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		Correspondence Can dietary fibre help provide safer food products for sufferers of gluten intolerance? A well-established biophysical probe may help towards providing an answer M Samil Kök, Richard Gillis, Shirley Ang, David Lafond, Arthur S Tatham, Gary Adams, Stephen E Harding BMC Biophysics 2012, 5:10 (17 May 2012) Abstract \| Provisional PDF \| PubMed \| 1 comment \| Editor’s summary Stephen Harding and colleagues speculate on the role that the ultracentrifuge assay procedure could play in detecting non-toxic biopolymers capable of sequestering ingested gluten peptides, with the eventual aim of reducing gluten intolerance symptoms.
		Software DelPhi: a comprehensive suite for DelPhi software and associated resources Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov BMC Biophysics 2012, 5:9 (14 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The DelPhi package is a comprehensive and user-friendly suite of tools for modelling electrostatic potentials in macromolecules using the Poisson-Boltzmann Equation, and is now enriched with additional features for greater usability.
		Research article Differences in adhesion and protrusion properties correlate with differences in migration speed under EGF stimulation Yue Hou, Sarah Hedberg, Ian C Schneider BMC Biophysics 2012, 5:8 (11 May 2012) Abstract \| Provisional PDF \| PubMed
		Research article Arbitrary protein-protein docking targets biologically relevant interfaces Juliette Martin, Richard Lavery BMC Biophysics 2012, 5:7 (6 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Docking of target proteins against an arbitrary set of partners generally leads to non-random localization of interaction interfaces as the false complexes favor residues from true interaction sites, allowing prediction of biologically relevant protein interfaces
		Research article Membrane microdomains emergence through non-homogeneous diffusion Hedi A Soula, Antoine Coulon, Guillaume Beslon BMC Biophysics 2012, 5:6 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Non-homogeneous diffusion in cell membranes leads to the formation of protein/ lipid enriched microdomains in a model of membrane dynamics, with domains of high viscosity tending to gather a statistically larger proportion of diffusive particles
		Research article Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: opposing responses to isoflurane Steven C Nelson, Steven K Neeley, Eric D Melonakos, John D Bell, David D Busath BMC Biophysics 2012, 5:5 (24 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Steady-state anisotropy of two fluorescent probes at different depths in a lipid bilayer reveals a decrease in anisotropy with increasing isoflurane anesthetic concentration, reflecting changes in the lateral pressure profile of the membrane.
		Software APM_GUI: analyzing particle movement on the cell membrane and determining confinement Silvia A Menchón, Mauricio G Martín, Carlos G Dotti BMC Biophysics 2012, 5:4 (20 February 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties Aliana López de Victoria, Chris A Kieslich, Apostolos K Rizos, Elias Krambovitis, Dimitrios Morikis BMC Biophysics 2012, 5:3 (7 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The spatial distributions of electrostatic potentials and charges in the V3 loop of HIV-1 protein gp120 may be responsible for both long- and short-range interactions with co-receptors, ultimately affecting viral entry into cells
		Research article Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations Haina Qin, Liangzhong Lim, Jianxing Song BMC Biophysics 2012, 5:2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Structural determination of the EphA4 ligand binding domain provides the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity.
		Research article Using default constraints of the spindle assembly checkpoint to estimate the associated chemical rates Khanh Dao Duc, David Holcman BMC Biophysics 2012, 5:1 (19 January 2012) Abstract \| Provisional PDF \| PubMed
		Research article Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data Mizuki Morita, AVSK Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi BMC Biophysics 2011, 4:21 (14 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner, largely explained by general lipophilicity, that suggests a common pattern of lipid tail-amino acid interactions
		Research article Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study Christian Trapp, Marc Schenkelberger, Albrecht Ott BMC Biophysics 2011, 4:20 (13 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Stable DNA duplexes with a bulged loop can form from short strands of unequal length with duplex stability decreasing monotonically with the length of the bulged loop, contributing substantially to microarray fluorescence intensity
		Research article Characterizing low affinity epibatidine binding to α4β2 nicotinic acetylcholine receptors with ligand depletion and nonspecific binding Alexandra M Person, Gregg B Wells BMC Biophysics 2011, 4:19 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Manipulation of maximum ligand and receptor concentrations and intentionally increasing ligand depletion are potentially helpful approaches to study low affinity binding of epibatidine to an independent binding site of alpha4beta2 nicotinic acetylcholine receptor.
