the goodman group this list is a product of research in the Goodman Group;
it is not the official department of chemistry list of
academics or academic publications
university of cambridge  

  • Peter J Bond
  • Current Options:
    All years, text only
  • Text / Pictures
  • People Index
  • Year Index
  • Search
  • Peter J Bond Publications

    2014


    Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations
    Jan K Marzinek, Peter J Bond, Guoping Lian, Yanyan Zhao, Lujia Han, Massimo G Noro, Efstratios N Pistikopoulos, and Athanasios Mantalaris
    Journal_of_Chemical_Information_and_Modeling DOI: 10.1021/ci500164q


    Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories:trj_cavity
    Teresa Paramo, Alexandra East, Diana Garzón, Martin B Ulmschneider, and Peter J Bond
    Journal_of_Chemical_Theory_and_Computation DOI: 10.1021/ct401098b

    2013


    The structural basis for endotoxin-induced allosteric regulation of the Toll-like receptor 4 (TLR4) innate immune receptor.
    Paramo T, Piggot TJ, Bryant CE, Bond PJ
    J Biol Chem, 2013, 51, 36215-36225. DOI: 10.1074/jbc.M113.501957


    Design, synthesis, and biological evaluation of an allosteric inhibitor of HSET that targets cancer cells with supernumerary centrosomes.
    Watts CA, Richards FM, Bender A, Bond PJ, Korb O, Kern O, Riddick M, Owen P, Myers RM, Raff J, Gergely F, Jodrell DI, Ley SV
    Chem Biol, 2013, 11, 1399-1410. DOI: 10.1016/j.chembiol.2013.09.012


    Selective inhibition of the unfolded protein response: targeting catalytic sites for Schiff base modification.
    Tomasio SM, Harding HP, Ron D, Cross BC, Bond PJ
    Mol Biosyst, 2013-10, 10, 2408-2416. DOI: 10.1039/C3MB70234K


    Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.
    Garzón D, Anselmi C, Bond PJ, Faraldo-Gómez JD
    J Biol Chem, 2013, 27, 19528-19536. DOI: 10.1074/jbc.M113.470179


    Structural and Thermodynamic Insights into Bacterial Outer Membrane Lipid Signaling by the Innate Immune System
    Paramo T, Tomasio S, Bond PJ
    BIOPHYSICAL JOURNAL, 2013, 2, 611A-611A.


    A Zoom on Membrane Fusion through Coarse-Grained, Atomistic and Hybrid Molecular Dynamics of SNARE Proteins
    Tek A, Darre L, Bond PJ, Sansom MSP, Pantano S, Baaden M
    BIOPHYSICAL JOURNAL, 2013, 2, 32A-32A.


    A Simulation Approach to Molecular Transport in Bacterial Reaction Chambers
    Roessler F, Cebo T, Heffernan S, Bond PJ
    BIOPHYSICAL JOURNAL, 2013, 2, 633A-633A.


    The simulation approach to lipid-protein interactions.
    Paramo T, Garzón D, Holdbrook DA, Khalid S, Bond PJ
    Methods Mol Biol, 2013, 435-455. DOI: 10.1007/978-1-62703-275-9_19


    Atomistic and Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins
    Piggot TJ, Bond PJ, Khalid S
    Proteins in Solution and at Interfaces: Methods and Applications in Biotechnology and Materials Science, 2013, 193-206.

    2012


    Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms.
    Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC
    J Chem Inf Model, 2012, 3, 617-648. DOI: 10.1021/ci200542m


    The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule.
    Cross BC, Bond PJ, Sadowski PG, Jha BK, Zak J, Goodman JM, Silverman RH, Neubert TA, Baxendale IR, Ron D, Harding HP
    Proc Natl Acad Sci U S A, 2012, 15, E869-E878. DOI: 10.1073/pnas.1115623109


    The Molecular Basis for Lipid Recognition and Signaling in the Toll-Like Receptor Complex and a Family of Lipid-Binding Proteins
    Paramo T, Higson S, Piggot TJ, Bond PJ
    BIOPHYSICAL JOURNAL, 2012, 3, 664A-664A.


    Insights into Membrane Fusion from Molecular Dynamics Simulations of SNARE Proteins
    Tek A, Bond PJ, Sansom MSP, Baaden M
    BIOPHYSICAL JOURNAL, 2012, 3, 499A-499A.


    Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1.
    Beale TM, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM
    Bioorg Med Chem, 2012, 5, 1749-1759. DOI: 10.1016/j.bmc.2012.01.010


    Increased endothelial cell selectivity of triazole-bridged dihalogenated A-ring analogues of combretastatin A-1
    Beale TM, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM
    Bioorganic and Medicinal Chemistry, 2012, 5, 1749-1759.


