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Daniel J Cole - Publications

Affiliations: 
Newcastle University, Newcastle upon Tyne, England, United Kingdom 
Area:
Computational chemistry, condensed matter physics, medicinal chemistry
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45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Behara PK, Jang H, Horton JT, Gokey T, Dotson DL, Boothroyd S, Bayly CI, Cole DJ, Wang LP, Mobley DL. Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields. The Journal of Physical Chemistry. B. PMID 39087913 DOI: 10.1021/acs.jpcb.4c03167  0.327
2021 Yang L, Horton JT, Payne MC, Penfold TJ, Cole DJ. Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field. Journal of Chemical Theory and Computation. PMID 34264669 DOI: 10.1021/acs.jctc.1c00135  0.317
2021 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. PMID 33886305 DOI: 10.1021/acs.jcim.1c00328  0.321
2020 Cole DJ, Mones L, Csányi G. A machine learning based intramolecular potential for a flexible organic molecule. Faraday Discussions. PMID 32955056 DOI: 10.1039/D0Fd00028K  0.401
2020 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. PMID 32433876 DOI: 10.1021/Acs.Jctc.0C00162  0.582
2020 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 SM, et al. The ONETEP linear-scaling density functional theory program. The Journal of Chemical Physics. 152: 174111. PMID 32384832 DOI: 10.1063/5.0004445  0.761
2020 Gougoula E, Cole DJ, Walker NR. Bifunctional Hydrogen Bonding of Imidazole with Water Explored by Rotational Spectroscopy and DFT Calculations. The Journal of Physical Chemistry. A. PMID 32141751 DOI: 10.1021/Acs.Jpca.0C00544  0.331
2020 al-Badri MA, Linscott E, Georges A, Cole DJ, Weber C. Superexchange mechanism and quantum many body excitations in the archetypal di-Cu oxo-bridge Communications Physics. 3. DOI: 10.1038/S42005-019-0270-1  0.393
2019 Manz TA, Chen T, Cole DJ, Limas NG, Fiszbein B. New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy. Rsc Advances. 9: 19297-19324. PMID 35519408 DOI: 10.1039/c9ra03003d  0.333
2019 Horton JT, Allen AEA, Cole DJ. Modelling flexible protein-ligand binding in p38α MAP kinase using the QUBE force field. Chemical Communications (Cambridge, England). PMID 31850454 DOI: 10.1039/C9Cc08574B  0.386
2019 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 Druglike Inhibitor. The Journal of Physical Chemistry. B. PMID 31553604 DOI: 10.1021/Acs.Jpcb.9B07588  0.547
2019 Allen AEA, Robertson MJ, Payne MC, Cole DJ. Development and Validation of the Quantum Mechanical Bespoke Protein Force Field. Acs Omega. 4: 14537-14550. PMID 31528808 DOI: 10.1021/acsomega.9b01769  0.658
2019 Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields. Medchemcomm. 10: 1116-1120. PMID 31391883 DOI: 10.1039/C9Md00017H  0.558
2019 Horton J, Allen AEA, Dodda LS, Cole DJ. QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics. Journal of Chemical Information and Modeling. PMID 30742438 DOI: 10.1021/Acs.Jcim.8B00767  0.422
2019 Manz TA, Chen T, Cole DJ, Limas NG, Fiszbein B. New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy Rsc Advances. 9: 19297-19324. DOI: 10.1039/C9Ra03003D  0.326
2018 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. 98. DOI: 10.1103/Physrevb.98.235157  0.479
2017 Allen AEA, Payne MC, Cole DJ. Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection. Journal of Chemical Theory and Computation. PMID 29161029 DOI: 10.1021/Acs.Jctc.7B00785  0.559
2017 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 (Cambridge, England). PMID 28787041 DOI: 10.1039/C7Cc05379G  0.681
2017 Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. Evidence for Correlated Static Disorder in the Fenna-Matthews-Olson Complex. The Journal of Physical Chemistry Letters. PMID 28485971 DOI: 10.1021/Acs.Jpclett.7B00669  0.595
2016 Morgan SE, Cole DJ, Chin AW. Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex. Scientific Reports. 6: 36703. PMID 27827409 DOI: 10.1038/Srep36703  0.334
2016 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. 6: 33213. PMID 27623708 DOI: 10.1038/Srep33213  0.344
2016 Cole DJ, Hine ND. Applications of large-scale density functional theory in biology. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 393001. PMID 27494095 DOI: 10.1088/0953-8984/28/39/393001  0.419
2016 Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation. PMID 27057643 DOI: 10.1021/Acs.Jctc.6B00027  0.7
2015 Cole DJ, Tirado-Rives J, Jorgensen WL. Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design. Biochimica Et Biophysica Acta. 1850: 966-71. PMID 25196360 DOI: 10.1016/J.Bbagen.2014.08.018  0.456
