Harel Weinstein

发表

A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes.

Hector Carrillo-Cabada, Trilce Estrada, Michela Taufer, 2019, IEEE/ACM transactions on computational biology and bioinformatics.

Quantitative Information Management for the Biochemical Computation of Cellular Networks

Ravi Iyengar, Harel Weinstein, Fabien Campagne, 2004, Science's STKE.

Quantification and Analysis of Combination Drug Synergy in High-Throughput Transcriptome Studies

Harel Weinstein, Zeynep H. Gümüs, Fernando Siso-Nadal, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

Epilogue: New Levels of Complexity in the Functional Roles of Modular Protein Interaction Domains: Switches and Sockets in the Circuit Diagrams of Cellular Systems Biology

Harel Weinstein, 2005 .

A lightweight method for evaluating in situ workflow efficiency

Trilce Estrada, Ewa Deelman, Loïc Pottier, 2020, J. Comput. Sci..

Rigorous Representation of Transporters as Allosteric Machines Enables a Quantitative Understanding of their Functional Mechanisms

George Khelashvili, Harel Weinstein, Michel A. Cuendet, 2017 .

Simulation and Modeling

Harel Weinstein, 2012 .

GPCRmd uncovers the dynamics of the 3D-GPCRome

Toni Giorgino, Davide Provasi, Gianni De Fabritiis, 2020, Nature Methods.

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

Toni Giorgino, Davide Provasi, Gianni De Fabritiis, 2020, Nature Methods.

A Novel Metric to Evaluate In Situ Workflows

Trilce Estrada, Ewa Deelman, Michela Taufer, 2020, ICCS.

Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis

Hector Carrillo-Cabada, Trilce Estrada, Ewa Deelman, 2018, BCB.

Characterizing In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-Generation Supercomputers

Trilce Estrada, Ewa Deelman, Loïc Pottier, 2019, 2019 15th International Conference on eScience (eScience).

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins

George Khelashvili, Harel Weinstein, Milka Doktorova, 2019, J. Comput. Chem..

New Computational Approaches for NMR-based Drug Design: A Protocol for Ligand Docking to Flexible Target Sites

Luis Gracia, Harel Weinstein, Joshua A. Speidel, 2006 .

A Machine Learning Algorithm for the Detection of Function-Related Rare Events in MD Trajectories of Biomolecular Systems

Harel Weinstein, Ambrose Plante, 2021 .

Modeling membrane deformations and lipid demixing upon protein-membrane interaction: the BAR dimer adsorption.

George Khelashvili, Harel Weinstein, Daniel Harries, 2009, Biophysical journal.

Oligomerization Domains of G Protein-Coupled Receptors

Jonathan A. Javitch, Marta Filizola, Harel Weinstein, 2005 .

Calmodulin structure and function: Implication of arginine in the compaction related to ligand binding

Harel Weinstein, Ernest L. Mehler, H. Weinstein, 1991 .

Structural models for dimerization of G-protein coupled receptors: the opioid receptor homodimers.

Marta Filizola, Harel Weinstein, H. Weinstein, 2002, Biopolymers.

The structure and dynamics of GPCR oligomers: a new focus in models of cell-signaling mechanisms and drug design.

Marta Filizola, Harel Weinstein, H. Weinstein, 2005, Current opinion in drug discovery & development.

Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study.

Harel Weinstein, Nathalie Basdevant, H. Weinstein, 2006, Journal of the American Chemical Society.

Pathways of Conformational Transitions in Proteins

Ron Elber, Harel Weinstein, H. Weinstein, 2008 .

The cost of living in the membrane: a case study of hydrophobic mismatch for the multi-segment protein LeuT.

George Khelashvili, Harel Weinstein, Lei Shi, 2013, Chemistry and physics of lipids.

Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT.

Harel Weinstein, Thijs Beuming, 2005, Protein engineering, design & selection : PEDS.

A misconception concerning the electronic density distribution of an atom

Harel Weinstein, Peter Politzer, H. Weinstein, 1975 .

Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP2-Regulated Dynamics of the N-Terminus

Gianni De Fabritiis, George Khelashvili, Harel Weinstein, 2015, ACS chemical neuroscience.

Conserved Helix 7 Tyrosine Acts as a Multistate Conformational Switch in the 5HT2C Receptor

Harel Weinstein, Stuart C. Sealfon, H. Weinstein, 2002, The Journal of Biological Chemistry.

Supporting Material

Harel Weinstein, Lei Shi, H. Weinstein, 2010 .

Protein Diffusion on Charged Membranes: A Dynamic Mean-Field Model Describes Time Evolution and Lipid Reorganization

George Khelashvili, Harel Weinstein, Daniel Harries, 2007, Biophysical journal.

Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters*

George Khelashvili, Jonathan A. Javitch, Harel Weinstein, 2015, The Journal of Biological Chemistry.

Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter:sodium symporters

Harel Weinstein, Lei Shi, Matthias Quick, 2010, Nature Structural &Molecular Biology.

Hinges, swivels and switches: the role of prolines in signalling via transmembrane α-helices

Mark S.P. Sansom, Harel Weinstein, H. Weinstein, 2000 .