    A-ring dihalogenation increases the cellular activity of combretastatin-templated tetrazoles
    Beale TM, Allwood DM, Bender A, Bond PJ, Brenton JD, Charnock-Jones DS, Ley SV, Myers RM, Shearman JW, Temple J, Unger J, Watts CA, Xian J
    ACS Medicinal Chemistry Letters, 2012, 3, 177-181.


    Minor pseudopilin self-assembly primes type II secretion pseudopilus elongation
    Cisneros DA, Bond PJ, Pugsley AP, Campos M, Francetic O
    EMBO Journal, 2012, 4, 1041-1053.


    Computational prediction of metabolism: Sites, products, SAR, P450 enzyme dynamics, and mechanisms
    Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC
    Journal of Chemical Information and Modeling, 2012, 3, 617-648.

    2011


    Molecular mechanism of selective recruitment of Syk kinases by the membrane antigen-receptor complex.
    Bond PJ, Faraldo-Gómez JD
    J Biol Chem, 2011, 29, 25872-25881. DOI: 10.1074/jbc.M111.223321


    From in silico target prediction to multi-target drug design: current databases, methods and applications.
    Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A
    J Proteomics, 2011, 12, 2554-2574. DOI: 10.1016/j.jprot.2011.05.011


    Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation.
    Bond PJ, Guy AT, Heron AJ, Bayley H, Khalid S
    Biochemistry, 2011, 18, 3777-3783. DOI: 10.1021/bi101404n


    Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study
    Piñeiro A, Bond PJ, Khalid S
    Biochimica et Biophysica Acta - Biomembranes, 2011, 6, 1746-1752.


    From in silico target prediction to multi-target drug design: Current databases, methods and applications
    Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, Young MP, Jenkins JL, Glick M, Glen RC, Bender A
    Journal of Proteomics, 2011, 12, 2554-2574.

    2010


    Antimicrobial and cell-penetrating peptides: structure, assembly and mechanisms of membrane lysis via atomistic and coarse-grained molecular dynamics simulations.
    Bond PJ, Khalid S
    Protein Pept Lett, 2010-11, 11, 1313-1327.


    Structural basis for the ion selectivity of F-ATP-synthase c-ring rotors
    Krah A, Pogoryelov D, Langer J, Bond PJ, Meier T, Faraldo-Gomez JD
    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 2010-07, 35-35. DOI: 10.1016/j.bbabio.2010.04.122


    Structural and energetic basis for H+ versus Na+ binding selectivity in ATP synthase Fo rotors.
    Krah A, Pogoryelov D, Langer JD, Bond PJ, Meier T, Faraldo-Gómez JD
    Biochim Biophys Acta, 2010-06, 06-Jul, 763-772. DOI: 10.1016/j.bbabio.2010.04.014


    Structural Basis for Regulation Specificity in Syk-Family Kinases
    Bond PJ, Faraldo-Gomez JD
    BIOPHYSICAL JOURNAL, 2010-01, 3, 442A-442A.


    Nanopores as Biosensors: DNA Sequencing and Chiral Discrimination
    Guy AT, Bond PJ, Khalid S
    BIOPHYSICAL JOURNAL, 2010-01, 3, 597A-597A.


    Multiscale Simulations of RNase E From E. coli: A Membrane Binding Protein
    Khalid S, Bond PJ, Luisi BF
    BIOPHYSICAL JOURNAL, 2010-01, 3, 81A-81A.


    Mechanisms of Selective Sodium/proton Binding and Coupled Rotation in F1fo ATP Synthases: Insights from Quantitative Computer Simulations
    Krah A, Bond PJ, Faraldo-Gomez JD
    BIOPHYSICAL JOURNAL, 2010-01, 3, 434A-434A.

