selected publications
- Mechanistic Understanding of the Modes of Ca2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration. ACS infectious diseases. 2024 Academic Article GET IT
- Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV). Virus research. 2023 Academic Article GET IT
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Allosterically coupled conformational dynamics in solution prepare the sterol transfer protein StarD4 to release its cargo upon interaction with target membranes.
Frontiers in molecular biosciences.
2023
Academic Article
GET IT
Times cited: 1 - Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. Science signaling. 2022 Academic Article GET IT
- Dual-Reporter System for Real-Time Monitoring of SARS-CoV-2 Main Protease Activity in Live Cells Enables Identification of an Allosteric Inhibition Path. ACS bio & med chem Au. 2022 Academic Article GET IT
- The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase. Communications biology. 2022 Academic Article GET IT
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Molecular determinants of pH sensing in the proton-activated chloride channel.
Proceedings of the National Academy of Sciences of the United States of America.
2022
Academic Article
GET IT
Times cited: 9 - The permeation of potassium ions through the lipid scrambling path of the membrane protein nhTMEM16. Frontiers in molecular biosciences. 2022 Academic Article GET IT
- Phosphatidylinositol Phosphates Modulate Interactions between the StarD4 Sterol Trafficking Protein and Lipid Membranes. The Journal of biological chemistry. 2022 Academic Article GET IT
- Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl-/H+ Antiporter. Molecules (Basel, Switzerland). 2021 Academic Article GET IT
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A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes.
IEEE/ACM transactions on computational biology and bioinformatics.
2021
Academic Article
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Times cited: 1 -
Localization atomic force microscopy.
Nature.
2021
Academic Article
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Times cited: 4 - Ligand-Dependent Conformational Transitions in Molecular Dynamics Trajectories of GPCRs Revealed by a New Machine Learning Rare Event Detection Protocol. Molecules (Basel, Switzerland). 2021 Academic Article GET IT
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Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide.
Biophysical journal.
2021
Academic Article
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Times cited: 46 -
GPCRmd uncovers the dynamics of the 3D-GPCRome.
Nature methods.
2020
Academic Article
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Times cited: 26 -
Use of paramagnetic 19F NMR to monitor domain movement in a glutamate transporter homolog.
Nature chemical biology.
2020
Academic Article
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Times cited: 30 -
Substrate-selective protein ectodomain shedding by ADAM17 and iRhom2 depends on their juxtamembrane and transmembrane domains.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
2020
Academic Article
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Times cited: 23 -
X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release.
Nature communications.
2020
Academic Article
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Times cited: 31 -
Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins.
Journal of computational chemistry.
2019
Academic Article
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Times cited: 13 -
Dynamic modulation of the lipid translocation groove generates a conductive ion channel in Ca2+-bound nhTMEM16.
Nature communications.
2019
Academic Article
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Times cited: 21 -
The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor.
Proceedings of the National Academy of Sciences of the United States of America.
2019
Academic Article
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Times cited: 19 - Channelrhodopsin-2 function is modulated by residual hydrophobic mismatch with the surrounding lipid environment. Applied Sciences (Switzerland). 2019 Article GET IT
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A Machine Learning Approach for the Discovery of Ligand-Specific Functional Mechanisms of GPCRs.
Molecules (Basel, Switzerland).
2019
Academic Article
GET IT
Times cited: 46 -
Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles.
Biophysical journal.
2019
Academic Article
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Times cited: 41 -
A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited.
Biophysical journal.
2019
Academic Article
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Times cited: 55 -
Accurate In Silico Modeling of Asymmetric Bilayers Based on Biophysical Principles.
Biophysical journal.
2018
Academic Article
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Times cited: 37 -
Gating mechanism of the extracellular entry to the lipid pathway in a TMEM16 scramblase.
Nature communications.
2018
Academic Article
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Times cited: 61 -
The LeuT-fold neurotransmitter:sodium symporter MhsT has two substrate sites.
Proceedings of the National Academy of Sciences of the United States of America.
2018
Academic Article
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Times cited: 19 -
An Amphipathic Helix Directs Cellular Membrane Curvature Sensing and Function of the BAR Domain Protein PICK1.
Cell reports.
2018
Academic Article
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Times cited: 15 -
How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties.
BMC biology.
2018
Academic Article
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Times cited: 29 -
A partially-open inward-facing intermediate conformation of LeuT is associated with Na+ release and substrate transport.
Nature communications.
2018
Academic Article
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Times cited: 35 -
Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin.
Structure (London, England : 1993).
2017
Academic Article
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Times cited: 43 -
Thermodynamic Coupling Function Analysis of Allosteric Mechanisms in the Human Dopamine Transporter.
Biophysical journal.
2017
Academic Article
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Times cited: 13 -
Single-molecule analysis of ligand efficacy in β2AR-G-protein activation.
Nature.
2017
Academic Article
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Times cited: 240 -
Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins.
Frontiers in molecular neuroscience.
2017
Academic Article
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Times cited: 20 -
The role of transmembrane segment 5 (TM5) in Na2 release and the conformational transition of neurotransmitter:sodium symporters toward the inward-open state.
The Journal of biological chemistry.
2017
Academic Article
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Times cited: 18 -
Structural modeling defines transmembrane residues in ADAM17 that are crucial for Rhbdf2-ADAM17-dependent proteolysis.
Journal of cell science.
2017
Academic Article
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Times cited: 35 -
A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter.
Scientific reports.
2017
Academic Article
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Times cited: 55 -
Combined in vitro and in silico approaches to the assessment of stimulant properties of novel psychoactive substances - The case of the benzofuran 5-MAPB.
