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1Academic Journal
المؤلفون: Panagiotis I. Koukos, Sepehr Dehghani-Ghahnaviyeh, Camilo Velez-Vega, John Manchester, D. Peter Tieleman, José S. Duca, Paulo C. T. Souza, Zoe Cournia
مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Molecular Biology, Biotechnology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, reproduces key dynamical, bilayer penetration depth, accessible surface area, grained force field, atom force field, tether lipid tails, martini 3 coarse, protein lipidation post, anchored proteins include, protein trafficking, grained models, anchored proteins, anchored peptides, vital co, various diseases, undergo farnesylation, translational modifications, thus crucial, targeting myristoylation, targeting farnesylation
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2Academic Journal
مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Molecular Biology, Pharmacology, Biotechnology, Infectious Diseases, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, performance gains allowed, drug molecule followed, aided drug design, find promising performance, successfully apply rbfe, relative binding free, apply rbfe, free energy, soluble proteins, predictive manner, p2y1 receptor, orthosteric site, microkinetic model, helical sites, helical site, gpcrs ), experiencing resurgence, embedded g, coupled receptors, congeneric series
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3Academic Journal
المؤلفون: Christos Lamprakis (10723116), Ioannis Andreadelis (6331535), John Manchester (2303572), Camilo Velez-Vega (1487623), José S. Duca (1487629), Zoe Cournia (650343)
مصطلحات موضوعية: Biophysics, Biochemistry, Physiology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, Martini open-beta 3, Study Protein Dimerization, supramolecular protein aggregation, association, membrane proteins, near-native dimer complexes, minima, coarse-grained force field, protein dimerization process, Martini 2.2 P, Martini Force Field, Martini 2.2 P multimer simulations, Martini 3 results
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4Report
المؤلفون: Christos Lamprakis (10695612), Ioannis Andreadelis (10695613), John Manchester (10695614), Camilo Velez-Vega (10695615), José S. Duca (6502057), Zoe Cournia (5849399)
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5Academic Journal
المؤلفون: Lieyang Chen, Anthony Cruz, Steven Ramsey, Callum J Dickson, Jose S Duca, Viktor Hornak, David R Koes, Tom Kurtzman
المصدر: PLoS ONE, Vol 14, Iss 8, p e0220113 (2019)
Relation: https://doi.org/10.1371/journal.pone.0220113; https://doaj.org/toc/1932-6203; https://doaj.org/article/1b18d4982db141da83dc26f8ff936f75
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6
المؤلفون: José S. Duca, Viktor Hornak, Callum J. Dickson
المصدر: Journal of chemical information and modeling. 61(12)
مصطلحات موضوعية: Binding Sites, Binding free energy, Intrinsic activity, Chemistry, Drug discovery, General Chemical Engineering, Entropy, General Chemistry, Library and Information Sciences, Drug molecule, Ligands, Small molecule, Lipids, P2y1 receptor, Computer Science Applications, Receptors, G-Protein-Coupled, Membrane, Biophysics, Thermodynamics, G protein-coupled receptor, Protein Binding
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7
المؤلفون: C. Wartchow, José S. Duca, Vibhas Aravamuthan, Sarah Williams, Robert A. Pearlstein, Hongbin Wan
مصطلحات موضوعية: chemistry.chemical_compound, Work (thermodynamics), Reaction rate constant, chemistry, Chemical physics, Dimer, Solvation, Potential energy, Ternary complex, Dissociation (chemistry), Topology (chemistry)
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8
المؤلفون: Matthias Zentgraf, Elizabeth Krutoholow, Thomas S. Rush, Chris Luebkemann, Kimito Funatsu, Gisbert Schneider, Jeff Blaney, Alleyn T. Plowright, Norman Sieroka, John Edward Hill, Petra Schneider, Jennifer Listgarten, José S. Duca, Robert Alan Goodnow, Johanna M. Jansen, Jasmin Fisher, Matthias Kohler, W. Patrick Walters
المصدر: Nature Reviews Drug Discovery. 19:353-364
مصطلحات موضوعية: 0301 basic medicine, Pharmacology, business.industry, media_common.quotation_subject, General Medicine, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Drug development, 030220 oncology & carcinogenesis, Political science, Drug Discovery, Artificial intelligence, business, Skepticism, media_common, Grand Challenges
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9Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability
المؤلفون: Anastasia Theodoropoulou, Camilo Velez-Vega, Ioannis Andreadelis, Zoe Cournia, Sofia Kiriakidi, José S. Duca, John I. Manchester, Christos Lamprakis, Stefan Doerr, Alexios Chatzigoulas
مصطلحات موضوعية: Cell signaling, education.field_of_study, Dimer, Population, Molecular Conformation, GTPase, Molecular Dynamics Simulation, Lipids, Surfaces, Coatings and Films, Proto-Oncogene Proteins p21(ras), Cell membrane, chemistry.chemical_compound, Molecular dynamics, Membrane, medicine.anatomical_structure, chemistry, Mole, Materials Chemistry, ras Proteins, Biophysics, medicine, lipids (amino acids, peptides, and proteins), Physical and Theoretical Chemistry, education, Protein Binding
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10
المؤلفون: Christos Lamprakis, Camilo Velez-Vega, José S. Duca, Zoe Cournia, Ioannis Andreadelis, John I. Manchester
المصدر: Journal of chemical theory and computation. 17(5)
مصطلحات موضوعية: 010304 chemical physics, Chemistry, Force field (physics), Cell Membrane, Metadynamics, Proteins, Water, Protein aggregation, 01 natural sciences, Computer Science Applications, Maxima and minima, Membrane protein, Chemical physics, 0103 physical sciences, Protein oligomerization, Thermodynamics, Parallel tempering, Physical and Theoretical Chemistry, Protein Multimerization, Protein Dimerization, Dimerization
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11
المؤلفون: Micholas Dean Smith, Jerry M. Parks, Daniel W. Kneller, Jeremy C. Smith, Andrei Golosov, Leighton Coates, Isabella Daidone, Camilo Velez-Vega, Atanu Acharya, Chris Chipot, Callum J. Dickson, Diane L. Lynch, Anna Pavlova, Yui Tik Pang, José S. Duca, James C. Gumbart, Josh V. Vermaas, Andrey Kovalevsky, Laura Zanetti-Polzi
المصدر: Chemical science (Camb. 2010. Online) 12 (2021): 1513–1527. doi:10.1039/d0sc04942e
info:cnr-pdr/source/autori:Pavlova A.; Lynch D.L.; Daidone I.; Zanetti-Polzi L.; Smith M.D.; Chipot C.; Kneller D.W.; Kovalevsky A.; Coates L.; Golosov A.A.; Dickson C.J.; Velez-Vega C.; Duca J.S.; Vermaas J.V.; Pang Y.T.; Acharya A.; Parks J.M.; Smith J.C.; Gumbart J.C./titolo:Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease/doi:10.1039%2Fd0sc04942e/rivista:Chemical science (Camb. 2010. Online)/anno:2021/pagina_da:1513/pagina_a:1527/intervallo_pagine:1513–1527/volume:12
Chemical Science
bioRxivمصطلحات موضوعية: Peptidomimetic, Stereochemistry, medicine.medical_treatment, viruses, Protonation, 010402 general chemistry, Cleavage (embryo), 01 natural sciences, Article, 03 medical and health sciences, 0103 physical sciences, medicine, Binding site, Histidine, 030304 developmental biology, 0303 health sciences, Protease, 010304 chemical physics, 010405 organic chemistry, Chemistry, Hydrogen bond, virus diseases, General Chemistry, Cysteine protease, 0104 chemical sciences
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12Academic Journal
المؤلفون: Charles A. Lesburg, Jose ́ S. Duca
المساهمون: The Pennsylvania State University CiteSeerX Archives
وصف الملف: application/pdf
Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.524.8289; http://nar.oxfordjournals.org/content/36/suppl_2/W252.full-text-lowres.pdf
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13
المؤلفون: Callum J. Dickson, Camilo Velez-Vega, José S. Duca
المصدر: Journal of chemical information and modeling. 60(1)
مصطلحات موضوعية: congenital, hereditary, and neonatal diseases and abnormalities, ERG1 Potassium Channel, Patch-Clamp Techniques, Protein Conformation, General Chemical Engineering, hERG, Datasets as Topic, Library and Information Sciences, Molecular Dynamics Simulation, 01 natural sciences, Sudden death, 0103 physical sciences, Humans, cardiovascular diseases, Binding site, Binding Sites, 010304 chemical physics, biology, Chemistry, Drug discovery, Cryoelectron Microscopy, General Chemistry, Small molecule, Potassium channel, 0104 chemical sciences, Computer Science Applications, Molecular Docking Simulation, 010404 medicinal & biomolecular chemistry, HEK293 Cells, Docking (molecular), biology.protein, Biophysics, Solvents, Pharmacophore
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14
المؤلفون: Petra, Schneider, W Patrick, Walters, Alleyn T, Plowright, Norman, Sieroka, Jennifer, Listgarten, Robert A, Goodnow, Jasmin, Fisher, Johanna M, Jansen, José S, Duca, Thomas S, Rush, Matthias, Zentgraf, John Edward, Hill, Elizabeth, Krutoholow, Matthias, Kohler, Jeff, Blaney, Kimito, Funatsu, Chris, Luebkemann, Gisbert, Schneider
المصدر: Nature reviews. Drug discovery. 19(5)
