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Staff Profile

Dr Daniel Cole

UKRI Future Leaders Fellow

  • Email: daniel.cole@ncl.ac.uk
  • Telephone: 0191 208 3614
  • Personal Website:
  • Address: School of Natural and Environmental Sciences
    Bedson Building
    Â鶹´«Ã½
    Â鶹´«Ã½ upon Tyne
    NE1 7RU
Background

I am a UKRI Future Leaders Fellow and Reader in computational medicinal chemistry in the School of Natural and Environmental Sciences, Â鶹´«Ã½. My research is aimed at the application of computational physics and chemistry to interesting and industrially-relevant questions in the biological and medicinal sciences. Much of my research is aimed at using electronic structure calculations to develop better models for the description of the structure, interactions and dynamics of molecules at the atomistic level, and ultimately for the design of pharmaceutical molecules. I am passionate about open research, and develop open software for force field development and computer-aided drug design.

Before taking up my post at Â鶹´«Ã½, I held a Marie Curie international outgoing fellowship, hosted by  at Yale University and at the University of Cambridge. I have also previously worked as a research associate at the National University of Singapore and the University of Cambridge.

Qualifications

  • M.Sci. and B.A. in Natural Sciences, University of Cambridge, 2004.
  • Ph.D. in Physics, , University of Cambridge, 2008

Area of expertise

  • Molecular and Materials Science

Google scholar:

SCOPUS:

Research

For more information, please see: 


Computer-aided Drug Design

Optimisation of protein-ligand binding affinity is a central goal of small molecule drug discovery. A wide range of computational methods have been developed for this purpose, but free energy methods are a particularly attractive option, because they provide a rigorous theoretical means to compute changes in the free energy of binding, limited only by the completeness of the sampling and the accuracy of the force field. Much of our work (see below) centres around developing force fields to improve the accuracy of free energy calculations, but we also contribute to areas including , , and . We work with the Â鶹´«Ã½ Centres for Cancer  and Rare Disease to apply these methods prospectively, and further efforts include the design of inhibitors of the  and the .


Open Force Field

We are passionate about open science, and proud to collaborate with the , and the wider . You can read a status report about the work of Open Force Field . We have contributed to of one of the mainline force fields (‘‘), and led the development of the  for fitting molecule-specific torsion parameters to high-level reference data. As an example proof-of-concept work, we experimented with using the Open Force Field software stack to replace the Lennard-Jones functional form with a more flexible . We are continuing to work with the community to further drive forward force field accuracy and ease-of-use.


Wider Force Field Design Efforts

Quantum mechanical calculations provide an accurate description of the electronic structure of matter, but the sampling of conformational dynamics of biomolecules is beyond the reach of these techniques. Our first forays into force field design revolved around methods to extract parameters of the classical force field directly from quantum mechanics. Outcomes included the  for bond and angle parameter derivation from the Hessian matrix, which is now used by Open Force Field, and  from atoms-in-molecule analysis. We developed the  software package to automate the entire force field assignment process, and benchmarked the accuracy on . More recently, we are pleased to collaborate with the  group in the development of ,  and machine learning potentials for organic molecules, and with , through a , for the development of graph neural network based charge models.


Large-scale Density Functional Theory

Recent progress in  (DFT) software allows electronic structure calculations of systems comprising many thousands of atoms to be performed on a routine basis, allowing access to . Some of the areas in the biological sciences where DFT can play an important role include the energetics of , binding of , and the parameterisation of model Hamiltonians to describe energy transfer in .