Progress in neuro-psychopharmacology & biological psychiatry.
2016
Academic Article
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Times cited: 10 -
The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems.
Journal of chemical theory and computation.
2016
Academic Article
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Times cited: 24 -
Conformational Dynamics on the Extracellular Side of LeuT Controlled by Na+ and K+ Ions and the Protonation State of Glu290.
The Journal of biological chemistry.
2016
Academic Article
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Times cited: 18 -
Augmenting drug-carrier compatibility improves tumour nanotherapy efficacy.
Nature communications.
2016
Academic Article
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Times cited: 116 -
Allosteric Mechanisms of Molecular Machines at the Membrane: Transport by Sodium-Coupled Symporters.
Chemical reviews.
2016
Information Resource
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Times cited: 49 -
Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles.
Biochemistry.
2016
Academic Article
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Times cited: 12 -
Computational approaches to detect allosteric pathways in transmembrane molecular machines.
Biochimica et biophysica acta.
2016
Academic Article
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Times cited: 51 -
A GIPC1-Palmitate Switch Modulates Dopamine Drd3 Receptor Trafficking and Signaling.
Molecular and cellular biology.
2016
Academic Article
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Times cited: 12 -
Substrate-induced unlocking of the inner gate determines the catalytic efficiency of a neurotransmitter:sodium symporter.
The Journal of biological chemistry.
2015
Academic Article
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Times cited: 29 -
Spontaneous inward opening of the dopamine transporter is triggered by PIP2-regulated dynamics of the N-terminus.
ACS chemical neuroscience.
2015
Academic Article
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Times cited: 85 -
Structure of Dimeric and Tetrameric Complexes of the BAR Domain Protein PICK1 Determined by Small-Angle X-Ray Scattering.
Structure (London, England : 1993).
2015
Academic Article
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Times cited: 34 - AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems. Entropy (Basel, Switzerland). 2015 Academic Article GET IT
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Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters.
The Journal of biological chemistry.
2015
Academic Article
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Times cited: 43 -
Functional mechanisms of neurotransmitter transporters regulated by lipid-protein interactions of their terminal loops.
Biochimica et biophysica acta.
2015
Information Resource
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Times cited: 26 -
Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2 -containing membranes.
Proteins.
2015
Academic Article
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Times cited: 41 -
Transport domain unlocking sets the uptake rate of an aspartate transporter.
Nature.
2015
Academic Article
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Times cited: 131 -
A mechanistic role of Helix 8 in GPCRs: Computational modeling of the dopamine D2 receptor interaction with the GIPC1-PDZ-domain.
Biochimica et biophysica acta.
2015
Academic Article
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Times cited: 35 -
A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2.
Journal of the American Chemical Society.
2014
Academic Article
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Times cited: 65 -
ESCRT-II/Vps25 constrains digit number by endosome-mediated selective modulation of FGF-SHH signaling.
Cell reports.
2014
Academic Article
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Times cited: 14 -
The second sodium site in the dopamine transporter controls cation permeation and is regulated by chloride.
The Journal of biological chemistry.
2014
Academic Article
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Times cited: 38 -
Not just an oil slick: how the energetics of protein-membrane interactions impacts the function and organization of transmembrane proteins.
Biophysical journal.
2014
Information Resource
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Times cited: 46 -
PIP2 regulates psychostimulant behaviors through its interaction with a membrane protein.
Nature chemical biology.
2014
Academic Article
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Times cited: 99 -
NbIT--a new information theory-based analysis of allosteric mechanisms reveals residues that underlie function in the leucine transporter LeuT.
PLoS computational biology.
2014
Academic Article
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Times cited: 79 -
Conformational dynamics of ligand-dependent alternating access in LeuT.
Nature structural & molecular biology.
2014
Academic Article
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Times cited: 118 -
Conformational changes in dopamine transporter intracellular regions upon cocaine binding and dopamine translocation.
Neurochemistry international.
2014
Academic Article
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Times cited: 13 -
Protein and lipid interactions driving molecular mechanisms of in meso crystallization.
Journal of the American Chemical Society.
2014
Academic Article
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Times cited: 17 -
Membrane driven spatial organization of GPCRs.
Scientific reports.
2013
Academic Article
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Times cited: 96 -
The membrane protein LeuT in micellar systems: aggregation dynamics and detergent binding to the S2 site.
Journal of the American Chemical Society.
2013
Academic Article
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Times cited: 30 -
Turkey must end violent response to protests.
Science (New York, N.Y.).
2013
Letter
GET IT
Times cited: 1 -
Chloride binding site of neurotransmitter sodium symporters.
Proceedings of the National Academy of Sciences of the United States of America.
2013
Academic Article
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Times cited: 70 -
The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT.
Chemistry and physics of lipids.
2013
Academic Article
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Times cited: 37 -
Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter.
The Journal of biological chemistry.
2012
Academic Article
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Times cited: 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
Academic Article
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Times cited: 26 -
Why GPCRs behave differently in cubic and lamellar lipidic mesophases.
Journal of the American Chemical Society.
2012
Academic Article
GET IT
Times cited: 43 -
Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT.
Biophysical journal.
2012
Academic Article
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Times cited: 76 -
In support of the BMRB.
Nature structural & molecular biology.
2012
Academic Article
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Times cited: 5 -
Structural intermediates in a model of the substrate translocation path of the bacterial glutamate transporter homologue GltPh.
The journal of physical chemistry. B.
2012
Academic Article
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Times cited: 37 -
Ligand-dependent conformations and dynamics of the serotonin 5-HT(2A) receptor determine its activation and membrane-driven oligomerization properties.