    2009


    Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens.
    Garzón D, Bond PJ, Faraldo-Gómez JD
    Mol Immunol, 2009-12, 02-Mar, 253-260. DOI: 10.1016/j.molimm.2009.09.029


    Complete ion-coordination structure in the rotor ring of Na+-dependent F-ATP synthases.
    Meier T, Krah A, Bond PJ, Pogoryelov D, Diederichs K, Faraldo-Gómez JD
    J Mol Biol, 2009, 2, 498-507. DOI: 10.1016/j.jmb.2009.05.082


    Coarse-Grain Simulations of the R-SNARE Fusion Protein in its Membrane Environment Detect Long-Lived Conformational Sub-States
    Durrieu MP, Bond PJ, Sansom MSR, Lavery R, Baaden M
    CHEMPHYSCHEM, 2009, 09-Oct, 1548-1552. DOI: 10.1002/cphc.200900216


    Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study.
    Balali-Mood K, Bond PJ, Sansom MS
    Biochemistry, 2009, 10, 2135-2145. DOI: 10.1021/bi8017398

    2008


    DNA and lipid bilayers: self-assembly and insertion
    Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP
    J R SOC INTERFACE, 2008, S241-S250. DOI: 10.1098/rsif.2008.0239.focus


    Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer.
    Bond PJ, Wee CL, Sansom MS
    Biochemistry, 2008, 43, 11321-11331. DOI: 10.1021/bi800642m


    Helix-helix interactions in membrane proteins: coarse-grained simulations of glycophorin a helix dimerization.
    Psachoulia E, Fowler PW, Bond PJ, Sansom MS
    Biochemistry, 2008, 40, 10503-10512. DOI: 10.1021/bi800678t


    Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.
    Carpenter T, Bond PJ, Khalid S, Sansom MS
    Biophys J, 2008-10, 8, 3790-3801. DOI: 10.1529/biophysj.108.131078


    Coarse-grained simulations of the membrane-active antimicrobial Peptide maculatin 1.1.
    Bond PJ, Parton DL, Clark JF, Sansom MS
    Biophys J, 2008-10, 8, 3802-3815. DOI: 10.1529/biophysj.108.128686


    OmpA: gating and dynamics via molecular dynamics simulations.
    Khalid S, Bond PJ, Carpenter T, Sansom MS
    Biochim Biophys Acta, 2008-09, 9, 1871-1880. DOI: 10.1016/j.bbamem.2007.05.024


    Coarse-grained MD simulations of membrane protein-bilayer self-assembly.
    Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MS
    Structure, 2008-04, 4, 621-630. DOI: 10.1016/j.str.2008.01.014


    Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers.
    Cox K, Bond PJ, Grottesi A, Baaden M, Sansom MS
    Eur Biophys J, 2008-02, 2, 131-141. DOI: 10.1007/s00249-007-0185-8


    Coarse-grained simulation: a high-throughput computational approach to membrane proteins.
    Sansom MS, Scott KA, Bond PJ
    Biochem Soc Trans, 2008-02, Pt 1, 27-32. DOI: 10.1042/BST0360027


    Molecular dynamics simulations of membrane proteins.
    Biggin PC, Bond PJ
    Methods Mol Biol, 2008, 147-160. DOI: 10.1007/978-1-59745-177-2_8

    2007


    Coarse-grained molecular dynamics simulations of membrane proteins and peptides.
    Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MS
    J Struct Biol, 2007-03, 3, 593-605. DOI: 10.1016/j.jsb.2006.10.004


    Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations.
    Bond PJ, Sansom MS
    Proc Natl Acad Sci U S A, 2007, 8, 2631-2636. DOI: 10.1073/pnas.0606822104


    Membrane simulations of OpcA: Gating in the loops?
    Bond PJ, Derrick JP, Sansom MSP
    BIOPHYS J, 2007-01, 2, L23-L25. DOI: 10.1529/biophysj.106.097311


    Bilayer deformation around voltage-dependent potassium channels revealed by self-assembly coarse-grained simulations
    Bond PJ, Sansom MSP
    BIOPHYSICAL JOURNAL, 2007-01, 617A-617A.


    Bacteriorhodopsin in the purple membrane
    D'Rozario RS, Bond PJ, Sansom MSP
    BIOPHYSICAL JOURNAL, 2007-01, 556A-556A.

    2006


    Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer.
    Cuthbertson JM, Bond PJ, Sansom MS
    Biochemistry, 2006, 48, 14298-14310. DOI: 10.1021/bi0610911


    Cysteine-scanning mutagenesis and disulfide mapping studies of the conserved domain of the twin-arginine translocase TatB component
    Lee PA, Orriss GL, Buchanan G, Greene NP, Bond PJ, Punginelli C, Jack RL, Sansom MSP, Berks BC, Palmer T
    J BIOL CHEM, 2006, 45, 34072-34085. DOI: 10.1074/jbc.M607295200


    MD simulations of Mistic: conformational stability in detergent micelles and water.
    Psachoulia E, Bond PJ, Sansom MS
    Biochemistry, 2006, 30, 9053-9058. DOI: 10.1021/bi0608818


    Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.
    Bond PJ, Faraldo-Gómez JD, Deol SS, Sansom MS
    Proc Natl Acad Sci U S A, 2006, 25, 9518-9523. DOI: 10.1073/pnas.0600398103


    Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa.
    Khalid S, Bond PJ, Deol SS, Sansom MS
    Proteins, 2006, 1, 6-15. DOI: 10.1002/prot.20845


    Molecular simulations of membrane proteins: Protein/membrane interactions
    Sansom M, Bond PJ, Khalid S, Balali-Mood K
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2006, -.


