List of works - Richard Bryce

Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories

scientific article published on 28 June 2010

Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region

scientific article published on 29 September 2011

Aminoimidazolylmethyluracil analogues as potent inhibitors of thymidine phosphorylase and their bioreductive nitroimidazolyl prodrugs.

scientific article published in January 2005

An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate-aromatic interactions.

scientific article published on 21 July 2010

Analysis of Enoyl-Acyl Carrier Protein Reductase Structure and Interactions Yields an Efficient Virtual Screening Approach and Suggests a Potential Allosteric Site.

scientific article published on 11 August 2015

Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors ⬇️

scientific article published on June 17, 2011

Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet

scientific article published on 01 June 2017

Ask the experts: focus on computational chemistry

scientific article published in June 2011

Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.

scientific article published in April 2009

Benzoic acid and pyridine derivatives as inhibitors of Trypanosoma cruzi trans-sialidase

scientific article published on 15 December 2006

Boron-Based Inhibitors of the NLRP3 Inflammasome

scientific article published in September 2017

Chlorine-35/37 NMR spectroscopy of solid amino acid hydrochlorides: refinement of hydrogen-bonded proton positions using experiment and theory

scientific article published on 01 December 2006

Comparative Molecular Dynamics Simulation of Aggregating and Non-Aggregating Inhibitor Solutions: Understanding the Molecular Basis of Promiscuity.

scientific article

Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study

scientific article

Conformational study of tylosin A in water and full assignments of 1 H and 13 C spectra of tylosin A in D2 O and tylosin B in CDCl3

scientific article published on 27 October 2016

Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

scientific article published on 01 September 2007

Coumarin-based inhibitors of human NAD(P)H:quinone oxidoreductase-1. Identification, structure-activity, off-target effects and in vitro human pancreatic cancer toxicity.

scientific article published on 14 November 2007

Design, synthesis and enzymatic evaluation of 6-bridged imidazolyluracil derivatives as inhibitors of human thymidine phosphorylase.

scientific article

Difluoro analogue of UCS15A triggers activation of exogenously expressed c-Src in HCT 116 human colorectal carcinoma cells

scientific article published on October 2007

Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening

scientific article published on 24 December 2008

Discovery of potent 4-aminoquinoline hydrazone inhibitors of NRH:quinoneoxidoreductase-2 (NQO2)

scientific article published on 27 August 2019

Effect of sequence and stereochemistry reversal on p53 peptide mimicry

scientific article (publication date: 2013)

Evaluation of analogues of furan-amidines as inhibitors of NQO2.

scientific article published on 12 March 2018

Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors

scientific article published on 8 December 2005

Exploring protein kinase conformation using swarm-enhanced sampling molecular dynamics

scientific article

Exploring reaction pathways with transition path and umbrella sampling: application to methyl maltoside.

scientific article published in March 2006

Fluorescent probe: complexation of Fe3+ with the myo-inositol 1,2,3-trisphosphate motif.

scientific article published on 29 September 2008

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

scientific article published on 29 September 2015

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics

scientific article

Identification of a novel class of inhibitor of human and Escherichia coli thymidine phosphorylase by in silico screening.

scientific article published in November 2003

Imidazoacridin-6-ones as novel inhibitors of the quinone oxidoreductase NQO2.

scientific article published on 15 March 2010

Improved Hydrogen Bonding at the NDDO-Type Semiempirical Quantum Mechanical/Molecular Mechanical Interface

scientific article published on 01 September 2009

In silico identification and biochemical characterization of novel inhibitors of NQO1

scientific article published on 29 September 2006

In silico identification and biochemical evaluation of novel inhibitors of NRH:quinone oxidoreductase 2 (NQO2).

scientific article published on 21 October 2010

In silico screening and biological evaluation of inhibitors of Src-SH3 domain interaction with a proline-rich ligand

scientific article

Insights into the Activity and Specificity of Trypanosoma cruzi trans-Sialidase from Molecular Dynamics Simulations ⬇️

scientific article published on May 14, 2013

Metabolic fate of 3α,5-cycloandrostanes in the endogenous lactonization pathway of Aspergillus tamarii KITA.

