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List of works by Sarah A Harris

A comparison of the electromechanical properties of structurally diverse proteins by molecular dynamics simulation

scientific article

A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy.

scientific article published on 23 January 2007

Affimer proteins inhibit immune complex binding to FcγRIIIa with high specificity through competitive and allosteric modes of action ⬇️

scientific article

An in silico design for a DNA nanomechanical switch.

scientific article published in October 2010

Atomistic Molecular Dynamics Simulations of DNA Minicircle Topoisomers: A Practical Guide to Setup, Performance, and Analysis

scientific article published on January 2016

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA.

scientific article published on 18 January 2011

Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

scientific article published on 16 February 2021

Bullied no more: when and how DNA shoves proteins around

scientific article published on 31 July 2012

Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA.

scientific article published on June 2015

Considerations in experimental and theoretical collision cross-section measurements of small molecules using travelling wave ion mobility spectrometry-mass spectrometry

article

Defining Dynamics of Membrane-Bound Pyrophosphatases by Experimental and Computational Single-Molecule FRET

scientific article published in 2018

Effect of sequence variation on the mechanical response of amyloid fibrils probed by steered molecular dynamics simulation

scientific article published on 7 February 2012

Erratum: Structural diversity of supercoiled DNA

scientific article published in Nature Communications

Exploring the dynamics of flagellar dynein within the axoneme with Fluctuating Finite Element Analysis

scientific article published on 10 August 2020

Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator ⬇️

scientific article

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules. ⬇️

scientific article published on 23 March 2018

In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

scientific article

Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations

scientific article published in February 2001

Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA. ⬇️

scientific article published on 17 January 2017

KOBRA: a fluctuating elastic rod model for slender biological macromolecules

scientific article published on 24 July 2020

Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation ⬇️

scientific article published on 22 September 2016

Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations

scientific article

Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design

scientific article published on 06 September 2021

Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA.

scientific article published on 30 December 2004

Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects ⬇️

scientific article published on 04 July 2013

Monitoring oligomer formation from self-aggregating amylin peptides using ESI-IMS-MS

Parmbsc1: a refined force field for DNA simulations ⬇️

scientific article

Peptide strand length controls the energetics of self-assembly and morphology of β-sheet fibrils ⬇️

scientific article

Peptide synthesis and self-assembly.

scientific article published on January 2012

Phosphorylation as a tool to modulate aggregation propensity and to predict fibril architecture

scientific article published on 15 December 2011

Protein/DNA interactions in complex DNA topologies: expect the unexpected ⬇️

scientific article

Protein/DNA interactions in complex DNA topologies: expect the unexpected. ⬇️

scientific article

Quantum-assisted biomolecular modelling.

scientific article published on August 2010

Securing the future of research computing in the biosciences

scientific article published on 16 May 2019

Seeing Supercoiled DNA with Atomistic Simulation: A New Twist on a Familiar Structure ⬇️

Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site

scientific article

Skp is a multivalent chaperone of outer-membrane proteins ⬇️

scientific article published on 25 July 2016

Small DNA circles as probes of DNA topology

scientific article published on April 2013

Spectrum of pathogenic variants and multiple founder effects in amelogenesis imperfecta associated with MMP20

scientific article

Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.

scientific article

Structural diversity of supercoiled DNA. ⬇️

scientific article

Structure of the microtubule-binding domain of flagellar dynein

scientific article

Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation ⬇️

scientific article published on May 4, 2011

Thermodynamic description of polymorphism in Q- and N-rich peptide aggregates revealed by atomistic simulation

scientific article published on July 2009

Thermodynamics of writhe in DNA minicircles from molecular dynamics simulations.

scientific article published on 5 April 2013

Topological aspects of DNA function and protein folding

scientific article published in April 2013

Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling ⬇️

scientific article published on 11 November 2014

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