		Research article Spindles and active vortices in a model of confined filament-motor mixtures David A Head, WJ Briels, Gerhard Gompper BMC Biophysics 2011, 4:18 (16 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discrete filament-motor protein model of subcellular microtubule self-assembly in fission yeast spontaneously generates a number of steady states, including spindles, nematics, and asters, highlighting potential mechanisms for self-organisation in filaments
		Research article Introduction of non-linear elasticity models for characterization of shape and deformation statistics: application to contractility assessment of isolated adult cardiocytes Carlos Bazan, Trevor Hawkins, David Torres-Barba, Peter Blomgren, Paul Paolini BMC Biophysics 2011, 4:17 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel image analysis approach to assess cardiocyte contractility successfully captures the full extent of contractile behavior by incorporating biomechanical properties, energy conservation principles and information content measures.
		Research article Sensing the Heat Stress by Mammalian Cells Jordan Cates, Garrett C Graham, Natalie Omattage, Elizabeth Pavesich, Ian Setliff, Jack Shaw, Caitlin Smith, Ovidiu Lipan BMC Biophysics 2011, 4:16 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new system-level mathematical approach is proposed to model the heat-shock response network in mammalian cells and the key heat-shock transcription factor-1 (HSF) which is transiently activated by elevated temperatures.
		Research article Probabilistic modeling and analysis of the effects of extra-cellular matrix density on the sizes, shapes, and locations of integrin clusters in adherent cells Erik S Welf, Ulhas P Naik, Babatunde A Ogunnaike BMC Biophysics 2011, 4:15 (9 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cells can sense the availability of extracellular matrix binding sites and in response they regulate the sizes, shapes, and locations of integrin clusters that mediate cell adhesion to surrounding tissues.
		Methodology article Detection and differentiation of bacterial spores in a mineral matrix by Fourier transform infrared spectroscopy (FTIR) and chemometrical data treatment Andrea Brandes Ammann, Helmut Brandl BMC Biophysics 2011, 4:14 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fourier transform infrared spectroscopy (FTIR) combined with chemometrical data treatment enables differentiation of Bacillus spores down to the species level in pure culture and in the presence of clay mineral matrix such as bentonite.
		Research article An upper limit for macromolecular crowding effects Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
		Research article Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics Yu-ming M Huang, Chia-en A Chang BMC Biophysics 2011, 4:12 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mechanism of phosphothreonine/serine recognition and specificity is elucidated for three well-known phosphopeptide-binding domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated domain (FHA) with the use of molecular dynamics simulations.
		Research article Thermotropic phase behavior and headgroup interactions of the nonbilayer lipids phosphatidylethanolamine and monogalactosyldiacylglycerol in the dry state Antoaneta V Popova, Dirk K Hincha BMC Biophysics 2011, 4:11 (10 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The thermotropic phase behavior and molecular interactions of the two biologically important non-bilayer lipids, egg phosphatidylethanolamine (EPE) and monogalactosyldiacylglycerol (MGDG) have been comprehensively characterized by Fourier-transform Infrared spectroscopy and Differential Scanning Calorimetry.
		Methodology article A Bayesian method for inferring quantitative information from FRET data Catherine A Lichten, Peter S Swain BMC Biophysics 2011, 4:10 (9 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new Bayesian algorithm is available for extracting quantitative information on molecular interactions from FRET (Forster resonance energy transfer) data which yields both an estimate of the dissociation constant and the uncertainty associated with that estimate.
		Research article Diffusion of hydrophobin proteins in solution and interactions with a graphite surface Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.
		Review Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations Balaji VS Iyer, Martin Kenward, Gaurav Arya BMC Biophysics 2011, 4:8 (15 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gaurav Arya and colleagues review results from state-of-the-art microscopy and chromosome conformation capture techniques that are being used to understand the three dimensional structure of the genome and the physical principles governing its folding.
		Research article Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.

