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List of works by Philip C. Biggin

A Hydrophobic Gating Mechanism for Nanopores

A Numbering System for MFS Transporter Proteins

scientific article

A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations

scientific article published on 18 November 2019

A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors.

scientific article published on 20 September 2010

A dynamically interacting flexible loop assists oligomerisation of the Caenorhabditis elegans centriolar protein SAS-6

scientific article published on 05 March 2019

A prokaryotic glutamate receptor: homology modelling and molecular dynamics simulations of GluR0.

scientific article published in October 2003

A role for Leu118 of loop E in agonist binding to the alpha 7 nicotinic acetylcholine receptor

scientific article published on 13 March 2008

A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval

A steroid in a lipid bilayer: localization, orientation, and energetics

scientific article published on 8 August 2008

A7DB: a relational database for mutational, physiological and pharmacological data related to the alpha7 nicotinic acetylcholine receptor

scientific article

Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide

scientific article published on 01 January 2018

Accurate calculation of the absolute free energy of binding for drug molecules

scientific article

Actions of agonists, fipronil and ivermectin on the predominant in vivo splice and edit variant (RDLbd, I/V) of the Drosophila GABA receptor expressed in Xenopus laevis oocytes

scientific article

Additional acetylcholine (ACh) binding site at alpha4/alpha4 interface of (alpha4beta2)2alpha4 nicotinic receptor influences agonist sensitivity

scientific article published on 14 July 2011

Agonist and antagonist binding in human glycine receptors

scientific article published on 15 September 2014

An interview with Philip Biggin, Section Editor for Computational, in silico and modelling studies ⬇️

scientific article published on August 13, 2012

Application of an Integrated GPCR SAR-Modeling Platform To Explain the Activation Selectivity of Human 5-HT2C over 5-HT2B.

scientific article

Atomistic mechanisms of human TRPA1 activation by electrophile irritants through molecular dynamics simulation and mutual information analysis

scientific article published in 2022

BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability

scientific article published on 15 May 2018

Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties

scientific article

Binding site flexibility: molecular simulation of partial and full agonists within a glutamate receptor.

scientific article

Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity

Bookshelf: a simple curation system for the storage of biomolecular simulation data

scientific article (publication date: 2010)

Channel gating: twist to open.

scientific article

Characterization of protein conformational states by normal-mode frequencies.

scientific article published on 23 August 2007

Chloride ions in the pore of glycine and GABA channels shape the time course and voltage dependence of agonist currents

scientific article published on October 2011

Comment on "On the Functional Annotation of Open-Channel Structures in the Glycine Receptor"

scientific article published on 01 June 2020

Comparative molecular dynamics--similar folds and similar motions?

scientific article published on December 2005

Computational Investigation of Voltage-Gated Sodium Channel β3 Subunit Dynamics

scientific article published on 18 March 2020

Computational methods to examine conformational changes and ligand-binding properties: Examples in neurobiology

scientific article published on 5 March 2018

Conformational preferences of a 14-residue fibrillogenic peptide from acetylcholinesterase

scientific article

Controlling Intramolecular Interactions in the Design of Selective, High-Affinity Ligands for the CREBBP Bromodomain

scientific article

Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers

scientific article published on 22 March 2022

Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals

scholarly article

Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.

scientific article

Defining the structural relationship between kainate-receptor deactivation and desensitization

scientific article published on 18 August 2013

Determination of Pore-Lining Residues in the Hepatitis C Virus p7 Protein

scientific article (publication date: 2009)

Discovery of the First Selective, Nonpeptidic Orexin 2 Receptor Agonists

scientific article published on 16 September 2015

Distinct Structural Pathways Coordinate the Activation of AMPA Receptor-Auxiliary Subunit Complexes

scientific article published on 24 February 2016

Distribution and dynamics of adamantanes in a lipid bilayer

scientific article published on 03 October 2008

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

scientific article

Edit, cut and paste in the nicotinic acetylcholine receptor gene family of Drosophila melanogaster.