2014 Lee LP, Limas NG, Cole DJ, Payne MC, Skylaris CK, Manz TA. Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms. Journal of Chemical Theory and Computation. 10: 5377-90. PMID 26583221 DOI: 10.1021/Ct500766V  0.609
2014 Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris CK, Payne MC. Large-Scale Density Functional Theory Transition State Searching in Enzymes. The Journal of Physical Chemistry Letters. 5: 3614-9. PMID 26278727 DOI: 10.1021/Jz5018703  0.598
2014 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. 122: 275-92. PMID 25034014 DOI: 10.1007/S11120-014-0027-3  0.394
2014 Belfield WJ, Cole DJ, Martin IL, Payne MC, Chau PL. Constrained geometric simulation of the nicotinic acetylcholine receptor. Journal of Molecular Graphics & Modelling. 52: 1-10. PMID 24955489 DOI: 10.1016/J.Jmgm.2014.05.001  0.492
2014 Cole DJ, Tirado-Rives J, Jorgensen WL. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering. Journal of Chemical Theory and Computation. 10: 565-571. PMID 24803853 DOI: 10.1021/Ct400989X  0.514
2014 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. 111: 5790-5. PMID 24717844 DOI: 10.1073/Pnas.1322966111  0.613
2014 Lever G, Cole DJ, Lonsdale R, Ranaghan KE, Wales DJ, Mulholland AJ, Skylaris CK, Payne MC. Large-scale density functional theory transition state searching in enzymes Journal of Physical Chemistry Letters. 5: 3614-3619. DOI: 10.1021/jz5018703  0.473
2014 Lee LP, Limas NG, Cole DJ, Payne MC, Skylaris CK, Manz TA. Expanding the scope of density derived electrostatic and chemical charge partitioning to thousands of atoms Journal of Chemical Theory and Computation. 10: 5377-5390. DOI: 10.1021/ct500766v  0.495
2013 Cole DJ, Chin AW, Hine ND, Haynes PD, Payne MC. Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex. The Journal of Physical Chemistry Letters. 4: 4206-12. PMID 26296166 DOI: 10.1021/Jz402000C  0.721
2013 Lee LP, Cole DJ, Skylaris CK, Jorgensen WL, Payne MC. Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning. Journal of Chemical Theory and Computation. 9: 2981-2991. PMID 23894231 DOI: 10.1021/Ct400279D  0.681
2013 Lever G, Cole DJ, Hine ND, Haynes PD, Payne MC. Electrostatic considerations affecting the calculated HOMO-LUMO gap in protein molecules. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 25: 152101. PMID 23470878 DOI: 10.1088/0953-8984/25/15/152101  0.717
2013 Lee LP, Cole DJ, Payne MC, Skylaris CK. Natural bond orbital analysis in the ONETEP code: applications to large protein systems. Journal of Computational Chemistry. 34: 429-44. PMID 23065758 DOI: 10.1002/Jcc.23150  0.615
2012 Cole DJ, O'Regan DD, Payne MC. Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U. The Journal of Physical Chemistry Letters. 3: 1448-52. PMID 26285620 DOI: 10.1021/Jz3004188  0.607
2011 Cole DJ, Rajendra E, Roberts-Thomson M, Hardwick B, McKenzie GJ, Payne MC, Venkitaraman AR, Skylaris CK. Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity. Plos Computational Biology. 7: e1002096. PMID 21789034 DOI: 10.1371/Journal.Pcbi.1002096  0.565
2010 Cole DJ, Skylaris CK, Rajendra E, Venkitaraman AR, Payne MC. Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations Epl. 91. DOI: 10.1209/0295-5075/91/37004  0.642
2010 Skylaris C, Cole DJ, Fox SJ, Rajendra E, Payne MC, Venkitaraman AR. Application of Large-Scale First Principles Quantum Mechanical Calculations With the ONETEP Program To Biophysical Problems Biophysical Journal. 98: 11a. DOI: 10.1016/J.Bpj.2009.12.064  0.604
2009 Cole DJ, Payne MC, Ciacchi LC. Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces. Physical Chemistry Chemical Physics : Pccp. 11: 11395-9. PMID 20024408 DOI: 10.1039/B816125A  0.516
2009 Kubair DV, Cole DJ, Ciacchi LC, Spearing SM. Multiscale mechanics modeling of direct silicon wafer bonding Scripta Materialia. 60: 1125-1128. DOI: 10.1016/J.Scriptamat.2009.02.058  0.318
2008 Ciacchi LC, Cole DJ, Payne MC, Gumbsch P. Stress-driven oxidation chemistry of wet silicon surfaces Journal of Physical Chemistry C. 112: 12077-12080. DOI: 10.1021/Jp804078N  0.507
2007 Cole DJ, Payne MC, Csányi G, Spearing SM, Colombi Ciacchi L. Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding. The Journal of Chemical Physics. 127: 204704. PMID 18052443 DOI: 10.1063/1.2799196  0.543
2007 Cole DJ, Payne MC, Colombi Ciacchi L. Stress development and impurity segregation during oxidation of the Si(1 0 0) surface Surface Science. 601: 4888-4898. DOI: 10.1016/J.Susc.2007.08.013  0.508
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