PLoS computational biology.
2012
Academic Article
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Times cited: 96 -
Experimental conditions can obscure the second high-affinity site in LeuT.
Nature structural & molecular biology.
2012
Academic Article
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Times cited: 77 -
Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors.
Biophysical journal.
2011
Academic Article
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Times cited: 77 -
The correlation between multidomain enzymes and multiple activation mechanisms--the case of phospholipase Cβ and its membrane interactions.
Biochimica et biophysica acta.
2011
Information Resource
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Times cited: 6 -
A dynamic model of membrane-bound phospholipase Cβ2 activation by Gβγ subunits.
Molecular pharmacology.
2011
Academic Article
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Times cited: 17 -
Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue.
Nature.
2011
Academic Article
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Times cited: 196 -
The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter.
PloS one.
2011
Academic Article
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Times cited: 106 -
Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms.
Biophysical journal.
2010
Academic Article
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Times cited: 41 -
Probing the structural determinants for the function of intracellular loop 2 in structurally cognate G-protein-coupled receptors.
Biochemistry.
2010
Academic Article
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Times cited: 19 -
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics.
Journal of molecular biology.
2010
Academic Article
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Times cited: 39 -
Cholesterol modulates the membrane effects and spatial organization of membrane-penetrating ligands for G-protein coupled receptors.
The journal of physical chemistry. B.
2010
Academic Article
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Times cited: 27 -
The binding sites for benztropines and dopamine in the dopamine transporter overlap.
Neuropharmacology.
2010
Academic Article
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Times cited: 57 -
Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1.
Organic & biomolecular chemistry.
2010
Academic Article
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Times cited: 33 -
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters.
Nature structural & molecular biology.
2010
Academic Article
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Times cited: 160 -
Single-molecule dynamics of gating in a neurotransmitter transporter homologue.
Nature.
2010
Academic Article
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Times cited: 215 -
Substrate-dependent proton antiport in neurotransmitter:sodium symporters.
Nature chemical biology.
2009
Academic Article
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Times cited: 45 -
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD.
Proceedings of the National Academy of Sciences of the United States of America.
2009
Academic Article
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Times cited: 99 -
Modeling membrane deformations and lipid demixing upon protein-membrane interaction: the BAR dimer adsorption.
Biophysical journal.
2009
Academic Article
GET IT
Times cited: 61 -
Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation.
Nature chemical biology.
2009
Academic Article
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Times cited: 304 -
Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations.
Proteins.
2009
Academic Article
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Times cited: 109 -
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation.
Proceedings of the National Academy of Sciences of the United States of America.
2009
Academic Article
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Times cited: 151 -
A juxtamembrane mutation in the N terminus of the dopamine transporter induces preference for an inward-facing conformation.
Molecular pharmacology.
2008
Academic Article
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Times cited: 63 -
Ligand selectivity of D2 dopamine receptors is modulated by changes in local dynamics produced by sodium binding.
The Journal of pharmacology and experimental therapeutics.
2008
Academic Article
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Times cited: 28 -
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
Academic Article
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Times cited: 21 -
The binding sites for cocaine and dopamine in the dopamine transporter overlap.
Nature neuroscience.
2008
Academic Article
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Times cited: 286 -
The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site.
Molecular cell.
2008
Academic Article
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Times cited: 322 -
Active state-like conformational elements in the beta2-AR and a photoactivated intermediate of rhodopsin identified by dynamic properties of GPCRs.
Biochemistry.
2008
Academic Article
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Times cited: 21 -
Membrane localization is critical for activation of the PICK1 BAR domain.
Traffic (Copenhagen, Denmark).
2008
Academic Article
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Times cited: 44 -
Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.
Proteins.
2008
Academic Article
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Times cited: 4 -
An intracellular interaction network regulates conformational transitions in the dopamine transporter.
The Journal of biological chemistry.
2008
Academic Article
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Times cited: 110 -
Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia.
Cancer prevention research (Philadelphia, Pa.).
2008
Academic Article
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Times cited: 56 -
Mutations affecting the oligomerization interface of G-protein-coupled receptors revealed by a novel de novo protein design framework.
Biophysical journal.
2008
Academic Article
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Times cited: 25 -
Protein diffusion on charged membranes: a dynamic mean-field model describes time evolution and lipid reorganization.
Biophysical journal.
2007
Academic Article
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Times cited: 48 -
Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects.
The Journal of chemical physics.
2007
Academic Article
GET IT
Times cited: 55 -
Topology of Type II REases revisited; structural classes and the common conserved core.
Nucleic acids research.
2007
Academic Article
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Times cited: 31 -
Modeling activated states of GPCRs: the rhodopsin template.
Journal of computer-aided molecular design.
2006
Academic Article
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Times cited: 64 -
Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer.
Journal of computer-aided molecular design.
2006
Academic Article
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Times cited: 69 -
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study.
Journal of the American Chemical Society.
2006
Academic Article
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Times cited: 107 -
Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin.
Proteins.
2006
Academic Article
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Times cited: 38 -
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.
Molecular pharmacology.
2006
Academic Article
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Times cited: 225 -
Functional selectivity and classical concepts of quantitative pharmacology.
The Journal of pharmacology and experimental therapeutics.
2006
Information Resource
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Times cited: 842 -
State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter:sodium symporter from Fusobacterium nucleatum.
The Journal of biological chemistry.
2006
Academic Article
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Times cited: 76 -
Trefoil factor family-1 mutations enhance gastric cancer cell invasion through distinct signaling pathways.