scientific article

Exploring the interaction of SV2A with racetams using homology modelling, molecular dynamics and site-directed mutagenesis

scientific article

Extending the structure of an ABC transporter to atomic resolution: modeling and simulation studies of MsbA.

scientific article published in April 2003

Fragment-Based Identification of Ligands for Bromodomain-Containing Factor 3 of Trypanosoma cruzi

scientific article published on 17 November 2020

Functional Validation of Heteromeric Kainate Receptor Models

scientific article

GPCR structure, function, drug discovery and crystallography: report from Academia-Industry International Conference (UK Royal Society) Chicheley Hall, 1-2 September 2014.

scientific article published on 14 March 2015

GPCRs: What Can We Learn from Molecular Dynamics Simulations?

scientific article published in January 2018

Glutamate receptors: desensitizing dimers

scientific article

Guiding lead optimization with GPCR structure modeling and molecular dynamics

scientific article

Homology modelling of human P-glycoprotein

scientific article

Identification of compounds that bind the centriolar protein SAS-6 and inhibit its oligomerisation

scientific article published on 01 September 2020

In silico mutation of cysteine residues in the ligand-binding domain of an N-methyl-D-aspartate receptor

scientific article published on 01 February 2007

Insect GABA receptors: splicing, editing, and targeting by antiparasitics and insecticides

scientific article

Insights into channel dysfunction from modelling and molecular dynamics simulations

scientific article published on 29 June 2017

Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.

scientific article published in August 2003

Intrinsic rectification of ion flux in alamethicin channels: studies with an alamethicin dimer ⬇️

scientific article published on August 1, 1997

Ion channel gating: insights via molecular simulations.

scientific article published on November 2003

JGromacs: a Java package for analyzing protein simulations

scientific article

K(+) versus Na(+) ions in a K channel selectivity filter: a simulation study

scientific article published on August 2002

Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism

scientific article published on 18 December 2015

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

Learning protein-ligand binding affinity with atomic environment vectors

scientific article published on 14 August 2021

MacroConf – dataset & workflows to assess cyclic peptide solution structures

scientific article published in 2023

Mass spectrometry reveals synergistic effects of nucleotides, lipids, and drugs binding to a multidrug resistance efflux pump

scientific article published on 20 May 2013

Mechanosensitive channels: stress relief.

scientific article

Molecular Basis of Kainate Receptor Modulation by Sodium

scientific article

Molecular basis for redox control by the human cystine/glutamate antiporter system xc−

scientific article published on 08 December 2021

Molecular basis for redox control by the human cystine/glutamate antiporter system xc−

preprint

Molecular determinants for competitive inhibition of alpha4beta2 nicotinic acetylcholine receptors.

scientific article

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 dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor.

scientific article published on 2 March 2006

Molecular dynamics simulations of the ligand-binding domain of the ionotropic glutamate receptor GluR2.

scientific article published on February 2002

Molecular dynamics studies of AChBP with nicotine and carbamylcholine: the role of water in the binding pocket

scientific article published on 26 June 2007

Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane

scientific article published on 2 September 2017

Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane

scientific article published on 30 December 2017

Muscle acetylcholine receptor conversion into chloride conductance at positive potentials by a single mutation

scientific article published on 30 September 2019

Mutational Analysis and Modeling of Negative Allosteric Modulator Binding Sites in AMPA Receptors

scientific article published on 03 October 2019

Mutationmapper: a tool to aid the mapping of protein mutation data

scientific article

Non-agonist-binding subunit interfaces confer distinct functional signatures to the alternate stoichiometries of the alpha4beta2 nicotinic receptor: an alpha4-alpha4 interface is required for Zn2+ potentiation

scientific article published on July 2008

Non-equivalent ligand selectivity of agonist sites in (α4β2)2α4 nicotinic acetylcholine receptors: a key determinant of agonist efficacy

scientific article published on 16 June 2014

On the atomic structure of cocaine in solution

scientific article

One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery

scientific article published on 5 August 2013

Open-state models of a potassium channel

scientific article published on October 2002

Oxidation Resistance 1 Modulates Glycolytic Pathways in the Cerebellum via an Interaction with Glucose-6-Phosphate Isomerase

scientific article published on 15 June 2018

Plastic wrap: journals, practise what you preach

scientific article published on 01 September 2019

Position and orientational preferences of drug-like compounds in lipid membranes: a computational and NMR approach

scientific article published on 01 August 2015

Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations

scientific article published on 01 February 2001

Potassium channels: structures, models, simulations.

