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1. Materials Informatics
by Hanoch Senderowitz and Alexander Tropsha
Journal of Chemical Information and Modeling, ISSN 1549-9596, 07/2018, Volume 58, Issue 7, p. 1313
Information science methodologies are key to bridging the gap between data creation, capture, and storage on one hand and the derivation and utilization of... 
Solar cells | Organic chemistry | Materials information | Media richness | Photovoltaic cells | Research methodology | Cosmetics | Nanomaterials | Knowledge | Bioinformatics
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2. Full Text Materials Informatics
by Senderowitz, Hanoch and Tropsha, Alexander
Journal of Chemical Information and Modeling, ISSN 1549-9596, 12/2018, Volume 58, Issue 12, pp. 2377 - 2379
COMPUTER SCIENCE, INFORMATION SYSTEMS | CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | CHEMISTRY, MULTIDISCIPLINARY
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3. Optimization of Molecular Representativeness
by Abraham Yosipof and Hanoch Senderowitz
Journal of Chemical Information and Modeling, ISSN 1549-9596, 06/2014, Volume 54, Issue 6, p. 1567
  Representative subsets selected from within larger data sets are useful in many chemoinformatics applications including the design of information-rich... 
Optimization algorithms | Parasitic protozoa | Information | Chemical compounds
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4. Full Text Visualization of Solar Cell Library Space by Dimensionality Reduction Methods
by Kaspi, Omer and Yosipof, Abraham and Senderowitz, Hanoch
Journal of Chemical Information and Modeling, ISSN 1549-9596, 12/2018, Volume 58, Issue 12, pp. 2428 - 2439
Visualizing high-dimensional data by projecting them into a two- or three-dimensional space is a popular approach in many scientific fields, including... 
CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | OXIDE | COMPUTER SCIENCE, INFORMATION SYSTEMS | SCIENCE | CHEMISTRY, MULTIDISCIPLINARY | TOOLS | Solar cells | Visualization | Cliffs | Identification methods | Principal components analysis | Energy sources | Clustering | Metal oxides | Organic chemistry | Reduction | Photovoltaic cells | Outliers (statistics) | Computer aided design--CAD | Dimensional analysis | Clean energy
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5. Docking Studies on DNA Intercalators
by Yocheved Gilad and Hanoch Senderowitz
Journal of Chemical Information and Modeling, ISSN 1549-9596, 01/2014, Volume 54, Issue 1, p. 96
  DNA is an important target for the treatment of multiple pathologies, most notably cancer. In particular, DNA intercalators have often been used as... 
Drugs | Chemistry | Research & development--R&D | Deoxyribonucleic acid--DNA
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6. Full Text Docking Studies on DNA Intercalators
by Gilad, Yocheved and Senderowitz, Hanoch
Journal of Chemical Information and Modeling, ISSN 1549-9596, 01/2014, Volume 54, Issue 1, pp. 96 - 107
DNA is an important target for the treatment of multiple pathologies, most notably cancer. In particular, DNA intercalators have often been used as anticancer... 
CHEMISTRY, MEDICINAL | RECOGNITION | ANTHRACYCLINE ANTIBIOTICS | MODE | CROSS-LINKING | COMPUTER SCIENCE, INFORMATION SYSTEMS | MOLECULAR DOCKING | CHEMISTRY, MULTIDISCIPLINARY | GENETIC ALGORITHM | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | SEQUENCE | AZINOMYCIN-B | BINDING | MINOR-GROOVE | Computational Biology | Models, Molecular | Intercalating Agents - pharmacology | Nucleic Acid Conformation - drug effects | Antineoplastic Agents - chemistry | Drug Discovery | DNA, B-Form - chemistry | Intercalating Agents - chemistry | Databases, Pharmaceutical | Databases, Chemical | Computer Simulation | Ligands | Antineoplastic Agents - pharmacology | Software | Computer-Aided Design | Decision Trees | Binding Sites | Databases, Nucleic Acid | DNA, B-Form - drug effects
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7. Full Text PV Analyzer: A Decision Support System for Photovoltaic Solar Cells Libraries
by Kaspi, Omer and Yosipof, Abraham and Senderowitz, Hanoch
Molecular Informatics, ISSN 1868-1743, 09/2018, Volume 37, Issue 9-10, pp. e1800067 - n/a
This work describes the integration of several data mining and machine learning tools for researching Photovoltaic (PV) solar cells libraries into a unified... 