Gastroenterology.
2006
Academic Article
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Times cited: 32 -
Hallucinogen actions on 5-HT receptors reveal distinct mechanisms of activation and signaling by G protein-coupled receptors.
The AAPS journal.
2006
Information Resource
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Times cited: 29 -
Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation.
Proceedings of the National Academy of Sciences of the United States of America.
2005
Academic Article
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Times cited: 256 -
A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains.
Journal of the American Chemical Society.
2005
Academic Article
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Times cited: 65 -
A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding.
Neuropharmacology.
2005
Academic Article
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Times cited: 34 -
The structure and dynamics of GPCR oligomers: a new focus in models of cell-signaling mechanisms and drug design.
Current opinion in drug discovery & development.
2005
Information Resource
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Times cited: 35 -
Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6.
Proceedings of the National Academy of Sciences of the United States of America.
2005
Academic Article
GET IT
Times cited: 86 -
Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT.
Protein engineering, design & selection : PEDS.
2005
Academic Article
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Times cited: 15 -
Molecular determinants for the complex binding specificity of the PDZ domain in PICK1.
The Journal of biological chemistry.
2005
Academic Article
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Times cited: 64 -
Certain 1,4-disubstituted aromatic piperidines and piperazines with extreme selectivity for the dopamine D4 receptor interact with a common receptor microdomain.
Molecular pharmacology.
2004
Academic Article
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Times cited: 35 -
Quantitative information management for the biochemical computation of cellular networks.
Science's STKE : signal transduction knowledge environment.
2004
Academic Article
GET IT
Times cited: 30 - Surface tension parameterization in molecular dynamics simulations of a phospholipid-bilayer membrane: Calibration and effects. Journal of Physical Chemistry B. 2004 Article GET IT
-
Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange.
Journal of molecular biology.
2004
Academic Article
GET IT
Times cited: 38 -
Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3.
The Journal of biological chemistry.
2004
Academic Article
GET IT
Times cited: 8 -
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.
Bioinformatics (Oxford, England).
2004
Academic Article
GET IT
Times cited: 62 -
Batch mode generation of residue-based diagrams of proteins.
Bioinformatics (Oxford, England).
2003
Academic Article
GET IT
Times cited: 8 -
Building protein diagrams on the web with the residue-based diagram editor RbDe.
Nucleic acids research.
2003
Academic Article
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Times cited: 23 -
A second site rescue mutation partially restores functional expression to the serotonin transporter mutant V382P.
Biochemistry.
2003
Academic Article
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Times cited: 7 -
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.
Biophysical journal.
2003
Academic Article
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Times cited: 28 -
Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
Proteins.
2003
Academic Article
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Times cited: 56 -
Molecular basis of partial agonism: orientation of indoleamine ligands in the binding pocket of the human serotonin 5-HT2A receptor determines relative efficacy.
Molecular pharmacology.
2003
Academic Article
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Times cited: 59 -
Key issues in the computational simulation of GPCR function: representation of loop domains.
Journal of computer-aided molecular design.
2002
Academic Article
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Times cited: 52 -
Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method.
Protein engineering.
2002
Academic Article
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Times cited: 76 -
The local environment at the cytoplasmic end of TM6 of the mu opioid receptor differs from those of rhodopsin and monoamine receptors: introduction of an ionic lock between the cytoplasmic ends of helices 3 and 6 by a L6.30(275)E mutation inactivates the mu opioid receptor and reduces the constitutive activity of its T6.34(279)K mutant.
Biochemistry.
2002
Academic Article
GET IT
Times cited: 28 -
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.
The Journal of biological chemistry.
2002
Academic Article
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Times cited: 98 -
Structural mimicry of proline kinks: tertiary packing interactions support local structural distortions.
Journal of molecular biology.
2002
Academic Article
GET IT
Times cited: 17 - Structural motifs as functional microdomains in G-protein-coupled receptors: Energetic considerations in the mechanism of activation of the serotonin 5-HT2A receptor by disruption of the ionic lock of the arginine cage. International Journal of Quantum Chemistry. 2002 Article GET IT
- Positioning and stabilization of dynorphin peptides in membrane bilayers: The mechanistic role of aromatic and basic residues revealed from comparative MD simulations. Journal of Physical Chemistry B. 2002 Article GET IT
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Three-dimensional representations of G protein-coupled receptor structures and mechanisms.
Methods in enzymology.
2002
Academic Article
GET IT
Times cited: 156 -
Functional role of a conserved motif in TM6 of the rat mu opioid receptor: constitutively active and inactive receptors result from substitutions of Thr6.34(279) with Lys and Asp.
Biochemistry.
2001
Academic Article
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Times cited: 77 -
Constitutive activation of the mu opioid receptor by mutation of D3.49(164), but not D3.32(147): D3.49(164) is critical for stabilization of the inactive form of the receptor and for its expression.
Biochemistry.
2001
Academic Article
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Times cited: 61 -
Comparison of the amino acid residues in the sixth transmembrane domains accessible in the binding-site crevices of mu, delta, and kappa opioid receptors.
Biochemistry.
2001
Academic Article
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Times cited: 29 -
Differences in conformational properties of the second intracellular loop (IL2) in 5HT(2C) receptors modified by RNA editing can account for G protein coupling efficiency.
Protein engineering.
2001
Academic Article
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Times cited: 23 -
Tas1r3, encoding a new candidate taste receptor, is allelic to the sweet responsiveness locus Sac.
Nature genetics.
2001
Academic Article
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Times cited: 440 -
Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA.
Protein engineering.
