Published in J Chem Phys on October 21, 2007
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol (2010) 3.65
Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol (2010) 2.14
Effect of macromolecular crowding on reaction rates: a computational and theoretical study. Biophys J (2009) 1.21
Influence of macromolecular crowding on protein-protein association rates--a Brownian dynamics study. Biophys J (2008) 1.20
Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures. Biophys J (2009) 1.17
Diffusion in crowded biological environments: applications of Brownian dynamics. BMC Biophys (2011) 1.06
Exploring the spatial and temporal organization of a cell's proteome. J Struct Biol (2010) 0.97
Stochastic simulation of signal transduction: impact of the cellular architecture on diffusion. Biophys J (2009) 0.96
The shape of protein crowders is a major determinant of protein diffusion. Biophys J (2013) 0.92
Reaching new levels of realism in modeling biological macromolecules in cellular environments. J Mol Graph Model (2013) 0.88
Validation of fractal-like kinetic models by time-resolved binding kinetics of dansylamide and carbonic anhydrase in crowded media. Biophys J (2011) 0.87
Crowding alone cannot account for cosolute effect on amyloid aggregation. PLoS One (2011) 0.87
Computer Simulations of the Bacterial Cytoplasm. Biophys Rev (2013) 0.87
A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion. PLoS One (2014) 0.85
A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling. J Comput Biol (2012) 0.83
Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage. PLoS Comput Biol (2010) 0.83
Spatial simulations in systems biology: from molecules to cells. Int J Mol Sci (2012) 0.83
Effects of macromolecular crowding on intracellular diffusion from a single particle perspective. Biophys Rev (2010) 0.82
Protein-protein interactions in dilute to concentrated solutions: α-chymotrypsinogen in acidic conditions. J Phys Chem B (2014) 0.81
A molecule-centered method for accelerating the calculation of hydrodynamic interactions in Brownian dynamics simulations containing many flexible biomolecules. J Chem Theory Comput (2013) 0.80
Computational modeling of the interplay between cadherin-mediated cell adhesion and Wnt signaling pathway. PLoS One (2014) 0.79
Control of translation initiation: a model-based analysis from limited experimental data. J R Soc Interface (2009) 0.78
Nonparametric simulation of signal transduction networks with semi-synchronized update. PLoS One (2012) 0.78
From microscopy data to in silico environments for in vivo-oriented simulations. EURASIP J Bioinform Syst Biol (2012) 0.78
Genome scale modeling in systems biology: algorithms and resources. Curr Genomics (2014) 0.75
Functional selectivity and classical concepts of quantitative pharmacology. J Pharmacol Exp Ther (2006) 7.03
The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell (2008) 4.29
A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol (2006) 3.23
Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation. Nat Chem Biol (2009) 2.98
The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci (2008) 2.72
PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics (2004) 2.55
Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature (2010) 2.41
Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation. Proc Natl Acad Sci U S A (2005) 2.33
Quantitative information management for the biochemical computation of cellular networks. Sci STKE (2004) 2.32
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A (2009) 2.25
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters. Nat Struct Mol Biol (2010) 2.20
Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue. Nature (2011) 2.18
An intracellular interaction network regulates conformational transitions in the dopamine transporter. J Biol Chem (2008) 2.07
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia. Cancer Prev Res (Phila) (2008) 2.04
State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter:sodium symporter from Fusobacterium nucleatum. J Biol Chem (2006) 2.01
The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter. PLoS One (2011) 1.48
Three-dimensional representations of G protein-coupled receptor structures and mechanisms. Methods Enzymol (2002) 1.38
Experimental conditions can obscure the second high-affinity site in LeuT. Nat Struct Mol Biol (2012) 1.37
Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT. Biophys J (2012) 1.30
Molecular determinants for the complex binding specificity of the PDZ domain in PICK1. J Biol Chem (2005) 1.28
Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms. Biophys J (2010) 1.27
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am Chem Soc (2006) 1.27
Membrane localization is critical for activation of the PICK1 BAR domain. Traffic (2008) 1.25
A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding. Neuropharmacology (2005) 1.24
Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials. Proteins (2003) 1.24
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD. Proc Natl Acad Sci U S A (2009) 1.23
Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6. Proc Natl Acad Sci U S A (2005) 1.23
The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics. FEBS J (2005) 1.20
Probing conformational changes in neurotransmitter transporters: a structural context. Eur J Pharmacol (2003) 1.17
Modeling membrane deformations and lipid demixing upon protein-membrane interaction: the BAR dimer adsorption. Biophys J (2009) 1.17
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins (2009) 1.16
Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors. Biophys J (2011) 1.15
A juxtamembrane mutation in the N terminus of the dopamine transporter induces preference for an inward-facing conformation. Mol Pharmacol (2008) 1.13
A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. J Am Chem Soc (2005) 1.12
Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic Acids Res (2007) 1.11
The binding sites for benztropines and dopamine in the dopamine transporter overlap. Neuropharmacology (2010) 1.11
Ligand-dependent conformations and dynamics of the serotonin 5-HT(2A) receptor determine its activation and membrane-driven oligomerization properties. PLoS Comput Biol (2012) 1.10
Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange. J Mol Biol (2004) 1.09
In support of the BMRB. Nat Struct Mol Biol (2012) 1.09
Chloride binding site of neurotransmitter sodium symporters. Proc Natl Acad Sci U S A (2013) 1.09
Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter. J Biol Chem (2012) 1.09
Modeling activated states of GPCRs: the rhodopsin template. J Comput Aided Mol Des (2006) 1.06
Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin. Proteins (2006) 1.06
Conserved helix 7 tyrosine acts as a multistate conformational switch in the 5HT2C receptor. Identification of a novel "locked-on" phenotype and double revertant mutations. J Biol Chem (2002) 1.05
Substrate-dependent proton antiport in neurotransmitter:sodium symporters. Nat Chem Biol (2009) 1.04
Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method. Protein Eng (2002) 1.03
Membrane driven spatial organization of GPCRs. Sci Rep (2013) 1.03
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics (2004) 1.02
Ligand selectivity of D2 dopamine receptors is modulated by changes in local dynamics produced by sodium binding. J Pharmacol Exp Ther (2008) 1.00
Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. J Comput Aided Mol Des (2006) 1.00
Protein diffusion on charged membranes: a dynamic mean-field model describes time evolution and lipid reorganization. Biophys J (2007) 1.00
The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT. Chem Phys Lipids (2013) 0.96
Structural models for dimerization of G-protein coupled receptors: the opioid receptor homodimers. Biopolymers (2002) 0.96
The structure and dynamics of GPCR oligomers: a new focus in models of cell-signaling mechanisms and drug design. Curr Opin Drug Discov Devel (2005) 0.96
The membrane protein LeuT in micellar systems: aggregation dynamics and detergent binding to the S2 site. J Am Chem Soc (2013) 0.95
Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh. J Phys Chem B (2012) 0.95
Structural mimicry of proline kinks: tertiary packing interactions support local structural distortions. J Mol Biol (2002) 0.95
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex. Biophys J (2003) 0.95
Building protein diagrams on the web with the residue-based diagram editor RbDe. Nucleic Acids Res (2003) 0.94
Certain 1,4-disubstituted aromatic piperidines and piperazines with extreme selectivity for the dopamine D4 receptor interact with a common receptor microdomain. Mol Pharmacol (2004) 0.92
Missense dopamine transporter mutations associate with adult parkinsonism and ADHD. J Clin Invest (2014) 0.92
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics. J Mol Biol (2010) 0.91
Molecular basis of partial agonism: orientation of indoleamine ligands in the binding pocket of the human serotonin 5-HT2A receptor determines relative efficacy. Mol Pharmacol (2003) 0.89
Batch mode generation of residue-based diagrams of proteins. Bioinformatics (2003) 0.88
Why GPCRs behave differently in cubic and lamellar lipidic mesophases. J Am Chem Soc (2012) 0.87
Cholesterol modulates the membrane effects and spatial organization of membrane-penetrating ligands for G-protein coupled receptors. J Phys Chem B (2010) 0.87
A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. J Am Chem Soc (2014) 0.86
Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework. Biophys J (2008) 0.86
Trefoil factor family-1 mutations enhance gastric cancer cell invasion through distinct signaling pathways. Gastroenterology (2006) 0.85
Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes. Proteins (2015) 0.83
Phosphatidylinositol 4,5-biphosphate (PIP(2)) lipids regulate the phosphorylation of syntaxin N-terminus by modulating both its position and local structure. Biochemistry (2012) 0.82
Probing the structural determinants for the function of intracellular loop 2 in structurally cognate G-protein-coupled receptors. Biochemistry (2010) 0.82
Active state-like conformational elements in the beta2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs. Biochemistry (2008) 0.82
A second site rescue mutation partially restores functional expression to the serotonin transporter mutant V382P. Biochemistry (2003) 0.81
Protein and lipid interactions driving molecular mechanisms of in meso crystallization. J Am Chem Soc (2014) 0.81
Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3. J Biol Chem (2004) 0.81
Towards a quantitative representation of the cell signaling mechanisms of hallucinogens: measurement and mathematical modeling of 5-HT1A and 5-HT2A receptor-mediated ERK1/2 activation. Neuropharmacology (2008) 0.81
A dynamic model of membrane-bound phospholipase Cβ2 activation by Gβγ subunits. Mol Pharmacol (2011) 0.80
How the dynamic properties and functional mechanisms of GPCRs are modulated by their coupling to the membrane environment. Adv Exp Med Biol (2014) 0.80
Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT. Protein Eng Des Sel (2005) 0.79
Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1. Org Biomol Chem (2010) 0.78
The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems. J Chem Theory Comput (2016) 0.75
Turkey must end violent response to protests. Science (2013) 0.75