scientific article published on 11 September 2015

Molecular Dynamics Study of Anhydrous Lamellar Structures of Synthetic Glycolipids: Effects of Chain Branching and Disaccharide Headgroup ⬇️

scientific article published on September 12, 2012

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene-Water Interface.

scientific article published on 27 May 2015

Molecular dynamics and free energy analysis of neuraminidase-ligand interactions

scientific article published on April 2004

Molecular dynamics simulation of monoalkyl glycoside micelles in aqueous solution: influence of carbohydrate headgroup stereochemistry.

scientific article published in March 2006

Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides ⬇️

scientific article published on August 4, 2010

Molecular dynamics study of chemically engineered green fluorescent protein mutants: comparison of intramolecular fluorescence resonance energy transfer rate

scientific article published in April 2009

Molecular probes: insights into design and analysis from computational and physical chemistry.

scientific article published on February 2008

Negative Cooperativity in NAD(P)H Quinone Oxidoreductase 1 (NQO1)

scientific article published on 20 September 2019

Non-enzymatic recombination of RNA: Ligation in loops.

scientific article

Non-symmetrical furan-amidines as novel leads for the treatment of cancer and malaria

scientific article

Novel inhibitors of NRH:quinone oxidoreductase 2 (NQO2): crystal structures, biochemical activity, and intracellular effects of imidazoacridin-6-ones

scientific article

Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

scientific article

Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening

scientific article

Rational drug design in parasitology: trans-sialidase as a case study for Chagas disease.

scientific article published on February 2008

Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

scientific article published on 04 November 2019

Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: Application to Influenza neuraminidase

article

Src family kinase inhibitor Saracatinib (AZD0530) impairs oxaliplatin uptake in colorectal cancer cells and blocks organic cation transporters

scientific article published on 15 June 2010

Stoichiometry and Folding of Linear Polypeptides—Reading Between the Lines ⬇️

scientific article published on 01 February 2011

Structure–activity relationship of 2,4,5-trioxoimidazolidines as inhibitors of thymidine phosphorylase

scientific article published in April 2011

The application of quantum mechanics in structure-based drug design ⬇️

scientific article published on 07 January 2013

The effects of perfluorination on carbohydrate-pi interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin.

scientific article published on 2 June 2010

Tracing the GSAP-APP C-99 Interaction Site in the β-Amyloid Pathway Leading to Alzheimer's Disease

scientific article published on 26 July 2019

Tryptophan as a molecular shovel in the glycosyl transfer activity of Trypanosoma cruzi trans-sialidase.

scientific article

What Next for Quantum Mechanics in Structure-Based Drug Discovery?

scientific article published on 01 January 2020

Xanthine oxidase-activated prodrugs of thymidine phosphorylase inhibitors

scientific article published in June 2008

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells

scientific article published on 13 January 2017

List of works by Richard Bryce

Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories

Accounting for non-optimal interactions in molecular recognition: a study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region

Aminoimidazolylmethyluracil analogues as potent inhibitors of thymidine phosphorylase and their bioreductive nitroimidazolyl prodrugs.

An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate-aromatic interactions.

Analysis of Enoyl-Acyl Carrier Protein Reductase Structure and Interactions Yields an Efficient Virtual Screening Approach and Suggests a Potential Allosteric Site.

Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors ⬇️

Approximate quantum chemical methods for modelling carbohydrate conformation and aromatic interactions: β-cyclodextrin and its adsorption on a single-layer graphene sheet

Ask the experts: focus on computational chemistry

Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.

Benzoic acid and pyridine derivatives as inhibitors of Trypanosoma cruzi trans-sialidase

Boron-Based Inhibitors of the NLRP3 Inflammasome

Chlorine-35/37 NMR spectroscopy of solid amino acid hydrochlorides: refinement of hydrogen-bonded proton positions using experiment and theory

Comparative Molecular Dynamics Simulation of Aggregating and Non-Aggregating Inhibitor Solutions: Understanding the Molecular Basis of Promiscuity.

Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study

Conformational study of tylosin A in water and full assignments of 1 H and 13 C spectra of tylosin A in D2 O and tylosin B in CDCl3

Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations

Coumarin-based inhibitors of human NAD(P)H:quinone oxidoreductase-1. Identification, structure-activity, off-target effects and in vitro human pancreatic cancer toxicity.

Design, synthesis and enzymatic evaluation of 6-bridged imidazolyluracil derivatives as inhibitors of human thymidine phosphorylase.

Difluoro analogue of UCS15A triggers activation of exogenously expressed c-Src in HCT 116 human colorectal carcinoma cells

Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening

Discovery of potent 4-aminoquinoline hydrazone inhibitors of NRH:quinoneoxidoreductase-2 (NQO2)

Effect of sequence and stereochemistry reversal on p53 peptide mimicry

Evaluation of analogues of furan-amidines as inhibitors of NQO2.

Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors

Exploring protein kinase conformation using swarm-enhanced sampling molecular dynamics

Exploring reaction pathways with transition path and umbrella sampling: application to methyl maltoside.

Fluorescent probe: complexation of Fe3+ with the myo-inositol 1,2,3-trisphosphate motif.

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics

Identification of a novel class of inhibitor of human and Escherichia coli thymidine phosphorylase by in silico screening.

Imidazoacridin-6-ones as novel inhibitors of the quinone oxidoreductase NQO2.

Improved Hydrogen Bonding at the NDDO-Type Semiempirical Quantum Mechanical/Molecular Mechanical Interface

In silico identification and biochemical characterization of novel inhibitors of NQO1

In silico identification and biochemical evaluation of novel inhibitors of NRH:quinone oxidoreductase 2 (NQO2).

In silico screening and biological evaluation of inhibitors of Src-SH3 domain interaction with a proline-rich ligand

Insights into the Activity and Specificity of Trypanosoma cruzi trans-Sialidase from Molecular Dynamics Simulations ⬇️

Metabolic fate of 3α,5-cycloandrostanes in the endogenous lactonization pathway of Aspergillus tamarii KITA.

Molecular Dynamics Study of Anhydrous Lamellar Structures of Synthetic Glycolipids: Effects of Chain Branching and Disaccharide Headgroup ⬇️

Molecular Dynamics of Cellulose Amphiphilicity at the Graphene-Water Interface.

Molecular dynamics and free energy analysis of neuraminidase-ligand interactions

Molecular dynamics simulation of monoalkyl glycoside micelles in aqueous solution: influence of carbohydrate headgroup stereochemistry.

Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides ⬇️

Molecular dynamics study of chemically engineered green fluorescent protein mutants: comparison of intramolecular fluorescence resonance energy transfer rate

Molecular probes: insights into design and analysis from computational and physical chemistry.

Negative Cooperativity in NAD(P)H Quinone Oxidoreductase 1 (NQO1)

Non-enzymatic recombination of RNA: Ligation in loops.

Non-symmetrical furan-amidines as novel leads for the treatment of cancer and malaria

Novel inhibitors of NRH:quinone oxidoreductase 2 (NQO2): crystal structures, biochemical activity, and intracellular effects of imidazoacridin-6-ones

Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies.

Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening

Rational drug design in parasitology: trans-sialidase as a case study for Chagas disease.

Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: Application to Influenza neuraminidase

Src family kinase inhibitor Saracatinib (AZD0530) impairs oxaliplatin uptake in colorectal cancer cells and blocks organic cation transporters

Stoichiometry and Folding of Linear Polypeptides—Reading Between the Lines ⬇️

Structure–activity relationship of 2,4,5-trioxoimidazolidines as inhibitors of thymidine phosphorylase

The application of quantum mechanics in structure-based drug design ⬇️

The effects of perfluorination on carbohydrate-pi interactions: computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin.

Tracing the GSAP-APP C-99 Interaction Site in the β-Amyloid Pathway Leading to Alzheimer's Disease

Tryptophan as a molecular shovel in the glycosyl transfer activity of Trypanosoma cruzi trans-sialidase.

What Next for Quantum Mechanics in Structure-Based Drug Discovery?

Xanthine oxidase-activated prodrugs of thymidine phosphorylase inhibitors

miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells