List of works - Peter J Bond

2016 update on APBioNet's annual international conference on bioinformatics (InCoB)

scientific article published on 22 December 2016

A Funneled Conformational Landscape Governs Flavivirus Fusion Peptide Interaction with Lipid Membranes.

scientific article published on 6 June 2018

A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone

scientific article published on 10 June 2017

A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice

scientific article published on 01 June 2019

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

scientific article published on 17 May 2018

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4.

scientific article

A study on Fe(2+) - α-helical-rich keratin complex formation using isothermal titration calorimetry and molecular dynamics simulation.

scientific article

A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles

scientific article

Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub.

scientific article

Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism.

scientific article

An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit

scientific article published on 13 December 2020

An Optical Technique for Mapping Microviscosity Dynamics in Cellular Organelles

scientific article published on 18 April 2018

Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.

scientific article

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.

scholarly article

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

scientific article

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

scientific article published on 20 January 2016

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

scientific article published in July 2009

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

scientific article

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

scientific article published on 20 October 2006

Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.

scientific article

Concentration- and pH-Dependent Oligomerization of the Thrombin-Derived C-Terminal Peptide TCP-25

scientific article published on 19 November 2020

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

scientific article

Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component.

scientific article

Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes

scientific article published on 24 October 2013

Directing GDNF-mediated neuronal signaling with proactively programmable cell-surface saccharide-free glycosaminoglycan mimetics

scientific article published on 01 January 2019

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

scientific article

Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.

scientific article published on 15 May 2013

Editorial

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

scientific article published in May 2014

Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway

scientific article published on 09 January 2019

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

scientific article published on 17 October 2016

Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response

scientific article

Engineering an Osmosensor by Pivotal Histidine Positioning within Disordered Helices

scientific article published on 29 November 2018

Evidence that TLR4 Is Not a Receptor for Saturated Fatty Acids but Mediates Lipid-Induced Inflammation by Reprogramming Macrophage Metabolism.

scientific article published on 13 April 2018

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

scientific article published on February 24, 2011

Extending the Martini Coarse-Grained Force Field to N-Glycans

scientific article published on 23 July 2020

Facile saccharide-free mimetics that recapitulate key features of glycosaminoglycan sulfation patterns

scientific article published on 24 August 2018

Flavivirus Cross-Reactivity to Dengue Nonstructural Protein 1 Antigen Detection Assays

scientific article published on 24 December 2019

Free energy predictions of ligand binding to an α-helix using steered molecular dynamics and umbrella sampling simulations

scientific article published on 17 July 2014

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

scientific article published on October 2016

Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States

scientific article published on 11 April 2017

Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.

scientific article published on 11 September 2008

How Ligand Binding Affects the Dynamical Transition Temperature in Proteins

scientific article published on 03 March 2020

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

scientific article

Impairing Cohesin Smc1/3 Head Engagement Compensates for the Lack of Eco1 Function.

scientific article published on 27 September 2016

Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.

scientific article published on 18 January 2012

Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations

scientific article published on 24 January 2019

Influence of pH on the activity of thrombin-derived antimicrobial peptides

scientific article published on 06 June 2018

Insertion and assembly of membrane proteins via simulation.

scientific article

Insights into water accessible pathways and the inactivation mechanism of proton translocation by the membrane-embedded domain of V-type ATPases

scientific article published on 01 March 2019

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

scientific article (publication date: April 2015)

Introductory note for JBCB special issue

scientific article published on 30 December 2016

Ion channel gating: insights via molecular simulations.

scientific article published on November 2003

Linker length affects photostability of protein-targeted sensor of cellular microviscosity

scientific article published on 10 October 2019

Lipid/protein interactions and the membrane/water interfacial region

scientific article published on 01 December 2003

MD simulations of spontaneous membrane protein/detergent micelle formation.

scientific article

Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody

scientific article published on 21 November 2018

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

scientific article

Membrane protein structure quality in molecular dynamics simulation.