The effect of a protein environment on the proposed activation mechanism of the histamine H2-receptor

Harel Weinstein, Eric E. J. Haaksma, H. Weinstein, 1991 .

Membrane Driven Spatial Organization of GPCRs

George Khelashvili, Marta Filizola, Jennifer M. Johnston, 2013, Scientific Reports.

Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects.

Harel Weinstein, H. Weinstein, Jian Sun, 2007, The Journal of chemical physics.

A Dynamic Model of Membrane-Bound Phospholipase Cβ2 Activation by Gβγ Subunits

Harel Weinstein, Sebastian Stolzenberg, H. Weinstein, 2011, Molecular Pharmacology.

A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains.

Harel Weinstein, Masha Y Niv, H. Weinstein, 2005, Journal of the American Chemical Society.

Not Just an Oil Slick: How the Energetics of Protein-Membrane Interactions Impacts the Function and Organization of Transmembrane Proteins

George Khelashvili, Harel Weinstein, Sayan Mondal, 2014, Biophysical journal.

Experimental conditions can obscure the second high-affinity site in LeuT

Jonathan A. Javitch, Harel Weinstein, Lei Shi, 2011, Nature Structural &Molecular Biology.

Gating mechanism of the extracellular entry to the lipid pathway in a TMEM16 scramblase

George Khelashvili, Harel Weinstein, H. Weinstein, 2018, Nature Communications.

How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties

George Khelashvili, Harel Weinstein, Asghar M. Razavi, 2018, BMC biology.

Computational approaches to detect allosteric pathways in transmembrane molecular machines.

Harel Weinstein, Lei Shi, Sebastian Stolzenberg, 2016, Biochimica et biophysica acta.

Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1.

Irina S. Moreira, Harel Weinstein, S. Brøgger Christensen, 2010, Organic & biomolecular chemistry.

Mechanisms of nucleophilic addition to activated double bonds : 1,2- and 1,4-Michael addition of ammonia

Harel Weinstein, Leonardo Pardo, Roman Osman, 1993 .

A New Computational Method for Membrane Compressibility: Bilayer Mechanical Thickness Revisited.

George Khelashvili, Harel Weinstein, Milka Doktorova, 2019, Biophysical journal.

Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homolog

Jonathan A. Javitch, Harel Weinstein, Lei Shi, 2011, Nature.

Single-molecule dynamics of gating in a neurotransmitter transporter homolog

Jonathan A. Javitch, Harel Weinstein, Lei Shi, 2010, Nature.

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

Sergio A Hassan, Harel Weinstein, Daqun Zhang, 2003, Proteins.

Single-molecule analysis of ligand efficacy in β2AR-G protein activation

Jonathan A. Javitch, Brian K. Kobilka, Harel Weinstein, 2017, Nature.

Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin.

George Khelashvili, Harel Weinstein, Asghar M. Razavi, 2017, Structure.

Probing conformational changes in neurotransmitter transporters: a structural context.

Orkun S. Soyer, Harel Weinstein, Thijs Beuming, 2003, European journal of pharmacology.

Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter*

Harel Weinstein, Lei Shi, Sebastian Stolzenberg, 2015, The Journal of Biological Chemistry.

Structure Calculation of Protein Segments Connecting Domains with Defined Secondary Structure: A Simulated Annealing Monte Carlo Combined with Biased Scaled Collective Variables Technique

Harel Weinstein, Ernest L. Mehler, Sergio A. Hassan, 2002 .

Three-dimensional representations of G protein-coupled receptor structures and mechanisms.

Harel Weinstein, J. Ballesteros, H. Weinstein, 2002, Methods in enzymology.

Membrane Localization is Critical for Activation of the PICK1 BAR Domain

Harel Weinstein, Masha Y Niv, Dimitrios Stamou, 2008, Traffic.

Hallucinogen actions on 5-HT receptors reveal distinct mechanisms of activation and signaling by G protein-coupled receptors

Harel Weinstein, H. Weinstein, 2005, The AAPS Journal.

Analytical calculation of atomic and molecular electrostatic potentials from the Poisson equation

Harel Weinstein, H. Weinstein, Shalom Srebrenik, 1973 .

Gramicidin Increases Lipid Flip-Flop in Symmetric and Asymmetric Lipid Vesicles.

Harel Weinstein, Milka Doktorova, John Katsaras, 2019, Biophysical journal.

The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site.

Harel Weinstein, Lei Shi, Matthias Quick, 2008, Molecular cell.

A Functional Selectivity Mechanism at the Serotonin-2A GPCR Involves Ligand-Dependent Conformations of Intracellular Loop 2

George Khelashvili, Jufang Shan, Harel Weinstein, 2014, Journal of the American Chemical Society.

Augmenting drug–carrier compatibility improves tumour nanotherapy efficacy

Harel Weinstein, Catharina de Lange Davies, Zahi A. Fayad, 2016, Nature Communications.

Functional Microdomains in G-protein-coupled Receptors

Robert P. Millar, Harel Weinstein, Stuart C. Sealfon, 1998, The Journal of Biological Chemistry.