RANSAC | Solar cell | Photovoltaic | QSAR | Machine learning | Decision Support System | Data mining | Material-Informatics | CHEMISTRY, MEDICINAL | VALIDATION | OUTLIER REMOVAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | OPTIMIZATION | Solar Energy | Software | Machine Learning | Quantitative Structure-Activity Relationship | Decision support systems | Solar cells | Data analysis | Statistical analysis | Independent variables | Data processing | Workflow | Statistical methods | Decision analysis | Learning algorithms | Embedded systems | Algorithms | Photovoltaic cells | Dependent variables | Graphical user interface | Libraries | Artificial intelligence | Photovoltaics
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8. Full Text Materials Informatics
by Senderowitz, Hanoch and Tropsha, Alexander
Journal of Chemical Information and Modeling, ISSN 1549-9596, 07/2018, Volume 58, Issue 7, pp. 1313 - 1314
COMPUTER SCIENCE, INFORMATION SYSTEMS | CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | CHEMISTRY, MULTIDISCIPLINARY
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9. Full Text Rescoring of docking poses under Occam’s Razor: are there simpler solutions?
by Zhenin, Michael and Bahia, Malkeet Singh and Marcou, Gilles and Varnek, Alexandre and Senderowitz, Hanoch and Horvath, Dragos
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 09/2018, Volume 32, Issue 9, pp. 877 - 888
Ligand affinity prediction from docking simulations is usually performed by means of highly empirical and diverse protocols. These protocols often involve the... 
Docking | Scoring | Force field calculations | Gold | Computer simulation | Calibration | Hydrophobicity | Complexity | Proteins | Solvation | Machine learning | Affinity | Ligands | Mathematical models | Binding sites | Cheminformatics | Chemical Sciences
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10. Full Text Plant phenolic volatiles inhibit quorum sensing in pectobacteria and reduce their virulence by potential binding to ExpI and ExpR proteins
by Joshi, Janak Raj and Khazanov, Netaly and Senderowitz, Hanoch and Burdman, Saul and Lipsky, Alexander and Yedidia, Iris
Scientific Reports, ISSN 2045-2322, 12/2016, Volume 6, Issue 1, p. 38126
Quorum sensing (QS) is a population density-dependent regulatory system in bacteria that couples gene expression to cell density through accumulation of... 
N-ACYLHOMOSERINE LACTONES | SOFT-ROT | CARVACROL | CAROTOVORA SUBSP CAROTOVORA | ESSENTIAL OILS | HOMOSERINE LACTONE SYNTHASE | PSEUDOMONAS-AERUGINOSA | MULTIDISCIPLINARY SCIENCES | STAPHYLOCOCCUS-AUREUS | ANTIMICROBIAL ACTIVITY | ERWINIA-CAROTOVORA | Enzymes | Essential oils | Cell walls | Carvacrol | Homology | Gene expression | Phenolic compounds | Volatiles | Eugenol | Allelochemicals | Cell density | Proteins | Soft rot | Quorum sensing | Population density
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11. G protein-coupled receptors: Target-based in silico screening
by Senderowitz, Hanoch and Marantz, Yael
Current Pharmaceutical Design, ISSN 1381-6128, 12/2009, Volume 15, Issue 35, pp. 4049 - 4068
In silico (or virtual) screening has become a common practice in current computer-aided drug design efforts. However, application to hit discovery in the G... 
Virtual screening | Docking | Structure-based drug design | In silico screening | PREDICT | GPCRs | structure-based drug design | HUMAN NEUROKININ-1 RECEPTOR | LIGAND-BINDING | virtual screening | CRYSTAL-STRUCTURE | DRUG DISCOVERY | SITE-DIRECTED MUTAGENESIS | MOLECULAR DOCKING | SCORING FUNCTION | docking | HOMOLOGY MODELS | BINDING-SITE | PHARMACOLOGY & PHARMACY | CANNABINOID CB1 RECEPTOR | Receptors, G-Protein-Coupled - metabolism | Computer Simulation | Humans | Drug Design | Models, Molecular | Protein Binding | Ligands | Computer-Aided Design | Receptors, G-Protein-Coupled - chemistry | Drug Delivery Systems
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12. A Multi-Objective Genetic Algorithm for Outlier Removal
by Oren E Nahum and Abraham Yosipof and Hanoch Senderowitz
Journal of Chemical Information and Modeling, ISSN 1549-9596, 12/2015, Volume 55, Issue 12, p. 2507
  Quantitative structure activity relationship (QSAR) or quantitative structure property relationship (QSPR) models are developed to correlate activities for... 
