Atomistic Simulations in Medicinal Chemistry & Biology at Newcastle University
Preprints
- Wang L, Alibay I, Boothroyd S, Cavender CE, Horton JT, McIsaac AR, Mitchell JA, Thompson MW, Wagner JR, Westbrook BR, Chodera JD, Cole DJ, Shirts MR, Mobley DL, Developing and benchmarking Sage 2.3.0 with the AshGC neural network charge model. chemrxiv.
- MacDermott-Opeskin H, Scheen J, Wognum C et al., A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data. chemrxiv
- Moore JH, Cole DJ, Csányi G, Computing Hydration Free Energies of Small Molecules with First Principles Accuracy. arxiv.
Published
- Adams C, Horton JT, Wang L, Boothroyd S, Mobley DL, Wright DW, Cole DJ, A Graph Neural Network Charge Model Targeting Accurate Electrostatic Properties of Organic Molecules. Journal of Chemical Theory and Computation, 2025 (in press).
- Morado J, Zinovjev K, Hedges LO, Cole DJ, Michel J, Enhancing Electrostatic Embedding for ML/MM Free Energy Calculation. Journal of Chemical Theory and Computation, 2025, 21(22), 11805-11819.
- Pirie R, Hall SJ, Cole DJ, Murphy T, Riemannian Geometry and Molecular Similarity II: Kähler Quantization. Proceedings of the Royal Society A, 2025, 481, 20240707.
- Herasymenko O, Silva M, Abu-Saleh AA, et al., CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. Journal of Chemical Information and Modelling, 2025, 65(13), 6884-6898.
- Kovács DP, Moore JH, Browning NJ, Batatia I, Horton JT, Pu Y, Kapil V, Witt WC, Magdau I-B, Cole DJ, Csányi G, MACE-OFF: Short-range Transferable Machine Learning Force Fields for Organic Molecules. Journal of the American Chemical Society, 2025, 147(21), 17598-17611.
- Wang Y, Takaba K, Chen MS, Wieder M, Xu Y, Zhang JZH, Yu K, Wang X, Zhang L, Cole DJ, Rackers JA, Greener JG, Eastman P, Martiniani S, Tuckerman ME, On the design space between molecular mechanics and machine learning force fields. Applied Physics Reviews 2025, 12(2), 021304.
- Cree B, Bieniek MK, Amin S, Kawamura A, Cole DJ, Active learning driven prioritisation of compounds from on-demand libraries targeting the SARS-CoV-2 main protease. Digital Discovery, 2025, 4, 438-450.
- Clark F, Cole DJ, Michel J, Robust Automated Truncation Point Detection for Molecular Simulations. Journal of Chemical Theory and Computation, 2025, 21, 88-101.
- Clark F, Robb G, Cole DJ, Michel J, Automated Adaptive Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation, 2024, 20, 7806-7828.
- Pirie R, Stanway-Gordon HA, Stewart HL, Wilson KL, Paton S, Tyerman J, Cole DJ, Fowler K, Waring MJ. An analysis of the physicochemical properties of oral drugs from 2000 to 2022. RSC Medicinal Chemistry, 2024, 15, 3125-3132.
- Behara PK, Jang H, Horton JT, Gokey T, Dotson DL, Boothroyd S, Bayly CI, Cole DJ, Wang L-P, Mobley DL, Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields. Journal of Physical Chemistry B, 2024, 128, 7888-7902.
- Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling. Journal of Physical Chemistry B, 2024, 128, 7043-7067.
- Hall SJ, Pirie R, Cole DJ, Riemannian Geometry and Molecular Surfaces I: Spectrum of the Laplacian. Proceedings of the Royal Society A, 2024, 480, 20230343.
- Horton JT, Boothroyd S, Behara PK, Mobley DL, Cole DJ, A transferable double exponential potential for condensed phase simulations of small molecules. Digital Discovery, 2023, 2, 1178-1187.
- Clark F, Robb G, Cole DJ, Michel J, Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations. Journal of Chemical Theory and Computation, 2023, 19, 3686-3704.
- Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang L-P, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL, Development and Benchmarking of Open Force Field 2.0.0 — the Sage Small Molecule Force Field. Journal of Chemical Theory and Computation, 2023, 19, 3251-3275.
- Jorge M, Barrera MC, Milne AW, Ringrose C, Cole DJ, What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids? Journal of Chemical Theory and Computation, 2023, 19, 1790-1804.
- Horton JT, Boothroyd S, Wagner J, Mitchell JA, Gokey T, Dotson DL, Behara PK, Ramaswamy VK, Mackey M, Chodera JD, Anwar J, Mobley DL, Cole DJ, Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale. Journal of Chemical Information and Modeling, 2022, 62.
- Bieniek MK, Cree B, Pirie R, Horton JT, Tatum NJ, Cole DJ, An Open-Source Molecular Builder and Free Energy Preparation Workflow. Communications Chemistry, 2022, 5, 136.
- Ringrose C, Horton JT, Wang L-P, Cole DJ. Exploration and Validation of Force Field Design Protocols through QM-to-MM Mapping. Physical Chemistry Chemical Physics, 2022, 24, 17014-17027.
- Kovács DP, van der Oord C, Kucera J, Allen AEA, Cole DJ, Ortner C, Csányi G. Linear Atomic Cluster Expansion Force Fields for Organic Molecules: beyond RMSE, Journal of Chemical Theory and Computation, 2021, 17, 7696-7711.
- Littlefair JD, Cole DJ, Penfold TJ. On Assessing Functional Errors in Density Functional Theory using Atomisation Energies and Electric Field Gradients, International Journal of Quantum Chemistry, 2021, e26799.
- Yang L, Horton JT, Payne MC, Penfold TJ, Cole DJ. Modelling Molecular Emitters in Organic Light Emitting Diodes with the Quantum Mechanical Bespoke Force Field, Journal of Chemical Theory and Computation, 2021, 17, 5021-5033.
- Nelson L, Bariami S, Ringrose C, Horton JT, Kurdekar V, Mey ASJS, Michel J, Cole DJ. Implementation of the QUBE force field in SOMD for high-throughput alchemical free energy calculations, Journal of Chemical Information and Modeling, 2021, 61, 2124-2130.
- Chaillet ML, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. Journal of Physical Chemistry Letters 2020, 11, 10306-10314.
- Linscott EB, Cole DJ, Hine NDM, Payne MC, Weber C. ONETEP+TOSCAM: Uniting dynamical mean field theory and linear-scaling density functional theory. Journal of Chemical Theory and Computation 2020, 16, 4899-4911.
- Cole DJ, Mones L, Csányi G. A Machine Learning Based Intramolecular Force Field for a Flexible Organic Molecule. Faraday Discussions 2020, 224, 247-264.
- Prentice JCA, Aarons J, Womack JC, Allen AEA, Andrinopoulos L, Anton L, Bell RA, Bhandari A, Bramley GA, Charlton RJ, Clements RJ, Cole DJ, Constantinescu G, Corsetti F, Dubois SMM, Duff KKB, Escartín JM, Greco A, Hill Q, Lee LP, Linscott E, O’Regan DD, Phipps MJS, Ratcliff LE, Serrano AR, Tait EW, Teobaldi G, Vitale V, Yeung N, Zuehlsdorff TJ, Dziedzic J, Haynes PD, Hine NDM, Mostofi AA, Payne MC, Skylaris CK. The ONETEP linear-scaling density functional theory program. Journal of Chemical Physics 2020, 152, 174111.
- Gougoula E, Cole DJ, Walker NR. Bifunctional Hydrogen Bonding of Imidazole with Water Explored by Rotational Spectroscopy and DFT Calculations. Journal of Physical Chemistry A 2020, 124, 2649-2659.