scientific article

Membrane recognition and dynamics of the RNA degradosome

scientific article

Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation.

scientific article

Molecular basis for the maintenance of lipid asymmetry in the outer membrane ofEscherichia coli

Molecular basis of dengue virus serotype 2 morphological switch from 29°C to 37°C

scientific article published on 19 September 2019

Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment.

scientific article

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

scientific article published on 13 April 2011

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment

scientific article published on 01 January 2005

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

scientific article published on 01 July 2020

Molecular dynamics simulations of membrane proteins

scientific article published on 01 January 2008

Molecular dynamics simulations of membrane proteins

scientific article published on 01 January 2015

Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.

scientific article published on 21 May 2011

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

scientific article published on 15 October 2020

Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions

scientific article published on 01 January 2019

Multiscale modeling of innate immune receptors: Endotoxin recognition and regulation by host defense peptides

scientific article published on 24 July 2019

Multiscale modelling and simulation of viruses

scientific article published on 25 January 2020

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses

scientific article

Multiscale molecular dynamics simulations of membrane proteins.

scientific article published on January 2013

Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab

scientific article published on 12 February 2020

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

scientific article published on 8 November 2016

On the ion coupling mechanism of the MATE transporter ClbM

scientific article published on 28 November 2019

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.

scientific article

Partial Intrinsic Disorder Governs the Dengue Capsid Protein Conformational Ensemble

scientific article published on 05 June 2018

Polar N-terminal Residues Conserved in Type 2 Secretion Pseudopilins Determine Subunit Targeting and Membrane Extraction Steps during Fibre Assembly

scientific article published on 17 April 2017

Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.

scientific article published on 13 October 2009

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

scientific article

Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold.

scientific article published on 10 October 2017

Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations

scientific article

Revisiting the interaction between the chaperone Skp and lipopolysaccharide

scientific article

Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification

scientific article published on October 2013

Selective inhibitors of trypanosomal uridylyl transferase RET1 establish druggability of RNA post-transcriptional modifications

scientific article

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

scientific article published on 11 July 2008

Single mutations in the ε subunit from thermophilic PS3 generate a high binding affinity site for ATP

scientific article published on 05 September 2018

Single-molecule studies of flavivirus envelope dynamics: Experiment and computation

scientific article published on 14 September 2018

Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis

scientific article

Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors

scientific article published on 21 April 2010

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides

scientific article published in Nature Communications

Structural basis for endotoxin neutralization and anti-inflammatory activity of thrombin-derived C-terminal peptides

Structure and subunit arrangement of Mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ

scientific article published on 24 May 2019

Structure mapping of dengue and Zika viruses reveals functional long-range interactions

scientific article published on 29 March 2019

Structure mapping of dengue and Zika viruses reveals new functional long-range interactions

scholarly article published 1 August 2018

Systematic analysis of protein identity between Zika virus and other arthropod-borne viruses

scientific article

The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain

scientific article

The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity.

scientific article published on 25 November 2015

The architecture of the OmpC-MlaA complex sheds light on the maintenance of outer membrane lipid asymmetry in

scientific article published in Journal of Biological Chemistry

The disordered plant dehydrin Lti30 protects the membrane during water-related stress by cross-linking lipids

scientific article published on 28 February 2019

The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule

scientific article

The role of protein-protein interactions in Toll-like receptor function.

scientific article published on 02 July 2015

The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6.

scientific article published on 10 August 2016

The simulation approach to bacterial outer membrane proteins.

scientific article published on May 2004

The simulation approach to lipid-protein interactions

scientific article published in January 2013

The structural basis for endotoxin-induced allosteric regulation of the Toll-like receptor 4 (TLR4) innate immune receptor.

scientific article published on 30 October 2013

The structural basis for membrane assembly of immunoreceptor signalling complexes

scientific article published on 27 August 2019

Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer

scientific article published on 01 December 2006

Understanding dengue virus capsid protein disordered N-Terminus and pep14-23-based inhibition

scientific article published on 20 November 2014

List of works by Peter J Bond

2016 update on APBioNet's annual international conference on bioinformatics (InCoB)

A Funneled Conformational Landscape Governs Flavivirus Fusion Peptide Interaction with Lipid Membranes.