Publications

  • Articles

    • Wang L, Alibay I, Behara PK, Boothroyd S, Cavender CE, Horton JT, McIsaac AR, Mitchell A, Morales B, Thompson MW, Wagner JR, Westbrook BR, Bayly CI, Chodera JD, Cole DJ, Eastwood JRB, Shirts MR, Mobley DL. . Journal of Chemical Theory and Computation 2026, epub ahead of print.
    • Moore JH, Cole DJ, Csányi G. . Journal of the American Chemical Society 2026, 148(5), 4928–4937.
    • MacDermott-Opeskin H, Scheen J, Wognum C, Horton JT, West D, Payne AM, Castellanos MA, Colby S, Griffen E, Cousins D, Stacey J, Reid L, Aschenbrenner JC, Fearon D, Balcomb B, Marples P, Tomlinson CWE, Lithgo R, Godoy AS, Winokan M, Barr H, Lahav N, Lavi M, Duberstein S, Cohen G, Fate G, Lefker B, Robinson R, Szommer T, Lynch N, Minh DDL, La VNT, Kang L, Huddleston K, Renslow R, Tollefson M, Walters WP, Xu C, Hsu J, St-Laurent J, Etsmoberg H, Zhu L, Quirke A, Haleem MIA, Alibay I, Baid G, Birnbaum B, Bishop KP, Bohorquez H, Bose A, Brown CJ, Burns J, Cai L, Cedeno R, de Cesco S, Chupakhin V, Clark F, Cole DJ, Corbi-Verge C, Danial M, Davi A, Dehaen W, Doering NP, Dougha A, Dréanic MP, Eakin B, Ehrlich A, Elijosius R, Fülöp J, Gitter A, Goossens K, Gu Y, Head-Gordon T, Hoffer L, Hofmans J, Jiang E, Kaminow B, Khosravi S, Khoualdi AF, Lenselink EB, Liu Z, Liu Y, Liu S, Ma Y, Maher P, Mayer I, Mendez-Lucio O, Mey ASJS, Michel J, Montanari F, Niu T, Ogino R, Palaniappan A, Pan X, Patnaik A, Pham LH, Pinto L, Purnomo J, Rich A, Schaaf L, Schran C, Singh RK, Srilakshmi M, Srivastava SP, Sun K, Sun Z, Talagayev V, Balakrishnan BTS, Titus I, Tkatchenko A, Treyde W, Tricarico G, Tripp A, Vithayapalert N, Wang Y, Wasi AT, Wedig S, Wolber G, Xu B, Zhou W, von Delft F, Lee A, Kirkegaard K, Sjö P, Fraser JS, Chodera JD. . Journal of Chemical Information and Modeling 2026, 66(6), 3129-3149.
    • Pirie R, Hall SJ, Cole DJ, Murphy T. . Proceedings of the Royal Society A 2025, 481(2323), 20240707.
    • Kovács DP, Moore JH, Browning NJ, Batatia I, Horton JT, Pu Y, Kapil V, Witt WC, Magdău IB, Cole DJ, Csányi G. . Journal of the American Chemical Society 2025, 147(21), 17598–17611.
    • Morado J, Zinovjev K, Hedges LO, Cole DJ, Michel J. . Journal of Chemical Theory and Computation 2025, 21(22), 11805-11819.
    • Herasymenko O, Silva M, Abu-Saleh AA, Ahmad A, Alvarado-Huayhuaz J, Arce OEA, Armstrong RJ, Arrowsmith C, Bachta KE, Beck H, Berta D, Bieniek MK, Blay V, Bolotokova A, Bourne PE, Breznik M, Brown PJ, Campbell ADG, Carosati E, Chau I, Cole DJ, Cree B, Dehaen W, Denzinger K, dos Santos Machado K, Dunn I, Durai P, Edfeldt K, Edwards A, Fayne D, Felfoldi D, Friston K, Ghiabi P, Gibson E, Guenther J, Gunnarsson A, Hillisch A, Houston DR, Halborg Jensen J, Harding RJ, Harris KS, Hoffer L, Hogner A, Horton JT, Houliston S, Hultquist JF, Hutchinson A, Irwin JJ, Jukic M, Kandwal S, Karlova A, Katis VL, Kich RP, Kireev D, Koes D, Inniss NL, Lessel U, Liu S, Loppnau P, Lu W, Martino S, McGibbon M, Meiler J, Mettu A, Money-Kyrle S, Moretti R, Moroz YS, Muvva C, Newman JA, Obendorf L, Paige B, Pandit A, Park K, Perveen S, Pirie R, Poda G, Protopopov M, Putter V, Ricci F, Roper NJ, Rosta E, Rzhetskaya M, Sabnis Y, Satchell KJF, Schmitt Kremer F, Scott T, Seitova A, Steinmann C, Talagayev V, Tarkhanova OO, Tatum NJ, Treleaven D, Velasque Werhli A, Walters WP, Wang X, Wells J, Wells G, Westermaier Y, Wolber G, Wortmann L, Zhang J, Zhao Z, Zheng S, Schapira M. . Journal of Chemical Information and Modeling 2025, 65(13), 6884-6898.
    • Cree B, Bieniek MK, Amin S, Kawamura A, Cole DJ. . Digital Discovery 2025, 4(2), 438-450.
    • Adams C, Horton JT, Wang L, Boothroyd S, Mobley DL, Wright DW, Cole DJ. . Journal of Chemical Theory and Computation 2025, 21(23), 12133-12148.
    • Clark F, Cole DJ, Michel J. . Journal of Chemical Theory and Computation 2024, 21(1), 88-101.
    • Hall SJ, Pirie R, Cole DJ. . Proceedings of the Royal Society A 2024, 480(2284), 20230343.
    • Behara PK, Jang H, Horton JT, Gokey T, Dotson DL, Boothroyd S, Bayly CI, Cole DJ, Wang L-P, Mobley DL. . Journal of Physical Chemistry B 2024, 128(32), 7888–7902.
    • Clark F, Robb GR, Cole DJ, Michel J. . Journal of Chemical Theory and Computation 2024, 20(18), 7806–7828.
    • Pirie R, Stanway-Gordon HA, Stewart HL, Wilson KL, Paton S, Tyerman J, Cole DJ, Fowler K, Waring MJ. . RSC Medicinal Chemistry 2024, 15(9), 3125-3132.
    • Jorge M, Barrera MC, Milne AW, Ringrose C, Cole DJ. . Journal of Chemical Theory and Computation 2023, 19(6), 1790–1804.
    • 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. . Journal of Chemical Theory and Computation 2023, 19(11), 3251–3275.
    • Clark F, Robb G, Cole DJ, Michel J. . Journal of Chemical Theory and Computation 2023, 19(12), 3429-3762.
    • Horton JT, Boothroyd S, Behara PK, Mobley DL, Cole DJ. . Digital Discovery 2023, 2(4), 1178-1187.
    • 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. . Journal of Chemical Information and Modeling 2022, 62(22), 5622-5633.
    • Ringrose C, Horton JT, Wang L-P, Cole DJ. . Physical Chemistry Chemical Physics 2022, 24, 17014-17027.
    • Bieniek MK, Cree B, Pirie R, Horton JT, Tatum NJ, Cole DJ. . Communications Chemistry 2022, 5, 136.
    • Littlefair J, Cole DJ, Penfold TJ. . International Journal of Quantum Chemistry 2021, 121(23), e26799.
    • Yang L, Horton JT, Payne MC, Penfold TJ, Cole DJ. . Journal of Chemical Theory and Computation 2021, 17(8), 5021–5033.
    • Kovács DP, van der Oord C, Kucera J, Allen AEA, Cole DJ, Ortner C, Csányi G. . Journal of Chemical Theory and Computation 2021, 17(12), 7696-7711.
    • Nelson L, Bariami S, Ringrose C, Horton JT, Kurdekar V, Mey ASJS, Michel J, Cole DJ. . Journal of Chemical Information and Modeling 2021, 61(5), 2124-2130.
    • al-Badri MA, Linscott EB, Georges A, Cole DJ, Weber C. . Communications Physics 2020, 3, 4.
    • Chaillet ML, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. . Journal of Physical Chemistry Letters 2020, 11(24), 10306-10314.
    • Linscott EB, Cole DJ, Hine NDM, Payne MC, Weber C. . Journal of Chemical Theory and Computation 2020, 16(8), 4899-4911.
    • Horton JT, Allen AEA, Cole DJ. . Chemical Communications 2020, 6, 932-935.
    • Gougoula E, Cole DJ, Walker NR. . Journal of Physical Chemistry A 2020, 124(13), 2649-2659.
    • Cole DJ, Mones L, Csanyi G. . Faraday Discussions 2020, 224, 247-264.
    • Horton J, Allen AEA, Dodda LS, Cole DJ. . Journal of Chemical Information and Modeling 2019, 59(4), 1366-1381.
    • Manz TA, Chen T, Cole DJ, Gabaldon Limas N, Fiszbein B. . RSC Advances 2019, 9, 19297-19324.
    • Allen AEA, Robertson MJ, Payne MC, Cole DJ. . ACS Omega 2019, 4(11), 14537-14550.
    • Cole DJ, Cabeza de Vaca I, Jorgensen WL. . MedChemComm 2019, 10(7), 1116-1120.
    • Qian Y, Cabeza de Vaca I, Vilseck JZ, Cole DJ, Tirado-Rives J, Jorgensen WL. . Journal of Physical Chemistry B 2019, 123(41), 8675-8685.
    • Linscott EB, Cole DJ, Payne MC, O'Regan DD. . Physical Review B 2018, 98(23), 235157.
    • Allen AEA, Payne MC, Cole DJ. . Journal of Chemical Theory and Computation 2018, 14(1), 274-281.
    • Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. . Journal of Physical Chemistry Letters 2017, 8, 2350–2356.
    • Joseph J, Baumann KN, Koehler P, Zuehlsdorff TJ, Cole DJ, Weber J, Bohndiek SE, Hernández-Ainsa S. . Nanoscale 2017, 9(42), 16193-16199.
    • Cole DJ, Janecek M, Stokes JE, Rossmann M, Faver JC, McKenzie GJ, Venkitaraman AR, Hyvönen M, Spring DR, Huggins DJ, Jorgensen WL. . Chemical Communications 2017, 53(67), 9372-9375.
    • Fokas AS, Cole DJ, Ahnert SE, Chin AW. . Scientific Reports 2016, 6, 33213.
    • Morgan SE, Cole DJ, Chin AW. . Scientific Reports 2016, 6, 36703.
    • Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. . Journal of Chemical Theory and Computation 2016, 12(5), 2312-2323.
    • Cole DJ, Tirado-Rives J, Jorgensen WL. . Biochimica et Biophysica Acta (BBA) General Subjects 2015, 1850(5), 966-971.
    • Weber C, Cole DJ, O'Regan DD, Payne MC. . Proceedings of the National Academy of Sciences of the United States of America 2014, 111(16), 5790-5795.
    • Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris C-K, Payne MC. . Journal of Physical Chemistry Letters 2014, 5(21), 3614-3619.
    • Kozuska JL, Paulsen IM, Belfield WJ, Martin IL, Cole DJ, Holt A, Dunn SMJ. . British Journal of Pharmacology 2014, 171(7), 1617-1628.
    • Lee LP, Gabaldon Limas N, Cole DJ, Payne MC, Skylaris C-K, Manz TA. . Journal of Chemical Theory and Computation 2014, 10(12), 5377-5390.
    • Cole DJ, Tirado-Rives J, Jorgensen WL. . Journal of Chemical Theory and Computation 2014, 10(2), 565-571.
    • Belfield WJ, Cole DJ, Martin IL, Payne MC, Chau P-L. . Journal of Molecular Graphics and Modelling 2014, 52, 1-10.
    • Fokas AS, Cole DJ, Chin AW. . Photosynthesis Research 2014, 122(3), 275-292.
    • Cole DJ, Chin AW, Hine NDM, Haynes PD, Payne MC. . Journal of Physical Chemistry Letters 2013, 4(24), 4206-4212.
    • 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.
    • 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.
    • 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).
    • 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, Ang PK, Loh KP. Ion Adsorption at the Graphene/Electrolyte Interface. Journal of Physical Chemistry Letters 2011, 2(14), 1799-1803.
    • 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. PLOS Computationsl Biology 2011, 7.
    • 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).
    • Cole DJ, Payne MC, Ciacchi LC. . Physical Chemistry Chemical Physics 2009, 11, 11395-11399.
    • 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, Colombi-Ciacchi L. Stress Development and Impurtity Segregation During Oxidation of the Si(1 0 0) Surface. Surface Science 2007, 601(21), 4888-4898.
    • Cole DJ, Payne MC, Csanyi G, Spearing SM, Colombi-Ciacchi L. . Journal of Chemical Physics 2007, 127(20), 204704.