2001
Academic Article
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Times cited: 18 -
Structural probing of a microdomain in the dopamine transporter by engineering of artificial Zn2+ binding sites.
Biochemistry.
2000
Academic Article
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Times cited: 36 -
A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding.
Journal of molecular biology.
2000
Academic Article
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Times cited: 124 -
Hinges, swivels and switches: the role of prolines in signalling via transmembrane alpha-helices.
Trends in pharmacological sciences.
2000
Information Resource
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Times cited: 256 -
Molecular dynamics simulations predict a tilted orientation for the helical region of dynorphin A(1-17) in dimyristoylphosphatidylcholine bilayers.
Biophysical journal.
2000
Academic Article
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Times cited: 49 -
The fourth transmembrane segment of the dopamine D2 receptor: accessibility in the binding-site crevice and position in the transmembrane bundle.
Biochemistry.
2000
Academic Article
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Times cited: 63 -
Prokink: a protocol for numerical evaluation of helix distortions by proline.
Protein engineering.
2000
Academic Article
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Times cited: 86 -
Multiple interactions of the Asp(2.61(98)) side chain of the gonadotropin-releasing hormone receptor contribute differentially to ligand interaction.
Biochemistry.
2000
Academic Article
GET IT
Times cited: 59 -
Interactive construction of residue-based diagrams of proteins: the RbDe web service.
Protein engineering.
2000
Academic Article
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Times cited: 21 -
Binding mechanisms of TATA box-binding proteins: DNA kinking is stabilized by specific hydrogen bonds.
Biophysical journal.
2000
Academic Article
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Times cited: 20 - Solvation in Simulated Annealing and High-Temperature Molecular Dynamics of Proteins: A Restrained Water Droplet Model. International Journal of Quantum Chemistry. 2000 Article
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The functional microdomain in transmembrane helices 2 and 7 regulates expression, activation, and coupling pathways of the gonadotropin-releasing hormone receptor.
The Journal of biological chemistry.
1999
Academic Article
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Times cited: 72 -
Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins.
Journal of molecular graphics & modelling.
1999
Academic Article
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Times cited: 13 -
The role of a conserved proline residue in mediating conformational changes associated with voltage gating of Cx32 gap junctions.
Biophysical journal.
1999
Academic Article
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Times cited: 97 - Molecular Dynamics Simulation of Membranes and a Transmembrane Helix. Journal of Computational Physics. 1999 Article GET IT
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Functional role of the spatial proximity of Asp114(2.50) in TMH 2 and Asn332(7.49) in TMH 7 of the mu opioid receptor.
FEBS letters.
1999
Academic Article
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Times cited: 42 -
Characterization of novel cathepsin K mutations in the pro and mature polypeptide regions causing pycnodysostosis.
The Journal of clinical investigation.
1999
Academic Article
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Times cited: 148 -
TIT for TAT: the properties of inosine and adenosine in TATA box DNA.
Journal of biomolecular structure & dynamics.
1999
Academic Article
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Times cited: 20 - How the TATA Box Selects Its Protein Partner. ACS Symposium Series. 1998 Article
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Selective binding of the TATA box-binding protein to the TATA box-containing promoter: analysis of structural and energetic factors.
Biophysical journal.
1998
Academic Article
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Times cited: 19 -
A proposed structure for transmembrane segment 7 of G protein-coupled receptors incorporating an asn-Pro/Asp-Pro motif.
Biophysical journal.
1998
Academic Article
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Times cited: 70 -
Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond.
Biophysical journal.
1998
Academic Article
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Times cited: 11 -
Functional microdomains in G-protein-coupled receptors. The conserved arginine-cage motif in the gonadotropin-releasing hormone receptor.
The Journal of biological chemistry.
1998
Academic Article
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Times cited: 225 -
Structure and dynamics of calmodulin in solution.
Biophysical journal.
1998
Academic Article
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Times cited: 135 -
Neurofilament (NF) assembly; divergent characteristics of human and rodent NF-L subunits.
The Journal of biological chemistry.
1998
Academic Article
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Times cited: 52 -
A cluster of aromatic residues in the sixth membrane-spanning segment of the dopamine D2 receptor is accessible in the binding-site crevice.
Biochemistry.
1998
Academic Article
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Times cited: 161 - On the structure and activity of membrane receptors: A computational simulation of ligand-triggered activation in a model 5-HT1A receptor. International Journal of Quantum Chemistry. 1997 Article
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Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor.
The EMBO journal.
1997
Academic Article
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Times cited: 359 -
Comparative modeling and molecular dynamics studies of the delta, kappa and mu opioid receptors.
Protein engineering.
1997
Academic Article
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Times cited: 73 -
Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.
Biophysical journal.
1997
Academic Article
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Times cited: 38 - Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix. Journal of Computational Chemistry. 1997 Article
-
Molecular mechanisms of ligand interaction with the gonadotropin-releasing hormone receptor.
Endocrine reviews.
1997
Information Resource
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Times cited: 416 -
A surface on the G protein beta-subunit involved in interactions with adenylyl cyclases.
Proceedings of the National Academy of Sciences of the United States of America.
1997
Academic Article
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Times cited: 46 -
Structural instability of a constitutively active G protein-coupled receptor. Agonist-independent activation due to conformational flexibility.
The Journal of biological chemistry.
1997
Academic Article
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Times cited: 255 -
Gbeta subunit interacts with a peptide encoding region 956-982 of adenylyl cyclase 2. Cross-linking of the peptide to free Gbetagamma but not the heterotrimer.
The Journal of biological chemistry.