Molecular structure | Protease inhibitors | Mathematical models | Chemical compounds | Genetic algorithms
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13. REMD Simulations Reveal the Dynamic Profile and Mechanism of Action of Deleterious, Rescuing, and Stabilizing Perturbations to NBD1 from CFTR
by Michael Zhenin and Efrat Noy and Hanoch Senderowitz
Journal of Chemical Information and Modeling, ISSN 1549-9596, 11/2015, Volume 55, Issue 11, p. 2349
  Cystic Fibrosis (CF) is a lethal, genetic disease caused by mutations to the CFTR chloride channel. The most common CF causing mutation is the deletion of... 
Genetic disorders | Genes | Cystic fibrosis | Mutation
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14. Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study
by Hannah H Avgy-David and Hanoch Senderowitz
Journal of Chemical Information and Modeling, ISSN 1549-9596, 10/2015, Volume 55, Issue 10, p. 2154
  The identification of bound conformations, namely, conformations adopted by ligands when binding their target is critical for target-based and ligand-based... 
Approximations | Ligands | Quantum physics | Biological activity | Crystal structure
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15. Full Text k‐Nearest neighbors optimization‐based outlier removal
by Yosipof, Abraham and Senderowitz, Hanoch
Journal of Computational Chemistry, ISSN 0192-8651, 03/2015, Volume 36, Issue 8, pp. 493 - 506
Datasets of molecular compounds often contain outliers, that is, compounds which are different from the rest of the dataset. Outliers, while often interesting... 
quantitative structure activity relationship | k‐nearest neighbors | optimization | outlier detection | distance‐based method | outlier removal | Outlier detection | Outlier removal | Quantitative structure activity relationship | Distance-based method | Optimization | k-nearest neighbors | SET | QSAR | CLASSIFICATION | SELECTION | distance-based method | CHEMISTRY, MULTIDISCIPLINARY | PREDICTION | Algorithms | Clathrate compounds | Mathematical optimization | Analysis
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16. Full Text RANdom SAmple Consensus (RANSAC) algorithm for material-informatics: application to photovoltaic solar cells
by Kaspi, Omer and Yosipof, Abraham and Senderowitz, Hanoch
Journal of Cheminformatics, ISSN 1758-2946, 06/2017, Volume 9, Issue 1, pp. 34 - 15
An important aspect of chemoinformatics and material-informatics is the usage of machine learning algorithms to build Quantitative Structure Activity... 
RANSAC | Material-informatics | QSAR | Solar Cells | Photovoltaics | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | VALIDATION | COMPUTER SCIENCE, INFORMATION SYSTEMS | OPTIMIZATION | SCIENCE | SELECTION | CHEMISTRY, MULTIDISCIPLINARY | Solar cells | Photovoltaic power generation | Computational chemistry | Solar batteries | Chemical research | Models | Research | Properties | Cell culture | Statistical analysis | Image processing | Statistical methods | Structure-activity relationships | Learning algorithms | Properties (attributes) | Algorithms | Photovoltaic cells | Samples | Data sets | Machine learning | Predictions | Libraries | Mathematical models | Informatics
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17. Full Text Materials Informatics: Statistical Modeling in Material Science
by Yosipof, Abraham and Shimanovich, Klimentiy and Senderowitz, Hanoch
Molecular Informatics, ISSN 1868-1743, 12/2016, Volume 35, Issue 11-12, pp. 568 - 579
Material informatics is engaged with the application of informatic principles to materials science in order to assist in the discovery and development of new... 