	All
		Correspondence Can dietary fibre help provide safer food products for sufferers of gluten intolerance? A well-established biophysical probe may help towards providing an answer M Samil Kök, Richard Gillis, Shirley Ang, David Lafond, Arthur S Tatham, Gary Adams, Stephen E Harding BMC Biophysics 2012, 5:10 (17 May 2012) Abstract \| Provisional PDF \| PubMed \| 1 comment \| Editor’s summary Stephen Harding and colleagues speculate on the role that the ultracentrifuge assay procedure could play in detecting non-toxic biopolymers capable of sequestering ingested gluten peptides, with the eventual aim of reducing gluten intolerance symptoms.
		Software DelPhi: a comprehensive suite for DelPhi software and associated resources Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov BMC Biophysics 2012, 5:9 (14 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The DelPhi package is a comprehensive and user-friendly suite of tools for modelling electrostatic potentials in macromolecules using the Poisson-Boltzmann Equation, and is now enriched with additional features for greater usability.
		Research article Differences in adhesion and protrusion properties correlate with differences in migration speed under EGF stimulation Yue Hou, Sarah Hedberg, Ian C Schneider BMC Biophysics 2012, 5:8 (11 May 2012) Abstract \| Provisional PDF \| PubMed
		Research article Arbitrary protein-protein docking targets biologically relevant interfaces Juliette Martin, Richard Lavery BMC Biophysics 2012, 5:7 (6 May 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Docking of target proteins against an arbitrary set of partners generally leads to non-random localization of interaction interfaces as the false complexes favor residues from true interaction sites, allowing prediction of biologically relevant protein interfaces
		Research article Membrane microdomains emergence through non-homogeneous diffusion Hedi A Soula, Antoine Coulon, Guillaume Beslon BMC Biophysics 2012, 5:6 (30 April 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Non-homogeneous diffusion in cell membranes leads to the formation of protein/ lipid enriched microdomains in a model of membrane dynamics, with domains of high viscosity tending to gather a statistically larger proportion of diffusive particles
		Research article Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: opposing responses to isoflurane Steven C Nelson, Steven K Neeley, Eric D Melonakos, John D Bell, David D Busath BMC Biophysics 2012, 5:5 (24 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Steady-state anisotropy of two fluorescent probes at different depths in a lipid bilayer reveals a decrease in anisotropy with increasing isoflurane anesthetic concentration, reflecting changes in the lateral pressure profile of the membrane.
		Software APM_GUI: analyzing particle movement on the cell membrane and determining confinement Silvia A Menchón, Mauricio G Martín, Carlos G Dotti BMC Biophysics 2012, 5:4 (20 February 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties Aliana López de Victoria, Chris A Kieslich, Apostolos K Rizos, Elias Krambovitis, Dimitrios Morikis BMC Biophysics 2012, 5:3 (7 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The spatial distributions of electrostatic potentials and charges in the V3 loop of HIV-1 protein gp120 may be responsible for both long- and short-range interactions with co-receptors, ultimately affecting viral entry into cells
		Research article Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations Haina Qin, Liangzhong Lim, Jianxing Song BMC Biophysics 2012, 5:2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Structural determination of the EphA4 ligand binding domain provides the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity.
		Research article Using default constraints of the spindle assembly checkpoint to estimate the associated chemical rates Khanh Dao Duc, David Holcman BMC Biophysics 2012, 5:1 (19 January 2012) Abstract \| Provisional PDF \| PubMed
		Research article Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data Mizuki Morita, AVSK Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi BMC Biophysics 2011, 4:21 (14 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner, largely explained by general lipophilicity, that suggests a common pattern of lipid tail-amino acid interactions
		Research article Stability of double-stranded oligonucleotide DNA with a bulged loop: a microarray study Christian Trapp, Marc Schenkelberger, Albrecht Ott BMC Biophysics 2011, 4:20 (13 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Stable DNA duplexes with a bulged loop can form from short strands of unequal length with duplex stability decreasing monotonically with the length of the bulged loop, contributing substantially to microarray fluorescence intensity
		Research article Characterizing low affinity epibatidine binding to α4β2 nicotinic acetylcholine receptors with ligand depletion and nonspecific binding Alexandra M Person, Gregg B Wells BMC Biophysics 2011, 4:19 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Manipulation of maximum ligand and receptor concentrations and intentionally increasing ligand depletion are potentially helpful approaches to study low affinity binding of epibatidine to an independent binding site of alpha4beta2 nicotinic acetylcholine receptor.