مصطلحات موضوعية: Artificial Intelligence, Drug Design, Drug Discovery, Humans
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15
المؤلفون: Tom Kurtzman, José S. Duca, Callum J. Dickson, David Ryan Koes, Steven Ramsey, Lieyang Chen, Anthony Cruz, Viktor Hornak
مصطلحات موضوعية: Virtual screening, Generalization, business.industry, Deep learning, Structure based, Artificial intelligence, Machine learning, computer.software_genre, business, Convolutional neural network, computer, Autodock vina
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16Academic Journal
المؤلفون: Amit S. Kulkarni, A. J. Hopfinger, José S. Duca
المساهمون: The Pennsylvania State University CiteSeerX Archives
مصطلحات موضوعية: molecular dynamics simulations
وصف الملف: application/pdf
Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.564.1668; http://www.aaai.org/Papers/Symposia/Spring/1999/SS-99-01/SS99-01-034.pdf
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17
المؤلفون: Subarna Shakya, José S. Duca, Elizabeth R. Sprague, Xin Chen, Zhuoliang Chen, Carol Joud, Yaping Wang, John William Giraldes, Wenlin Shao, Simon Mathieu, Chen Christine Hiu-Tung, Yanqiu Yuan, Kristen Hurov, B. Barry Touré, Christopher Sean Straub
المصدر: Journal of Medicinal Chemistry. 60:2155-2161
مصطلحات موضوعية: 0301 basic medicine, Leucine Zippers, Leucine zipper, 010405 organic chemistry, Chemistry, Kinase, Protein Serine-Threonine Kinases, Crystallography, X-Ray, 01 natural sciences, 0104 chemical sciences, Maternal embryonic leucine zipper kinase, 03 medical and health sciences, 030104 developmental biology, Biochemistry, Drug Discovery, Molecular Medicine, Enzyme Inhibitors, Selectivity
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18
المؤلفون: John Reilly, José S. Duca, Robin Alec Fairhurst, David Andrew Sandham, Steven J. Charlton, Daniel J. McKay, Callum J. Dickson, Camilo Velez-Vega, David A. Sykes, Robert A. Pearlstein, Duncan Shaw, Viktor Hornak
المصدر: Journal of Medicinal Chemistry. 59:5780-5789
مصطلحات موضوعية: Models, Molecular, 0301 basic medicine, Binding Sites, Ligand efficiency, Dose-Response Relationship, Drug, Molecular Structure, Chemistry, Cell Membrane, Plasma protein binding, Ligands, Ligand (biochemistry), Small molecule, Structure-Activity Relationship, 03 medical and health sciences, 030104 developmental biology, Membrane, Biochemistry, Membrane protein, Drug Discovery, Biophysics, Humans, Molecular Medicine, Structure–activity relationship, Receptors, Adrenergic, beta-2, Binding site
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19
المؤلفون: Yaping Wang, Xin Chen, Zhuoliang Chen, John William Giraldes, Kirk Wright, Sean Kim, José S. Duca, Eric J. Martin, J. Tres Brazell, Kristen Hurov, Elizabeth R. Sprague, Yun Feng, David E. Puleo, Subarna Shakya, Yanqiu Yuan, David Sage, Matthew J. Meyer, Yuji Mishina, Yan Yan-Neale, Christopher Sean Straub, Li Tian, Simon Mathieu, Dongshu Chen, Wenlin Shao, B. Barry Touré, Troy Smith
المصدر: Journal of Medicinal Chemistry. 59:4711-4723
مصطلحات موضوعية: Male, Models, Molecular, 0301 basic medicine, Protein Serine-Threonine Kinases, Maternal embryonic leucine zipper kinase, Small hairpin RNA, Mice, Structure-Activity Relationship, 03 medical and health sciences, 0302 clinical medicine, In vivo, Cell Line, Tumor, Drug Discovery, Animals, Humans, Structure–activity relationship, Protein Kinase Inhibitors, Cell Proliferation, Gene knockdown, Dose-Response Relationship, Drug, Molecular Structure, Drug discovery, Chemistry, Kinase, Cell cycle, Cell biology, Mice, Inbred C57BL, 030104 developmental biology, Biochemistry, 030220 oncology & carcinogenesis, MCF-7 Cells, Molecular Medicine
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20
المؤلفون: José S. Duca, Viktor Hornak, Callum J. Dickson, Dallas Bednarczyk
المصدر: Journal of chemical information and modeling. 59(1)
مصطلحات موضوعية: Cell Membrane Permeability, Membrane permeability, General Chemical Engineering, Molecular Conformation, Library and Information Sciences, Molecular Dynamics Simulation, 01 natural sciences, Polar surface area, Madin Darby Canine Kidney Cells, Molecular dynamics, Dogs, 0103 physical sciences, Molecule, Animals, 010304 chemical physics, Chemistry, Hydrogen Bonding, General Chemistry, Permeation, 0104 chemical sciences, Computer Science Applications, Partition coefficient, 010404 medicinal & biomolecular chemistry, Membrane, Pharmaceutical Preparations, Chemical physics, Permeability (electromagnetism), Thermodynamics
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