photovoltaic cells | chemoinformatics | solar cells | QSAR | Material informatics | material science | QSPR | CHEMISTRY, MEDICINAL | GLASS-TRANSITION TEMPERATURES | PROPERTY RELATIONSHIP MODELS | PREDICTION | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | NEURAL-NETWORKS | MOLECULAR DESCRIPTOR | IMPACT SENSITIVITY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | OPTIMIZATION | IONIC LIQUIDS | ORGANIC PHOTOVOLTAICS | Combinatorial Chemistry Techniques - methods | Metals - chemistry | Drug Design | Models, Statistical | Data Mining - methods | Quantitative Structure-Activity Relationship | Information Science - methods | Materials Science - methods | Photovoltaic cells | Materials science | Informatics
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18. Molecular Dynamics Flexible Fitting Simulations Identify New Models of the Closed State of the Cystic Fibrosis Transmembrane Conductance Regulator Protein
by Luba Simhaev and Nael A McCarty and Robert C Ford and Hanoch Senderowitz
Journal of Chemical Information and Modeling, ISSN 1549-9596, 08/2017, Volume 57, Issue 8, p. 1932
Cystic fibrosis (CF) is a lethal, genetic disease found in particular in humans of European origin which is caused by mutations in the cystic fibrosis... 
High resolution | Computer simulation | Molecular dynamics | Cystic fibrosis | Homology | Zebrafish | Trajectories | Electron microscopy | Modulators | Proteins | Resistance | Molecules | Maps | Simulation | Fibrosis | Mutation | Trajectory analysis | Binding sites | Adenosine triphosphatase | Adenosine triphosphate
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19. Full Text Hsp104 facilitates the endoplasmic‐reticulum–associated degradation of disease‐associated and aggregation‐prone substrates
by Doonan, Lynley M and Guerriero, Christopher J and Preston, G. Michael and Buck, Teresa M and Khazanov, Netaly and Fisher, Edward A and Senderowitz, Hanoch and Brodsky, Jeffrey L
Protein Science, ISSN 0961-8368, 07/2019, Volume 28, Issue 7, pp. 1290 - 1306
Misfolded proteins in the endoplasmic reticulum (ER) are selected for ER‐associated degradation (ERAD). More than 60 disease‐associated proteins are substrates... 
endoplasmic‐reticulum–associated degradation | proteasome | molecular chaperone | Hsp104 | protein aggregation | cystic fibrosis transmembrane conductance regulator | AAA‐ATPase | apolipoprotein B | ubiquitin | yeast | BIOCHEMISTRY & MOLECULAR BIOLOGY | LIPID PARTICLES | ER-ASSOCIATED DEGRADATION | PARTICLE MESH EWALD | NUCLEOTIDE-BINDING DOMAIN | APOLIPOPROTEIN-B | INSERTION-DELETION POLYMORPHISM | TRANSMEMBRANE CONDUCTANCE REGULATOR | IN-VITRO | endoplasmic-reticulum-associated degradation | PROTEIN-QUALITY CONTROL | AAA-ATPase | MISFOLDED PROTEINS | Ubiquitin | Detergents, Synthetic | Codon | Molecular dynamics | Heat shock proteins | Cystic fibrosis | Apolipoproteins | Cells | Adenosine triphosphatase | Protein binding | Biodegradation | Yeast | Disease | Nonsense mutation | Stop codon | Lipids | Agglomeration | Hydrophobicity | Substrates | Degradation | Resistance | Apolipoprotein B | Proteins | Protein folding | Fibrosis | Conductance | Mutation | Chimeras | Endoplasmic reticulum
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20. Full Text Optimization of Molecular Representativeness
by Yosipof, Abraham and Senderowitz, Hanoch
Journal of Chemical Information and Modeling, ISSN 1549-9596, 06/2014, Volume 54, Issue 6, pp. 1567 - 1577
Representative subsets selected from within larger data sets are useful in many chemoinformatics applications including the design of information-rich compound... 
K-DISSIMILARITY | LIBRARIES | DISSIMILARITY SELECTION | CHEMISTRY, MEDICINAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | SET | COMPUTER SCIENCE, INFORMATION SYSTEMS | DIVERSITY | ALGORITHMS | CHEMISTRY, MULTIDISCIPLINARY | Databases, Pharmaceutical | Malaria, Falciparum - drug therapy | Algorithms | Models, Biological | Humans | Antiparasitic Agents - pharmacology | Models, Molecular | Drug Discovery - methods | Plasmodium falciparum - drug effects | Quantitative Structure-Activity Relationship | Cluster Analysis
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