    Insertion and assembly of membrane proteins via simulation.
    Bond PJ, Sansom MS
    J Am Chem Soc, 2006, 8, 2697-2704. DOI: 10.1021/ja0569104


    Anionic phospholipid interactions with the potassium channel KcsA: simulation studies.
    Deol SS, Domene C, Bond PJ, Sansom MS
    Biophys J, 2006, 3, 822-830. DOI: 10.1529/biophysj.105.071407


    Membrane Protein Simulations: Modelling a Complex Environment
    Bond PJ, Cuthbertson J, Deol SS, Forrest LR, Johnston J, Patargias G, Sansom MSP
    Lecture Notes in Computational Science and Engineering, 2006, 1-20.

    2005


    Simulation studies of the interactions between membrane proteins and detergents.
    Bond PJ, Cuthbertson J, Sansom MS
    Biochem Soc Trans, 2005-11, Pt 5, 910-912. DOI: 10.1042/BST20050910


    Molecular simulations and lipid-protein interactions: potassium channels and other membrane proteins.
    Sansom MS, Bond PJ, Deol SS, Grottesi A, Haider S, Sands ZA
    Biochem Soc Trans, 2005-11, Pt 5, 916-920. DOI: 10.1042/BST20050916


    Membrane protein structure quality in molecular dynamics simulation.
    Law RJ, Capener C, Baaden M, Bond PJ, Campbell J, Patargias G, Arinaminpathy Y, Sansom MS
    J Mol Graph Model, 2005-10, 2, 157-165. DOI: 10.1016/j.jmgm.2005.05.006


    Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.
    Patargias G, Bond PJ, Deol SS, Sansom MS
    J Phys Chem B, 2005, 1, 575-582. DOI: 10.1021/jp046727h


    On the convergence of the conformational sampling in molecular dynamics simulations of membrane proteins
    Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Mark SPS
    BIOPHYSICAL JOURNAL, 2005-01, 1, 150A-150A.


    Molecular Dynamics simulations of spontaneous micelle formation around membrane proteins.
    Bond PJ, Sansom MSP
    BIOPHYSICAL JOURNAL, 2005-01, 1, 356A-356A.

    2004


    MD simulations of spontaneous membrane protein/detergent micelle formation.
    Bond PJ, Cuthbertson JM, Deol SS, Sansom MS
    J Am Chem Soc, 2004, 49, 15948-15949. DOI: 10.1021/ja044819e


    Lipid-protein interactions of integral membrane proteins: a comparative simulation study.
    Deol SS, Bond PJ, Domene C, Sansom MS
    Biophys J, 2004-12, 6, 3737-3749. DOI: 10.1529/biophysj.104.048397


    Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations
    Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cuthbertson J, Sansom MSP
    PROTEINS, 2004, 4, 783-791. DOI: 10.1002/prot.20257


    The simulation approach to bacterial outer membrane proteins.
    Bond PJ, Sansom MS
    Mol Membr Biol, 2004-05, 3, 151-161. DOI: 10.1080/0968760410001699169


    Conformational dynamics of OmpA: MD simulations of a bacterial outer membrane protein
    Bond PJ, Sansom MSP
    BIOPHYSICAL JOURNAL, 2004-01, 1, 257A-257A.

    2003


    Lipid/protein interactions and the membrane/water interfacial region.
    Domene C, Bond PJ, Deol SS, Sansom MS
    J Am Chem Soc, 2003, 49, 14966-14967. DOI: 10.1021/ja0364874


    Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.
    Bond PJ, Sansom MS
    J Mol Biol, 2003, 5, 1035-1053.


    Membrane protein simulations: ion channels and bacterial outer membrane proteins.
    Domene C, Bond PJ, Sansom MS
    Adv Protein Chem, 2003, 159-193.

    2002


    OmpA: a pore or not a pore? Simulation and modeling studies.
    Bond PJ, Faraldo-Gómez JD, Sansom MS
    Biophys J, 2002-08, 2, 763-775. DOI: 10.1016/S0006-3495(02)75207-7



    © Goodman Group, 2005-2015; privacy

    department of chemistry University of Cambridge