Topology of Type II REases revisited; structural classes and the common conserved core

Adam Liwo, Harel Weinstein, Harold A. Scheraga, 2007, Nucleic acids research.

Certain 1,4-Disubstituted Aromatic Piperidines and Piperazines with Extreme Selectivity for the Dopamine D4 Receptor Interact with a Common Receptor Microdomain

Peter Gmeiner, Sandhya Kortagere, Harel Weinstein, 2004, Molecular Pharmacology.

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

Harel Weinstein, Thijs Beuming, Jonathan A Javitch, 2006, Molecular Pharmacology.

On the basis set dependence of reported limitations in predictions from electrostatic potentials

Harel Weinstein, H. Weinstein, W. Daniel Edwards, 1978 .

Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations

George Khelashvili, Harel Weinstein, Alan Grossfield, 2009, Proteins.

The study of G‐protein coupled receptor oligomerization with computational modeling and bioinformatics

Marta Filizola, Harel Weinstein, H. Weinstein, 2005, The FEBS journal.

Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation

Jonathan A. Javitch, Harel Weinstein, Poul Nissen, 2009, Proceedings of the National Academy of Sciences.

Functional Selectivity and Classical Concepts of Quantitative Pharmacology

Arthur Christopoulos, Jonathan A. Javitch, Bryan L. Roth, 2007, Journal of Pharmacology and Experimental Therapeutics.

Ab initio computational modeling of loops in G‐protein‐coupled receptors: Lessons from the crystal structure of rhodopsin

Sergio A Hassan, Sandhya Kortagere, Harel Weinstein, 2006, Proteins.

Molecular dynamics simulation of the hydrated d(CGCGAATTCGCG)2 dodecamer

Harel Weinstein, Roman Osman, R. Osman, 1993 .

Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation.

Marta Filizola, Harel Weinstein, Jonathan A Javitch, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Conformational dynamics of ligand-dependent alternating access in LeuT

Benoît Roux, Harel Weinstein, Matthias Quick, 2014, Nature Structural &Molecular Biology.

Allosteric communication between protomers of dopamine Class A GPCR dimers modulates activation

Irina S. Moreira, Jonathan A. Javitch, Harel Weinstein, 2009, Nature chemical biology.

The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems

Harel Weinstein, Michel A. Cuendet, Michael V. LeVine, 2016, Journal of Chemical Theory and Computation.

Localized Molecular Orbitals

Harel Weinstein, H. Weinstein, Maurice Cohen, 1971 .

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

Harel Weinstein, John A. Schetz, Zeynep H. Gümüş, 2009, Neuropharmacology.

State-dependent Conformations of the Translocation Pathway in the Tyrosine Transporter Tyt1, a Novel Neurotransmitter:Sodium Symporter from Fusobacterium nucleatum*

Harel Weinstein, Lei Shi, Thijs Beuming, 2006, Journal of Biological Chemistry.

Dynamic modulation of the lipid translocation groove generates a conductive ion channel in Ca2+-bound nhTMEM16

George Khelashvili, Harel Weinstein, Xiaolu Cheng, 2019, Nature Communications.

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter

George Khelashvili, Harel Weinstein, Asghar M. Razavi, 2017, Scientific Reports.

Quantitative modeling of membrane deformations by multihelical membrane proteins: application to G-protein coupled receptors.

George Khelashvili, Jufang Shan, Harel Weinstein, 2011, Biophysical journal.

Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD

Harel Weinstein, Thijs Beuming, Irina S Moreira, 2009, Proceedings of the National Academy of Sciences.

The Molecular Basis of Structure-Activity Relationships: Quantum Chemical Recognition Mechanisms in Drug-Receptor Interactions

Harel Weinstein, Roman Osman, R. Osman, 1979 .

Ion-controlled conformational dynamics in the outward-open transition from an occluded state of LeuT.

Harel Weinstein, Lei Shi, Sebastian Stolzenberg, 2012, Biophysical journal.

An Intracellular Interaction Network Regulates Conformational Transitions in the Dopamine Transporter*

Harel Weinstein, Lei Shi, Jonathan A Javitch, 2008, Journal of Biological Chemistry.

Structural Instability of a Constitutively Active G Protein-coupled Receptor

Brian K. Kobilka, Harel Weinstein, Roland Seifert, 1997, The Journal of Biological Chemistry.

The Membrane Protein LeuT in Micellar Systems: Aggregation Dynamics and Detergent Binding to the S2 Site

George Khelashvili, Jonathan A. Javitch, Harel Weinstein, 2013, Journal of the American Chemical Society.

Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method.

Marta Filizola, Harel Weinstein, Osvaldo Olmea, 2002, Protein engineering.

Ligand Selectivity of D2 Dopamine Receptors Is Modulated by Changes in Local Dynamics Produced by Sodium Binding

Harel Weinstein, Spencer S Ericksen, Spencer S. Ericksen, 2009, Journal of Pharmacology and Experimental Therapeutics.

Electrostatic Potentials as Descriptors of Molecular Reactivity: The Basis for Some Successful Predictions of Biological Activity

Harel Weinstein, Roman Osman, Sid Topiol, 1981 .