A Spring-Loaded Mechanism Governs the Clamp-like Dynamics of the Skp Chaperone

A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4.

A study on Fe(2+) - α-helical-rich keratin complex formation using isothermal titration calorimetry and molecular dynamics simulation.

A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles

Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub.

Aggregation of thrombin-derived C-terminal fragments as a previously undisclosed host defense mechanism.

An Alternative HIV-1 Non-Nucleoside Reverse Transcriptase Inhibition Mechanism: Targeting the p51 Subunit

An Optical Technique for Mapping Microviscosity Dynamics in Cellular Organelles

Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.

Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.

Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016).

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.

Concentration- and pH-Dependent Oligomerization of the Thrombin-Derived C-Terminal Peptide TCP-25

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component.

Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes

Directing GDNF-mediated neuronal signaling with proactively programmable cell-surface saccharide-free glycosaminoglycan mimetics

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.

Editorial

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway

Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity

Energetics of Endotoxin Recognition in the Toll-Like Receptor 4 Innate Immune Response

Engineering an Osmosensor by Pivotal Histidine Positioning within Disordered Helices

Evidence that TLR4 Is Not a Receptor for Saturated Fatty Acids but Mediates Lipid-Induced Inflammation by Reprogramming Macrophage Metabolism.

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

Extending the Martini Coarse-Grained Force Field to N-Glycans

Facile saccharide-free mimetics that recapitulate key features of glycosaminoglycan sulfation patterns

Flavivirus Cross-Reactivity to Dengue Nonstructural Protein 1 Antigen Detection Assays

Free energy predictions of ligand binding to an α-helix using steered molecular dynamics and umbrella sampling simulations

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

Full-length, Oligomeric Structure of Wzz Determined by Cryoelectron Microscopy Reveals Insights into Membrane-Bound States

Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.

How Ligand Binding Affects the Dynamical Transition Temperature in Proteins

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

Impairing Cohesin Smc1/3 Head Engagement Compensates for the Lack of Eco1 Function.

Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.

Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations

Influence of pH on the activity of thrombin-derived antimicrobial peptides

Insertion and assembly of membrane proteins via simulation.

Insights into water accessible pathways and the inactivation mechanism of proton translocation by the membrane-embedded domain of V-type ATPases

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

Introductory note for JBCB special issue

Ion channel gating: insights via molecular simulations.

Linker length affects photostability of protein-targeted sensor of cellular microviscosity

Lipid/protein interactions and the membrane/water interfacial region

MD simulations of spontaneous membrane protein/detergent micelle formation.

Mechanism of Enhanced Immature Dengue Virus Attachment to Endosomal Membrane Induced by prM Antibody

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

Membrane protein structure quality in molecular dynamics simulation.

Membrane recognition and dynamics of the RNA degradosome

Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation.

Molecular basis for the maintenance of lipid asymmetry in the outer membrane ofEscherichia coli

Molecular basis of dengue virus serotype 2 morphological switch from 29°C to 37°C

Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment.

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

Molecular dynamics simulations of membrane proteins

Molecular dynamics simulations of membrane proteins

Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.

Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein

Multiscale Modeling and Simulation Approaches to Lipid-Protein Interactions

Multiscale modeling of innate immune receptors: Endotoxin recognition and regulation by host defense peptides

Multiscale modelling and simulation of viruses

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses

Multiscale molecular dynamics simulations of membrane proteins.

Not all therapeutic antibody isotypes are equal: the case of IgM versus IgG in Pertuzumab and Trastuzumab

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

On the ion coupling mechanism of the MATE transporter ClbM