1996
Academic Article
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Times cited: 46 -
Residues in the seventh membrane-spanning segment of the dopamine D2 receptor accessible in the binding-site crevice.
Biochemistry.
1996
Academic Article
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Times cited: 121 -
Contribution of a helix 5 locus to selectivity of hallucinogenic and nonhallucinogenic ligands for the human 5-hydroxytryptamine2A and 5-hydroxytryptamine2C receptors: direct and indirect effects on ligand affinity mediated by the same locus.
Molecular pharmacology.
1996
Academic Article
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Times cited: 71 -
Mapping the binding site pocket of the serotonin 5-Hydroxytryptamine2A receptor. Ser3.36(159) provides a second interaction site for the protonated amine of serotonin but not of lysergic acid diethylamide or bufotenin.
The Journal of biological chemistry.
1996
Academic Article
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Times cited: 128 - Conformational memories and the exploration of biologically relevant peptide conformations: An illustration for the gonadotropin-releasing hormone. Journal of the American Chemical Society. 1996 Article GET IT
- Structure and Activity of Membrane Receptors: Modeling and Computational Simulation of Ligand Recognition in a Three-Dimensional Model of the 5-Hydroxytryptamine(1A) Receptor. Journal of biomedical science. 1996 Academic Article GET IT
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Structural change mechanisms in regulatory proteins.
Science (New York, N.Y.).
1996
Article
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Times cited: 1 - [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods in Neurosciences. 1995 Article GET IT
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A locus of the gonadotropin-releasing hormone receptor that differentiates agonist and antagonist binding sites.
The Journal of biological chemistry.
1995
Academic Article
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Times cited: 92 -
Related contribution of specific helix 2 and 7 residues to conformational activation of the serotonin 5-HT2A receptor.
The Journal of biological chemistry.
1995
Academic Article
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Times cited: 200 -
Functional role of arginine-11 in the N-terminal helix of skeletal troponin C: combined mutagenesis and molecular dynamics investigation.
Biochemistry.
1995
Academic Article
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Times cited: 11 -
Electrostatic analysis of DNA binding properties in lysine to leucine mutants of TATA-box binding proteins.
Protein engineering.
1995
Academic Article
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Times cited: 8 -
Ligand-induced domain motion in the activation mechanism of a G-protein-coupled receptor.
Protein engineering.
1994
Academic Article
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Times cited: 61 -
A reciprocal mutation supports helix 2 and helix 7 proximity in the gonadotropin-releasing hormone receptor.
Molecular pharmacology.
1994
Academic Article
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Times cited: 266 -
Polarity conserved positions in transmembrane domains of G-protein coupled receptors and bacteriorhodopsin.
FEBS letters.
1994
Academic Article
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Times cited: 46 -
Ca(2+)-binding and structural dynamics in the functions of calmodulin.
Annual review of physiology.
1994
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Times cited: 111 - Consequences of sequential Ca2+ occupancy for the structure and dynamics of calbindinD9K: computational simulations and comparison to experimental determinations in solution. Molecular Simulation. 1993 Article
- Molecular dynamics simulation of the hydrated d(CGCGAATTCGCG)2 dodecamer. Journal of the American Chemical Society. 1993 Article
- Mechanisms of nucleophilic addition to activated double bonds: 1,2- and 1,4-Michael addition of ammonia. Journal of the American Chemical Society. 1993 Article
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On the use of the transmembrane domain of bacteriorhodopsin as a template for modeling the three-dimensional structure of guanine nucleotide-binding regulatory protein-coupled receptors.
Proceedings of the National Academy of Sciences of the United States of America.
1992
Academic Article
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Times cited: 94 -
Analysis and refinement of criteria for predicting the structure and relative orientations of transmembranal helical domains.
Biophysical journal.
1992
Academic Article
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Times cited: 102 -
The role of Pro/Hyp-kinks in determining the transmembrane helix length and gating mechanism of a [Leu]zervamicin channel.
Biophysical journal.
1992
Academic Article
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Times cited: 13 - Calmodulin structure and function: Implication of arginine in the compaction related to ligand binding. Molecular Engineering. 1991 Article GET IT
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Structural dynamics of calmodulin and troponin C.
Protein engineering.
1991
Academic Article
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Times cited: 38 -
Molecular mechanisms of radiation induced DNA damage: H-abstraction and beta-cleavage.
Free radical research communications.
1991
Academic Article
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Times cited: 4 -
Molecular mechanisms of radiation induced DNA damage: H-addition to bases, direct ionization and double strand break.
Free radical research communications.
1991
Academic Article
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Times cited: 6 -
Structure-function relations in radiation damaged DNA.
Basic life sciences.
1991
Information Resource
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Times cited: 4 - Nucleophilic addition to activated double bonds: Predictions of reactivity from the Laplacian of the charge density. Journal of Physical Chemistry. 1989 Article
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On the ion selectivity in Ca-binding proteins: the cyclo(-L-Pro-Gly-)3 peptide as a model.
Proceedings of the National Academy of Sciences of the United States of America.
1989
Academic Article
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Times cited: 39 -
A metactoid sensitization model to describe multiple receptors linked to a common response: application to histamine receptors coupled to [3H]cyclic AMP accumulation in guinea pig cortex.
Molecular pharmacology.
1989
Academic Article
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Times cited: 1 -
A molecular theoretical model of recognition and activation at a 5-HT receptor.
Progress in clinical and biological research.
1989
Academic Article
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Times cited: 3 -
Theoretical studies of molecular mechanisms of DNA damage induced by hydroxyl radicals.
Free radical research communications.