scientific article

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

scientific article (publication date: 18 January 2017)

Protein dynamics--a moving target: comment on "Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments" by C. Micheletti

scientific article published on 26 October 2012

Proton Control of Transitions in an Amino Acid Transporter

scientific article published on 26 August 2019

Quantifying water-mediated protein-ligand interactions in a glutamate receptor: a DFT study

scientific article published on 5 May 2011

Rapid and accurate prediction and scoring of water molecules in protein binding sites

scientific article

Recovery from desensitization in GluA2 AMPA receptors is affected by a single mutation in the N-terminal domain interface

scientific article published in 2024

Rigid body essential X-ray crystallography: distinguishing the bend and twist of glutamate receptor ligand binding domains

scientific article published on July 2008

Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors

scientific article published on 29 January 2016

Role of the Cys Loop and Transmembrane Domain in the Allosteric Modulation of α4β2 Nicotinic Acetylcholine Receptors

scientific article

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance.

scientific article published on 13 November 2015

Selectivity and cooperativity of modulatory ions in a neurotransmitter receptor

scientific article published on March 2009

Simulation of voltage-dependent interactions of alpha-helical peptides with lipid bilayers

scientific article published on 01 June 1996

Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study

scientific article published on 8 August 2017

Steered Molecular Dynamics Simulations Predict Conformational Stability of Glutamate Receptors

scientific article published on 2 August 2016

Structural basis of antifolate recognition and transport by PCFT

scholarly article

Structure and orientation of the mammalian antibacterial peptide cecropin P1 within phospholipid membranes

scientific article published on 01 May 1996

Structure of the Inhibited State of the Sec Translocon

scientific article published on 09 July 2020

Structure-function relationships in helix-bundle channels probed via total chemical synthesis of alamethicin dimers: effects of a Gln7 to Asn7 mutation

scientific article published on 01 November 1997

Study of Human Orexin-1 and -2 G-Protein-Coupled Receptors with Novel and Published Antagonists by Modeling, Molecular Dynamics Simulations, and Site-Directed Mutagenesis

scientific article (publication date: 17 April 2012)

Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase

scientific article published on 01 November 2019

Substrate versus inhibitor dynamics of P-glycoprotein

scientific article published on 17 June 2013

The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy

scientific article published on 09 July 2009

The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions.

scientific article published on 7 December 2015

The KDEL trafficking receptor exploits pH to tune the strength of an unusual short hydrogen bond

scientific article published on 09 October 2020

The Startle Disease Mutation E103K Impairs Activation of Human Homomeric α1 Glycine Receptors by Disrupting an Intersubunit Salt Bridge across the Agonist Binding Site

scientific article published on 7 February 2017

The dielectric properties of water within model transbilayer pores.

scientific article published on November 1997

The dynamics of camphor in the cytochrome P450 CYP101D2.

scientific article published on 12 August 2013

The influence of different lipid environments on the structure and function of the hepatitis C virus p7 ion channel protein

scientific article published on 23 May 2011

The role of flexibility and conformational selection in the binding promiscuity of PDZ domains

scientific article

The solvation structure of alprazolam

scientific article published on 28 July 2016

The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif

scientific article published on 15 October 2021

The α7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics.

scientific article published in May 2005

Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site-directed mutagenesis

scientific article published on 8 November 2013

Towards understanding promiscuity in multidrug efflux pumps

scientific article published on 06 December 2013

Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions

scientific article (publication date: 15 April 2016)

Water at the nanoscale

scientific article published in Nature

Water in ion channels and pores--simulation studies

scientific article

Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin

scientific article

spyrmsd: symmetry-corrected RMSD calculations in Python

scientific article published on 31 August 2020

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