Weinstein Lab

The Weinstein lab studies complex systems in physiology with methods of molecular and computational biophysics, bioinformatics and mathematical models. The work addresses structural and dynamic mechanisms in fundamental biological processes such as signal transduction, neuronal signaling and regulation of cell growth mechanisms, and the expression of these processes in the physiological functions of tissues and organs.

Current Members

Shana Bergman
Xiaolu Cheng
George Khelashvili
Giulia Morra
Shayantani Mukherjee
Ambrose Plante
Asghar Razavi
Derek Shore

Former Members

 

 

 

 

 

Pedro Blecua Albornoz
Matthew Diamond
Milka Doktorova
Luis Gracia
Zeynep H. Gumus
Marta Filizola
Niklaus Johner
Sayan Mondal
Irina Moreira
Masha Niv
Lei Shi
Lucy Skrabanek
Daniel Terry

Older Presentations

Postdoc Research Day Oral Presentation (WMC, NY)
Thijs Beuming, Marianne L. Bergmann, Lei Shi, Luis Gracia, Klaudia Raniszewska, Amy Hauck Newman, Jonathan A. Javitch, Harel Weinstein, Ulrik Gether, and Claus J. Loland
The Binding Sites for Cocaine and Dopamine in the Dopamine Transporter are Overlapping

 

Projects presented at the 2007 Biophysical Society meeting (Baltimore)
George A. Khelashvili, Daniel Harries and H. Weinstein Macromolecule Adsorption Macromolecule Adsorption on charged bilayers: A dynamic mean-field model accounts for the evolution of lateral reorganization and demixing
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Daniel Han, S. X. Wang, and H. Weinstein The dynamics of the conformational modulation of rhodopsin by the NPxxY motif in transmembrane helix 7 depends on the interaction of Y7.53 with F7.60 in the juxtamembrane helix 8
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Masha Y. Niv, D. Han, K. Madsen, U. Gether and H. Weinstein Interaction between the PDZ and the BAR Domains in PICK1: Structural Modeling and Phenotypic Characterization of the Functional Modulation
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Projects presented at the 2006 European Conference on Computational Biology (Eilat, Israel)
Masha Y. Niv, L. Skrabanek, R. J. Roberts, H. Scheraga, H. Weinstein Scan2S, a novel regular expression scan with secondary structure constraints applied to Type II Restriction Endonucleases
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Projects presented at the 2005 Biophysical Society meeting (Los Angeles)
Nathalie Basdevant, H. Weinsteinand M. Ceruso Recognition of peptides by PDZ domains: A Computational Study
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Thijs Beuming, M. Niv, L. Skrabanek, P. Mukherjee, M. Ceruso and H. Weinstein. Specific PDZ-peptide interactions identified with PDZBase: a database of PDZ-domain mediated protein-protein interactions.
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Sandhya Kortagere, T. Beuming and H. Weinstein Mapping the Parameters of Amino Acid Interactions with Halogenated Ligands as a Tool for Structure Based Drug Design
Masha Y. Niv and H. Weinstein Flexible Docking of Peptides to PDZ Structures and Homology Models
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Simon X. Wang, M. Filizola, M. Ceruso and H. Weinstein Rhodopsin Dimers: Molecular Dynamics Simulations Using Discrete Representations of the Membrane and Water Environment
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Projects presented at the 2002 Biophysical Society meeting (San Francisco)
Marc A. Ceruso, X. Periole, and H. Weinstein Role of the Inter-Domain Motions in the Regulation of Nucleotide Exchange and GTPase Activity in Transducin
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Marta Filizola, O. Olmea, and H. Weinstein Using Correlated Mutation Analysis to Predict the Heterodimerization Interface of GPCRs
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Sergio A. Hassan, and E. Mehler, Alanine Dipeptide and Discrimination of Misfolded Structures of Proteins with the Screened Coulomb Potential Continuum Model
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Sergio A. Hassan, D. Zhang,E. Mehler, and H. Weinstein A Fast and General Continuum Approach for Describing Electrostatic Effects in Molecular Dynamics Simulations of Biomolecules
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Ramasubbu Sankararamakrishnan, and H. Weinstein Comparison of NVE and NPT Ensembles and the Effect of g Values in the Simulation of a Peptide Imbedded in DMPC Bilayers
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Jian Sun, and H. Weinstein The Restriction Enzyme BamHI is Poised for Sliding Along DNA in the Nonspecific Complex
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Irache Visiers, B.J. Ebersole, S. Dracheva, J. Ballesteros, S. Sealfon, and H. Weinstein Energetic Considerations in the Mechanism of Activation of Rhodopsin-Like Receptors
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Projects presented at the 2001 Biophysical Society meeting (Boston)
L. Pardo, D. Bosch, M. Campillo, Nina Pastor, and H. Weinstein Sequence Specificity Dictated by the Interplay Between Direct Readout and DNA Flexibility at the TATA Box-Binding Protein – TATA Box Interface
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Nina Pastor, and H. Weinstein The Effect of High Salt Concentration on Protein Dynamics: Molecular Dynamics Simulations of P.woesei TATA Box-Binding Protein
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Sergio A. Hassan, E. Mehler, and H. Weinstein Structure Calculations of Protein Surface Segments: Monte Carlo Simulated Annealing with Scaled Collective Variables and Force Constant Annealing
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Jian Sun, Nina Pastor, and H. Weinstein MD Simulation of TATA-Box DNA: PME Calculations and the Effect of Electrostatic Cut-off
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Ramasubbu Sankararamakrishnan, and H. Weinstein Dynorphin A-(1-23) and DES-TYR Dynorphin Behave Differently in Phosphlopid Bilayers
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Xavier Periole, E. Mehler, and H. Weinstein Interaction of a Bromodomain with a Peptide Containing Acetylated Lysine: a Dynamic Simulation Study
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Barbara J. Ebersole, Irache Visiers, Daqun Zhang, Harel Weinstein, Stuart Sealfon – Ligand position in the GPCR binding site determines efficacy

Projects presented at the 2000 Biophysical Society meeting (New Orleans)
Irache Visiers, J.A, Ballesteros, B.B. Braunheim, and H. Weinstein A spatially ordered sequence of intramolecular rearrangements observed from simulations of agonist-related activation of 5ht2c receptors
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Irache Visiers, M. Stephan, G. Ruchick, and H. Weinstein A rescue mutation recovers the lost transport activity in T382P mutant
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Irache Visiers, S.A. Hassan, and H. Weinstein Differences in conformational properties of the second intracellular loop (IL2) in 5ht2c receptors modified by RNA editing can account for the silencing of constitutive activity
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Irache Visiers, L. Norregaard, C.J. Loland, J.A. Ballasteros, U. Gether, and H. Weinstein Inferences from molecular models of Zn-binding pockets in hDAT
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