1989
Academic Article
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Times cited: 6 - Reactivities of acrylic and methacrylic acids in a nucleophilic addition model of their biological activity. Journal of the American Chemical Society. 1988 Article
-
Structural and energetic parameters of Ca2+ binding to peptides and proteins.
Biopolymers.
1988
Academic Article
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Times cited: 22 - A metactoid-sensitization model for the classification of histamine receptors coupled to [3H]cAMP accumulation in a vesicular preparation of guinea pig cerebral cortex. Annals of the New York Academy of Sciences. 1987 Article
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A molecular model for activation of a 5-hydroxytryptamine receptor.
Molecular pharmacology.
1987
Academic Article
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Times cited: 26 -
Analysis of the molecular electrostatic potential for the prediction of N-oxidation and biological activity of substituted pyridines.
Molecular toxicology.
1987
Academic Article
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Times cited: 5 -
Molecular determinants for recognition of triazole and tetrazole analogs of histamine at H2-receptors.
Molecular pharmacology.
1987
Academic Article
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Times cited: 13 -
Pharmacological characterization of two 5-hydroxytryptamine receptors coupled to adenylate cyclase in guinea pig hippocampal membranes.
Molecular pharmacology.
1987
Academic Article
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Times cited: 114 -
Molecular determinants for the agonist activity of 2-methylhistamine and 4-methylhistamine at H2-receptors.
Journal of medicinal chemistry.
1986
Academic Article
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Times cited: 14 - Molecular models for muscarinic ligands. Trends in Pharmacological Sciences. 1986 Article GET IT
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On the role of computational approaches to enzyme structure and function in the study of molecular processes in biology. An introduction.
Enzyme.
1986
Academic Article
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Times cited: 2 -
Theoretical studies on the activation mechanism of the histamine H2-receptor: the proton transfer between histamine and a receptor model.
Molecular pharmacology.
1986
Academic Article
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Times cited: 56 -
Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity.
Biopolymers.
1985
Academic Article
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Times cited: 46 -
Two 5-HT receptors linked to adenylate cyclase in guinea pig hippocampus are discriminated by 5-carboxamidotryptamine and spiperone.
European journal of pharmacology.
1985
Academic Article
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Times cited: 94 -
A molecular theory of recognition and activation at a 5-HT receptor based on a quantum chemical approach to structure activity relationships.
Clinical physiology and biochemistry.
1985
Academic Article
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Times cited: 12 -
A theoretical investigation of histamine tautomerism.
Journal of medicinal chemistry.
1984
Academic Article
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Times cited: 54 -
Differences in d-[3H]lysergic acid diethylamide binding in mouse cortex and hippocampus in vivo and in vitro revealed by radioautography and rapid filtration studies.
The Journal of pharmacology and experimental therapeutics.
1984
Academic Article
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Times cited: 11 -
Discriminant effects of behaviorally active and inactive analogs of phencyclidine on membrane electrical excitability.
The Journal of pharmacology and experimental therapeutics.
1984
Academic Article
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Times cited: 4 -
Multiple actions of phencyclidine: discriminant structure-activity relationships from molecular conformations and assay conditions.
Federation proceedings.
1983
Academic Article
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Times cited: 5 -
Enhanced serotonin-stimulated adenylate cyclase activity in membranes from adult guinea pig hippocampus.
Life sciences.
1983
Academic Article
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Times cited: 27 -
Effects of phencyclidine on cardiac action potential: pH dependence and structure-activity relationships.
European journal of pharmacology.
1983
Academic Article
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Times cited: 12 -
Site of action of phencyclidine. IV. Interaction of phencyclidine and its analogues on ionic channels of the electrically excitable membrane and nicotinic receptor: implications for behavioral effects.
Molecular pharmacology.
1982
Academic Article
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Times cited: 15 - Comparison of 2-bromo-D-LSD (BOL) and D-LSD interaction with 5HT and LSD binding sites in rat cortex. Federation Proceedings. 1982 Article
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Response of the histamine h2-receptor in brain to antidepressant drugs.
Advances in biochemical psychopharmacology.
1982
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Times cited: 16 -
The behavioral effects of phencyclidines may be due to their blockade of potassium channels.
Proceedings of the National Academy of Sciences of the United States of America.
1981
Academic Article
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Times cited: 64 -
Models for active sites of metalloenzymes. II. Interactions with a model substrate.
Annals of the New York Academy of Sciences.
1981
Academic Article
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Times cited: 13 - Phencyclidine (PCP) and its analogs on ionic channels of the nicotinic receptor and electrogenic membrane: Role in behavioral effects. Federation Proceedings. 1981 Article
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Quantum chemical studies on molecular determinants for drug action.
Annals of the New York Academy of Sciences.
1981
Academic Article
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Times cited: 33 - Regulation of muscarinic binding sites by carbachol and guanylnucleotides. Federation Proceedings. 1981 Article
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Phencyclidine (PCP) and derivatives: pharmacology and structure-activity relationships [proceedings].
Psychopharmacology bulletin.
1980
Academic Article
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Times cited: 2 -
"Specific binding" of 3H-phencyclidine: artifacts of the rapid filtration method.
Life sciences.
1980
Academic Article
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Times cited: 30 -
Histamine and psychotropic drugs.
Psychopharmacology bulletin.
1980
Academic Article
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Times cited: 3 -
One agonist and two receptors mediating the same effect: histamine receptors linked to adenylate cyclase in the brain.
Advances in biochemical psychopharmacology.