		Research article Spindles and active vortices in a model of confined filament-motor mixtures David A Head, WJ Briels, Gerhard Gompper BMC Biophysics 2011, 4:18 (16 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discrete filament-motor protein model of subcellular microtubule self-assembly in fission yeast spontaneously generates a number of steady states, including spindles, nematics, and asters, highlighting potential mechanisms for self-organisation in filaments
		Research article Introduction of non-linear elasticity models for characterization of shape and deformation statistics: application to contractility assessment of isolated adult cardiocytes Carlos Bazan, Trevor Hawkins, David Torres-Barba, Peter Blomgren, Paul Paolini BMC Biophysics 2011, 4:17 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel image analysis approach to assess cardiocyte contractility successfully captures the full extent of contractile behavior by incorporating biomechanical properties, energy conservation principles and information content measures.
		Research article Sensing the Heat Stress by Mammalian Cells Jordan Cates, Garrett C Graham, Natalie Omattage, Elizabeth Pavesich, Ian Setliff, Jack Shaw, Caitlin Smith, Ovidiu Lipan BMC Biophysics 2011, 4:16 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new system-level mathematical approach is proposed to model the heat-shock response network in mammalian cells and the key heat-shock transcription factor-1 (HSF) which is transiently activated by elevated temperatures.
		Research article Probabilistic modeling and analysis of the effects of extra-cellular matrix density on the sizes, shapes, and locations of integrin clusters in adherent cells Erik S Welf, Ulhas P Naik, Babatunde A Ogunnaike BMC Biophysics 2011, 4:15 (9 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cells can sense the availability of extracellular matrix binding sites and in response they regulate the sizes, shapes, and locations of integrin clusters that mediate cell adhesion to surrounding tissues.
		Methodology article Detection and differentiation of bacterial spores in a mineral matrix by Fourier transform infrared spectroscopy (FTIR) and chemometrical data treatment Andrea Brandes Ammann, Helmut Brandl BMC Biophysics 2011, 4:14 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fourier transform infrared spectroscopy (FTIR) combined with chemometrical data treatment enables differentiation of Bacillus spores down to the species level in pure culture and in the presence of clay mineral matrix such as bentonite.
		Research article An upper limit for macromolecular crowding effects Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
		Research article Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics Yu-ming M Huang, Chia-en A Chang BMC Biophysics 2011, 4:12 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mechanism of phosphothreonine/serine recognition and specificity is elucidated for three well-known phosphopeptide-binding domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated domain (FHA) with the use of molecular dynamics simulations.
		Research article Thermotropic phase behavior and headgroup interactions of the nonbilayer lipids phosphatidylethanolamine and monogalactosyldiacylglycerol in the dry state Antoaneta V Popova, Dirk K Hincha BMC Biophysics 2011, 4:11 (10 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The thermotropic phase behavior and molecular interactions of the two biologically important non-bilayer lipids, egg phosphatidylethanolamine (EPE) and monogalactosyldiacylglycerol (MGDG) have been comprehensively characterized by Fourier-transform Infrared spectroscopy and Differential Scanning Calorimetry.
		Methodology article A Bayesian method for inferring quantitative information from FRET data Catherine A Lichten, Peter S Swain BMC Biophysics 2011, 4:10 (9 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new Bayesian algorithm is available for extracting quantitative information on molecular interactions from FRET (Forster resonance energy transfer) data which yields both an estimate of the dissociation constant and the uncertainty associated with that estimate.
		Research article Diffusion of hydrophobin proteins in solution and interactions with a graphite surface Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.
		Review Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations Balaji VS Iyer, Martin Kenward, Gaurav Arya BMC Biophysics 2011, 4:8 (15 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gaurav Arya and colleagues review results from state-of-the-art microscopy and chromosome conformation capture techniques that are being used to understand the three dimensional structure of the genome and the physical principles governing its folding.
		Research article Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.