Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix. - Arnaud J. A. Soirat; Chung F. Wong; Roman Osman; Harel Weinstein (J. Comput. Chem., 1997)

Key issues in the computational simulation of GPCR function: representation of loop domains. - Ernest L. Mehler; Xavier Periole; S. A. Hassan; Harel Weinstein (J. Comput. Aided Mol. Des., 2002)

Batch mode generation of residue-based diagrams of proteins. - Fabien Campagne; Emmanuel Bettler; Gert Vriend; Harel Weinstein (Bioinform., 2003)

Building protein diagrams on the web with the residue-based diagram editor RbDe. - Lucy Skrabanek; Fabien Campagne; Harel Weinstein (Nucleic Acids Res., 2003)

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. - Thijs Beuming; Harel Weinstein (Bioinform., 2004)

PDZBase: a protein?Cprotein interaction database for PDZ-domains. - Thijs Beuming; Lucy Skrabanek; Masha Y. Niv; Piali Mukherjee; Harel Weinstein (Bioinform., 2005)

Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. - Marta Filizola; Simon X. Wang; Harel Weinstein (J. Comput. Aided Mol. Des., 2006)

Modeling activated states of GPCRs: the rhodopsin template. - Masha Y. Niv; Lucy Skrabanek; Marta Filizola; Harel Weinstein (J. Comput. Aided Mol. Des., 2006)

Quantification and Analysis of Combination Drug Synergy in High-Throughput Transcriptome Studies. - Zeynep H. Gümüs; Fernando Siso-Nadal; Ada Gjrezi; Paul McDonagh; Iya Khalil; Paraskevi Giannakakou; Harel Weinstein (BIBE, 2010)

TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from Bioinformatics and Biomedical Literature. - Lei Shi 006; Marko Srdanovic; Thijs Beuming; Lucy Skrabanek; Jonathan A. Javitch; Harel Weinstein (BIBE, 2010)

Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties. - Jufang Shan; George Khelashvili; Sayan Mondal; Ernest L. Mehler; Harel Weinstein (PLoS Comput. Biol., 2012)

N-body Information Theory (NbIT) Analysis of Rigid-Body Dynamics in Intracellular Loop 2 of the 5-HT2A Receptor. - Michael V. LeVine; Jose Manuel Perez-Aguilar; Harel Weinstein (IWBBIO, 2014)

NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT. - Michael V. LeVine; Harel Weinstein (PLoS Comput. Biol., 2014)

AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems. - Michael V. LeVine; Harel Weinstein (Entropy, 2015)

Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis. - Trilce Estrada; Jeremy Benson; Hector Carrillo-Cabada; Asghar M. Razavi; Michel A. Cuendet; Harel Weinstein; Ewa Deelman; Michela Taufer (BCB, 2018)

Characterizing In Situ and In Transit Analytics of Molecular Dynamics Simulations for Next-Generation Supercomputers. - Michela Taufer; Ewa Deelman; Stephen Thomas; Michael R. Wyatt II; Tu Mai Anh Do; Loïc Pottier; Rafael Ferreira da Silva; Harel Weinstein; Michel A. Cuendet; Trilce Estrada (eScience, 2019)

A Novel Metric to Evaluate In Situ Workflows. - Tu Mai Anh Do; Loïc Pottier; Stephen Thomas; Rafael Ferreira da Silva; Michel A. Cuendet; Harel Weinstein; Trilce Estrada; Michela Taufer; Ewa Deelman (ICCS (1), 2020)

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins. - George Khelashvili; Xiaolu Cheng; Maria E. Falzone; Milka Doktorova; Alessio Accardi; Harel Weinstein (J. Comput. Chem., 2020)

A lightweight method for evaluating in situ workflow efficiency. - Tu Mai Anh Do; Loïc Pottier; Silvina Caíno-Lores; Rafael Ferreira da Silva; Michel A. Cuendet; Harel Weinstein; Trilce Estrada; Michela Taufer; Ewa Deelman (J. Comput. Sci., 2021)

A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes. - Hector Carrillo-Cabada; Jeremy Benson; Asghar M. Razavi; Brianna Mulligan; Michel A. Cuendet; Harel Weinstein; Michela Taufer; Trilce Estrada (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Online Boosted Gaussian Learners for In-Situ Detection and Characterization of Protein Folding States in Molecular Dynamics Simulations. - Harshita Sahni; Hector Carrillo-Cabada; Ekaterina D. Kots; Silvina Caíno-Lores; Jack Marquez; Ewa Deelman; Michel A. Cuendet; Harel Weinstein; Michela Taufer; Trilce Estrada (e-Science, 2023)

Runtime Steering of Molecular Dynamics Simulations Through In Situ Analysis and Annotation of Collective Variables. - Silvina Caíno-Lores; Michel A. Cuendet; Jack Marquez; Ekaterina D. Kots; Trilce Estrada; Ewa Deelman; Harel Weinstein; Michela Taufer (PASC, 2023)