Publications by Dr Daniel Cole - ePrints

Browsing publications by Dr Daniel Cole.

Newcastle Authors	Title	Year
Dr Rachael Pirie Dr Harriet Annabella Stanway-Gordon Dr Hannah Stewart Dr Kirsty Wilson Dr Daniel Cole et al.	An analysis of the physicochemical properties of oral drugs from 2000 to 2022	2024
Dr Daniel Cole	Automated Adaptive Absolute Binding Free Energy Calculations	2024
Josh Horton Dr Daniel Cole	Benchmarking Quantum Mechanical Levels of Theory for Valence Parametrization in Force Fields	2024
Dr Stuart Hall Dr Rachael Pirie Dr Daniel Cole	Riemannian geometry and molecular similarity I: spectrum of the Laplacian	2024
Dr Daniel Cole	The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling	2024
Josh Horton Dr Daniel Cole	A transferable double exponential potential for condensed phase simulations of small molecules	2023
Dr Daniel Cole	Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations	2023
Josh Horton Dr Daniel Cole	Development and benchmarking of an open, self-consistent force field for proteins and small molecules from the open force field initiative	2023
Josh Horton Dr Daniel Cole	Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field	2023
Josh Horton Dr Daniel Cole	Fast, conformation-independent charges with graph convolutional networks	2023
Dr Chris Ringrose Dr Daniel Cole	What is the Optimal Dipole Moment for Nonpolarizable Models of Liquids?	2023
Dr Mat Bieniek Ben Cree Dr Rachael Pirie Josh Horton Dr Natalie Tatum et al.	An Open-Source Molecular Builder and Free Energy Preparation Workflow	2022
Dr Chris Ringrose Josh Horton Dr Daniel Cole	Exploration and Validation of Force Field Design Protocols through QM-to-MM Mapping	2022
Josh Horton Dr Daniel Cole	Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization At Scale	2022
Lauren Nelson Dr Chris Ringrose Josh Horton Dr Vadiraj Kurdekar Dr Daniel Cole et al.	Implementation of the QUBE Force Field in SOMD for High-Throughput Alchemical Free-Energy Calculations	2021
Dr Daniel Cole	Linear Atomic Cluster Expansion Force Fields for Organic Molecules: Beyond RMSE	2021
Josh Horton Professor Thomas Penfold Dr Daniel Cole	Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field	2021
Josh Littlefair Dr Daniel Cole Professor Thomas Penfold	On assessing functional errors in density functional theory using atomisation energies and electric field gradients	2021
Dr Daniel Cole	A machine learning based intramolecular potential for a flexible organic molecule	2020
Eva Gougoula Dr Daniel Cole Dr Nick Walker	Bifunctional Hydrogen Bonding of Imidazole with Water Explored by Rotational Spectroscopy and DFT Calculations	2020
Dr Daniel Cole Dr Dumitru Sirbu	Challenges for large scale simulation: general discussion	2020
Joshua Horton Dr Daniel Cole	Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field	2020
Dr Daniel Cole	ONETEP + TOSCAM: uniting dynamical mean field theory and linear-scaling density functional theory	2020
Dr Daniel Cole	Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment	2020
Dr Daniel Cole	Superexchange mechanism and quantum many body excitations in the archetypal di-Cu oxo-bridge	2020
Dr Daniel Cole	The ONETEP linear-scaling density functional theory program	2020
Dr Daniel Cole	Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor	2019
Dr Daniel Cole	Computation of Protein-Ligand Binding Free Energies using Quantum Mechanical Bespoke Force Fields	2019
Dr Daniel Cole	Development and Validation of the Quantum Mechanical Bespoke Protein Force Field	2019
Dr Daniel Cole	New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy	2019
Josh Horton Dr Daniel Cole	QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics	2019
Dr Daniel Cole Joshua Horton Lauren Nelson Dr Vadiraj Kurdekar	The Future of Force Fields in Computer Aided Drug Design	2019
Dr Daniel Cole	Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection	2018
Dr Daniel Cole	Role of spin in the calculation of Hubbard U and Hund's J parameters from first principles	2018
Dr Daniel Cole	Computationally-Guided Optimization of Small-Molecule Inhibitors of the Aurora A Kinase – TPX2 Protein-Protein Interaction	2017
Dr Daniel Cole	Distance dependent photoacoustics revealed through DNA nanostructures	2017
Dr Daniel Cole	Evidence of Correlated Static Disorder in the Fenna–Matthews–Olson Complex	2017
Dr Daniel Cole	Applications of Large-Scale Density Functional Theory in Biology	2016
Dr Daniel Cole	Biomolecular Force Field Parameterization via Atoms-in-Molecular Electron Density Partitioning	2016
Dr Daniel Cole	Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex	2016
Dr Daniel Cole	Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis	2016
Dr Daniel Cole	Molecular Dynamics and Monte Carlo Simulations for Protein-Ligand Binding and Inhibitor Design	2015
Dr Daniel Cole	Constrained geometric dynamics of the Fenna–Matthews–Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer	2014
Dr Daniel Cole	Constrained geometric simulation of the nicotinic acetylcholine receptor	2014
Dr Daniel Cole	Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering	2014
Dr Daniel Cole	Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms	2014
Dr Daniel Cole	Impact of Intracellular Domain Flexibility upon Properties of Activated Human 5-HT₃ Receptors	2014
Dr Daniel Cole	Large-Scale Density Functional Theory Transition State Searching in Enzymes	2014
Dr Daniel Cole	Renormalization of Myoglobin-ligand Binding Energetics by Quantum Many-body Effects	2014
Dr Daniel Cole	Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex	2013
Dr Daniel Cole	Water Structuring and Collagen Adsorption at Hydrophilic and Hydrophobic Silicon Surfaces	2009
Dr Daniel Cole	Development of a classical force field for the oxidized Si surface: Application to Hydrophilic Wafer Bonding	2007