- Horton JT, Allen AEA, Cole DJ. Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field. Chemical Communications 2020, 56, 932-935.
- al-Badri MA, Linscott EB, Georges A, Cole DJ, Weber C. Super-exchange mechanism and quantum many body excitations in the archetypal hemocyanin/tyrosinase di-Cu oxo-bridge. Communications Physics 2020, 3, 4.
- Qian Y, Cabeza de Vaca I, Vilseck JZ, Cole DJ, Tirado-Rives J, Jorgensen WL. Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor. Journal of Physical Chemistry B 2019, 123, 8675-8685.
- Allen AEA, Robertson MJ, Payne MC, Cole DJ. Development and Validation of the Quantum Mechanical Bespoke Protein Force Field. ACS Omega 2019, 4, 14537-14550.
- Cole DJ, Horton JT, Nelson L, Kurdekar V. The Future of Force Fields in Computer Aided Drug Design. Future Medicinal Chemistry 2019, 11, 2359-2363.
- Manz T, Chen T, Cole DJ, Gabaldon Limas N, Fiszbein B. New Scaling Relations to Compute Atom-in-Material Polarizabilities and Dispersion Coefficients: Part 1. Theory and Accuracy. RSC Advances 2019, 9, 19297-19324.
- Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of Protein-Ligand Binding Free Energies using Quantum Mechanical Bespoke Force Fields. MedChemComm 2019, 10, 1116-1120. New Talent in Medicinal Chemistry Themed Collection.
- Horton JT, Allen AEA, Dodda L, Cole DJ. QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics. Journal of Chemical Information and Modeling 2019, 59(4), 1366-1381.
- Linscott EB, Cole DJ, Payne MC, O’Regan DD. Role of spin in the calculation of Hubbard U and Hund’s J parameters from first principles. Physical Review B 2018, 98, 235157.
- Allen AEA, Payne MC, Cole DJ. Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection. Journal of Chemical Theory and Computation 2018, 14(1), 274-281.
- Cole DJ, Janecek M, Stokes JE, Rossmann M, Faver JC, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR, Huggins DJ, Jorgensen WL. Computationally-Guided Optimization of Small-Molecule Inhibitors of the Aurora A Kinase – TPX2 Protein-Protein Interaction. Chemical Communications 2017, 53(67), 9372-9375.
- Joseph J, Baumann KN, Koehler P, Zuehlsdorff TJ, Cole DJ, Weber J, Bohndiek SE, Hernández-Ainsa S. Distance dependent photoacoustics revealed through DNA nanostructures. Nanoscale 2017, 9(42), 16193-16199.
- Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. Evidence of Correlated Static Disorder in the Fenna–Matthews–Olson Complex. Journal of Physical Chemistry Letters 2017, 8, 2350–2356.
- Cole DJ, Hine NDM. Applications of Large-Scale Density Functional Theory in Biology. Journal of Physics: Condensed Matter 2016, 28(39), 393001.
- Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. Biomolecular Force Field Parameterization via Atoms-in-Molecular Electron Density Partitioning. Journal of Chemical Theory and Computation 2016, 12(5), 2312-2323.
- Morgan SE, Cole DJ, Chin AW. Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex. Scientific Reports 2016, 6, 36703.
- Fokas AS, Cole DJ, Ahnert SE, Chin AW. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis. Scientific Reports 2016, 6, 33213.
- Cole DJ, Tirado-Rives J, Jorgensen WL. Molecular Dynamics and Monte Carlo Simulations for Protein-Ligand Binding and Inhibitor Design. Biochimica et Biophysica Acta (BBA) General Subjects 2015, 1850(5), 966-971.
- Fokas AS, Cole DJ, Chin AW. Constrained geometric dynamics of the Fenna–Matthews–Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer. Photosynthesis Research 2014, 122(3), 275-292.
- Belfield WJ, Cole DJ, Martin IL, Payne MC, Chau P-L. Constrained geometric simulation of the nicotinic acetylcholine receptor. Journal of Molecular Graphics and Modelling 2014, 52, 1-10.