1980
Academic Article
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Times cited: 11 - Psychiatry on trial: clinical and ethical problems in the psychiatric assessment of competency to stand trial. Annals of the New York Academy of Sciences. 1980 Academic Article GET IT
- Specific binding of [3H]-PCP: Artifacts of the rapid filtration method. Federation Proceedings. 1980 Article
- Some relations between electronic distribution and electronegativity. The Journal of Chemical Physics. 1979 Article
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[13C]NMR chemical shifts and calculated electronic structures of serotonin congeners: relation to biological activity.
Molecular pharmacology.
1979
Academic Article
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Times cited: 2 -
Studies on histamine H2 receptors coupled to cardiac adenylate cyclase. Effects of guanylnucleotides and structural requirements for agonist activity.
Biochimica et biophysica acta.
1979
Academic Article
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Times cited: 22 -
Studies on histamine H2 receptors coupled to cardiac adenylate cyclase. Blockade by H2 and H1 receptor antagonists.
Molecular pharmacology.
1979
Academic Article
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Times cited: 26 - Brain 5-HT and LSD binding sites. Federation Proceedings. 1979 Article
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Some structure activity relationships of phencyclidine derivatives as anticholinergic agents in vitro and in vivo.
Progress in clinical and biological research.
1979
Academic Article
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Times cited: 9 - On the basis set dependence of reported limitations in predictions from electrostatic potentials. Chemical Physics Letters. 1978 Article GET IT
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Defining the histamine H2-receptor in brain: the interaction with LSD.
NIDA research monograph.
1978
Information Resource
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Times cited: 8 - Electron charge redistribution following electrophilic attack on heterocycles: nitrogen as a charge transducer. Tetrahedron. 1978 Article GET IT
- LSD, tricyclic antidepressants and neuroleptics inhibit histamine stimulated adenylate cyclase in brain. Federation Proceedings. 1978 Article
- Mechanism of activation of the histamine H2-receptor. Federation Proceedings. 1978 Article
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Recognition and activation mechanisms on the LSD/serotonin receptor: the molecular basis of structure activity relationships.
NIDA research monograph.
1978
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Times cited: 7 -
Antagonism of histamine-activated adenylate cyclase in brain by D-lysergic acid diethylamide.
Proceedings of the National Academy of Sciences of the United States of America.
1977
Academic Article
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Times cited: 94 - Molecular determinants for the action of tryptamines on an LSD receptor. Federation Proceedings. 1977 Article
- A modified hamiltonian method for the study of multiple site reactivity: comparison with perturbation results. Chemical Physics Letters. 1977 Article GET IT
- Near ab-initio methods for the calculations of large molecules: Comparison of pseudopotential and ab-initio results. Chemical Physics Letters. 1977 Article GET IT
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A theoretical model study of the comparative effectiveness of atropine and scopolamine action in the central nervous system.
Journal of theoretical biology.
1977
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Times cited: 6 - Evaluation of cardiac shunt flow from tracer measurements. Federation Proceedings. 1977 Article
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Tautomerism and the receptor action of histamine: a mechanistic model.
Molecular pharmacology.
1976
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Times cited: 100 - Perturbation treatment of multiple site reactivity: Molecule-molecule interactions. Chemical Physics Letters. 1976 Article GET IT
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A theoretical and experimental study of the semirigid cholinergic agonist 3-acetoxyquinuclidine.
Molecular pharmacology.
1975
Academic Article
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Times cited: 24 - A misconception concerning the electronic density distribution of an atom. Theoretica Chimica Acta. 1975 Article GET IT
- Some definitions of atomic regions in molecules and solids. Chemical Physics Letters. 1975 Article GET IT
- Theoretical treatment of multiple site reactivity in large molecules. Chemical Physics Letters. 1975 Article GET IT
- Molecular electrostatic potentials-II. Mechanistic aspects of electrophilic interactions of some five-membered heterocycles. Tetrahedron. 1975 Article GET IT
- The effect of substitution on protonation sites: evidence for protonation at N(3) in N(7)-substituted adenine. Journal of Molecular Structure. 1975 Article GET IT
- Formulation of molecular forces and their analytical calculation. The Journal of Chemical Physics. 1974 Article
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Psychotomimetics as anticholinergic agents. I. 1-Cyclohexylpiperidine derivatives: anticholinesterase activity and antagonistic activity to acetylcholine.
Biochemical pharmacology.
1974
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Times cited: 118 -
Cholinolytic action of phencyclidine derivatives.
European journal of pharmacology.
1974
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Times cited: 27 - Quantum mechanical analysis of electronic transitions in some cyanine dye photosensitizers. Photochemistry and Photobiology. 1973 Article
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Acetylcholine-like molecular arrangement in psychomimetic anticholinergic drugs.
Proceedings of the National Academy of Sciences of the United States of America.
1973
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Times cited: 36 -
Psychotomimetic drugs as anticholinergic agents. II. Quantum-mechanical study of molecular interaction potentials of 1-cyclohexylpiperidine derivatives with the cholinergic receptor.
Molecular pharmacology.
1973
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Times cited: 63 - Analytical calculation of atomic and molecular electrostatic potentials from the Poisson equation. Chemical Physics Letters. 1973 Article GET IT
- Direct optimization approach to molecular electron density calculation. Chemical Physics Letters. 1972 Article GET IT
- Localized Molecular Orbitals. Advances in Atomic, Molecular and Optical Physics. 1971 Article GET IT
- Molecular orbital set determined by a localization procedure. Symposia of the Faraday Society. 1968 Article
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The treatment of acute pulmonary edema with furosemide.
Current therapeutic research, clinical and experimental.
1966
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Times cited: 5