaris, E. Rajendra, A. R. Venkitaraman, M. C. Payne
Protein-Protein Interactions from Linear-Scaling First-Principles Quantum-Mechanical Calculations
Europhysics Letters, 91, 37004 (2010) Abstract Full text

[5] D. J. Cole, M. C. Payne, L. Colombi Ciacchi
Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces
Phys. Chem. Chem. Phys., 11, 11395 (2009) Abstract Full text

[4] D. V. Kubair, D. J. Cole, L. Colombi Ciacchi, S. M. Spearing
Multiscale Mechanics Modeling of Direct Silicon Wafer Bonding
Scripta Materialia 60, 1125 (2009) Abstract Full text

[3] L. Colombi Ciacchi, D. J. Cole, M. C. Payne, P. Gumbsch
Stress-driven oxidation chemistry of wet silicon surfaces
Journal of Physical Chemistry C 112, 12077 (2008) Abstract Full text

[2] D. J. Cole, G. Csányi, M. C. Payne, S. M. Spearing, L. Colombi Ciacchi
Development of a classical force field for the oxidised Si surface: Application to hydrophilic wafer bonding
Journal of Chemical Physics 127, 204704 (2007) Abstract Full text

[1] D. J. Cole, M. C. Payne, L. Colombi Ciacchi
Stress development and impurity segregation during oxidation of the Si(100) surface
Surface Science 601, 4888 (2007) Abstract Full text

My Ph.D. thesis is available here

Selected Presentations

"Biomolecular force field parameterisation from atoms-in-molecule electron density partitioning"
American Chemical Society spring meeting, San Diego, U.S.A. (2016);
CECAM workshop: "Beyond point charges: novel electrostatic developments in force fields", Lausanne, Switzerland (2016);
Lennard-Jones Centre computational drug discovery masterclass, Cambridge (2016);
Recent Appointees in Materials Modelling conference, Queen Mary's University London (2016).

"Applications of Large-Scale Electronic Structure Calculations in Biology"
CCP9 Young Researchers' Event, University of York (2016);
Psi-K Conference, San Sebastian, Spain (2015);
Centre for Scientific Computing Seminar, University of Warwick (2015);
Physics at the Nanoscale Seminar, King's College London (2014).

"Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering"
2014 Workshop on Free Energy Methods in Drug Design, Boston, U.S.A (2014);
American Chemical Society March Meeting, Dallas, U.S.A. (2014).

"Optimisation of non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase (NNRTIs)"
Schrödinger User Group Meeting, Boston, U.S.A. (2014).

"Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U"
American Chemical Society March Meeting, San Diego, U.S.A. (2012).

"Biomolecular Simulation with ONETEP"
India-UK workshop on "Trends in protein biophysics: from in silico molecules to in vivo and vitro proteins" (2011).

"Protein-Protein Interactions from Linear-Scaling DFT Calculations"
Psi-K Conference, Berlin, Germany (2010);
American Physical Society March Meeting, Portland, U.S.A. (2010);
British Biophysical Society Meeting, Cambridge, U.K. (2010).

"pH Sensitivity of Solution-Gated Graphene"
International Conference on Materials for Advanced Technologies, Singapore (2009).

"Biomolecular Adsorption at a Si/Water Interface Driven by Water-Structure Effects"
Microstructure and Fracture Seminar, Cavendish Laboratory (2009).

"ONETEP and Protein Adsorption Simulations on the Darwin Cluster"
SciComp@Cam, Centre for Mathematical Sciences, Cambridge (2008).

"Molecular Dynamics Simulations of Protein-Surface Interactions"
Physics of Medicine Roadshow, Cambridge Institute for Medical Research (2008).

"Development of a Classical Force Field for the Simulation of Solvated Proteins on Oxidised Si Surfaces"
International Conference on Materials for Advanced Technologies, Singapore (2007).