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List of works by Daniel J Cole

A machine learning based intramolecular potential for a flexible organic molecule

scientific article published on 21 September 2020

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor

scientific article published on 07 October 2019

An open-source molecular builder and free energy preparation workflow

scientific article published in 2022

Applications of large-scale density functional theory in biology.

scientific article

Challenges for large scale simulation: general discussion

scientific article published on 23 November 2020

Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields

scientific article published on 27 February 2019

Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction

scientific article published on 8 August 2017

Constrained geometric dynamics of the Fenna-Matthews-Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer ⬇️

scientific article published on 18 July 2014

Constrained geometric simulation of the nicotinic acetylcholine receptor

scientific article published on 6 June 2014

Development and Validation of the Quantum Mechanical Bespoke Protein Force Field

scientific article published on 27 August 2019

Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding

scientific article published on 01 November 2007

Distance dependent photoacoustics revealed through DNA nanostructures.

scientific article published on 18 October 2017

Electrostatic considerations affecting the calculated HOMO–LUMO gap in protein molecules

scientific article published on 07 March 2013

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering

scientific article published on 17 January 2014

Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex.

scientific article published on 9 May 2017

Harmonic Force Constants for Molecular Mechanics Force Fields via Hessian Matrix Projection.

scientific article published on 21 November 2017

Impact of intracellular domain flexibility upon properties of activated human 5-HT3 receptors.

scientific article published on April 2014

Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity

scientific article

Large-Scale Density Functional Theory Transition State Searching in Enzymes

scientific article published on 09 October 2014

Ligand Discrimination in Myoglobin from Linear-Scaling DFT+U

scientific article published on 14 May 2012

Modeling Molecular Emitters in Organic Light-Emitting Diodes with the Quantum Mechanical Bespoke Force Field

scientific article published on 15 July 2021

Modelling flexible protein-ligand binding in p38α MAP kinase using the QUBE force field

scientific article published on 18 December 2019

Natural bond orbital analysis in the ONETEP code: Applications to large protein systems ⬇️

scientific article published on October 15, 2012

Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex

scientific article

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

scientific article published in 2022

Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning ⬇️

scientific article published on June 11, 2013

QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics

scientific article published on 22 February 2019

Renormalization of myoglobin-ligand binding energetics by quantum many-body effects ⬇️

scientific article published on 09 April 2014

Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis

scientific article

Riemannian geometry and molecular similarity I: spectrum of the Laplacian

scientific article published in 2024

Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment

scientific article published on 23 November 2020

The future of force fields in computer-aided drug design

scientific article published on 23 September 2019

Toward Ab Initio Optical Spectroscopy of the Fenna-Matthews-Olson Complex.

scientific article published on 27 November 2013

Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces

scientific article published on 20 October 2009

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