  • Conference Proceedings (inc. Abstract)

    • Brandenburg JG, Burke K, Civalleri B, Cole DJ, Csanyi G, David G, Gidopoulos NI, Gowland D, Helgaker T, Herbst MF, Hourahine B, Irons TJP, Jacob CR, Loos PF, Mehta N, Mulay MR, Neugebauer J, Pernal K, Pribram-Jones A, Romaniello P, Ryder MR, Savin A, Sirbu D, Skylaris C-K, Truhlar DG, Wetherell J, Yang W. . In: Faraday Discussions. 2020, Royal Society of Chemistry.

  • Letter

    • 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.

  • Reviews

    • Wang Y, Takaba K, Chen MS, Wieder M, Xu Y, Zhu T, Zhang JZH, Nagle A, Yu K, Wang X, Cole DJ, Rackers JA, Cho K, Greener JG, Eastman P, Martiniani S, Tuckerman ME. . Applied Physics Reviews 2025, 12(2), 021304.
    • Wang L, Behara PK, Thompson MW, Gokey T, Wang Y, Wagner JR, Cole DJ, Gilson MK, Shirts MR, Mobley DL. . Journal of Physical Chemistry B 2024, 128(29), 7043–7067.
    • 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. . Journal of Chemical Physics 2020, 152(17), 174111.
    • Cole DJ, Horton JT, Nelson L, Kurdekar V. . Future Medicinal Chemistry 2019, 11(18), 2359-2363.
    • Cole DJ, Hine NDM. . Journal of Physics: Condensed Matter 2016, 28(39), 393001.