- Cole DJ, Tirado-Rives J, Jorgensen WL. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering.Journal of Chemical Theory and Computation 2014, 10(2), 565-571.
- Lee LP, Gabaldon Limas N, Cole DJ, Payne MC, Skylaris C-K, Manz TA. Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms. Journal of Chemical Theory and Computation 2014, 10(12), 5377-5390.
- Kozuska JL, Paulsen IM, Belfield WJ, Martin IL, Cole DJ, Holt A, Dunn SMJ. Impact of Intracellular Domain Flexibility upon Properties of Activated Human 5-HT3 Receptors. British Journal of Pharmacology 2014, 171(7), 1617-1628.
- Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris C-K, Payne MC. Large-Scale Density Functional Theory Transition State Searching in Enzymes. Journal of Physical Chemistry Letters 2014, 5(21), 3614-3619.
- Weber C, Cole DJ, O’Regan DD, Payne MC. Renormalization of Myoglobin-ligand Binding Energetics by Quantum Many-body Effects. Proceedings of the National Academy of Sciences of the United States of America 2014, 111(16), 5790-5795.
- Lever G, Cole DJ, Hine NDM, Haynes PD, Payne MC. Electrostatic Considerations Affecting the Calculated HOMO-LUMO Gap in Protein Molecules. Journal of Physics: Condensed Matter 2013, 25(15).
- Lee LP, Cole DJ, Payne MC, Skylaris C-K. Natural Bond Orbital Analysis in the ONETEP Code: Applications to Large Protein Systems. Journal of Computational Chemistry 2013, 34(6), 429-444.
- Lee LP, Cole DJ, Skylaris C-K, Jorgensen WL, Payne MC. Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation 2013, 9(7), 2981-2991.
- Cole DJ, Chin AW, Hine NDM, Haynes PD, Payne MC. Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex. Journal of Physical Chemistry Letters 2013, 4(24), 4206-4212.
- Cole DJ, O’Regan DD, Payne MC. Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U. Journal of Physical Chemistry Letters 2012, 3(11), 1448-1452.
- Cole DJ, Rajendra E, Roberts-Thomson M, Hardwick B, McKenzie GJ, Payne MC, Venkitaraman AR, Skylaris C-K. Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity. PLOS Computational Biology 2011, 7:e1002096.
- Cole DJ, Ang PK, Loh KP. Ion Adsorption at the Graphene/Electrolyte Interface. Journal of Physical Chemistry Letters 2011, 2(14), 1799-1803.
- Cole DJ, Skylaris C-K, Rajendra E, Venkitaraman AR, Payne MC. Protein-protein Interactions form Linear-scaling First-principles Quantum-mechanical Calculations. Europhysics Letters Association 2010, 91(3).
- Kubair DV, Cole DJ, Colombi-Ciacchi L, Spearing SM. Multiscale Mechanics Modeling of Direct Silicon Wafer Bonding.Scripta Materialia 2009, 60(12), 1125-1128.
- Cole DJ, Payne MC, Ciacchi LC. Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces. Physical Chemistry Chemical Physics 2009, 11, 11395-11399.
- Colombi-Ciacchi L, Cole DJ, Payne MC, Gumbsch P. Stress-Driven Oxidation Chemistry of Wet Silicon Surfaces. Journal of Physical Chemistry 2008, 112(32), 12077-12080.
- Cole DJ, Payne MC, Csanyi G, Spearing SM, Colombi-Ciacchi L. Development of a classical force field for the oxidized Si surface: Application to Hydrophilic Wafer Bonding. Journal of Chemical Physics 2007, 127(20), 204704.
- Cole DJ, Payne MC, Colombi-Ciacchi L. Stress Development and Impurtity Segregation During Oxidation of the Si(1 0 0) Surface. Surface Science 2007, 601(21), 4888-4898.