المؤلفون: Manuel Pastor, José Carlos Gómez-Tamayo, Ferran Sanz

المصدر: Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-15 (2021)

مصطلحات موضوعية: Modeling framework, Modeling tools, Reproducibility, Model management, Workflow, QSAR, Information technology, T58.5-58.64, Chemistry, QD1-999

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1758-2946

URL الوصول: https://doaj.org/article/c352a6410d554ee2ba850498ce5d4d80

المؤلفون: Tsehai A.J. Grell, Mark Mason, Aaron A. Thompson, Jose Carlos Gómez-Tamayo, Daniel Riley, Michelle V. Wagner, Ruth Steele, Rodrigo F. Ortiz-Meoz, Jay Wadia, Paul L. Shaffer, Gary Tresadern, Sujata Sharma, Xiaodi Yu

المصدر: Heliyon, Vol 8, Iss 12, Pp e12392- (2022)

مصطلحات موضوعية: Malic enzymes, X-ray crystallography, Single particle Cryo-EM, Allostery, Drug discovery, Science (General), Q1-390, Social sciences (General), H1-99

Relation: http://www.sciencedirect.com/science/article/pii/S2405844022036805; https://doaj.org/toc/2405-8440; https://doaj.org/article/0f71dae03abd4550a60deb71f7723386

الاتاحة: https://doi.org/10.1016/j.heliyon.2022.e12392
https://doaj.org/article/0f71dae03abd4550a60deb71f7723386

المؤلفون: Wanda van der Stel (Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University), Giada Carta (Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam), Julie Eakins (Cyprotex Discovery Ltd.), Johannes Delp (In vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz), Ilinca Suciu (In vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz), Anna Forsby (Department of Biochemistry and Biophysics, Stockholm University), Andrea Cediel-Ulloa (Department of Organismal Biology, Uppsala University), Kristina Attoff (Department of Biochemistry and Biophysics, Stockholm University), Florentina Troger (Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna), Hennicke Kamp (BASF), Iain Gardner (Certara UK Limited), Barbara Zdrazil (Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna), Martijn J. Moné (Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University), Gerhard F. Ecker (Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna), Manuel Pastor (Department of Experimental and Health Sciences, Universitat Pompeu Fabra), Jose Carlos Gómez-Tamayo (Department of Experimental and Health Sciences, Universitat Pompeu Fabra), Andrew White (Unilever), Erik H. J. Danen (Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University), Marcel Leist (In vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz), Paul Walker (Cyprotex Discovery Ltd.), Paul Jennings (Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, AIMMS, Vrije Universiteit Amsterdam), Susanne Hougaard (Bennekou National Food Institute, Technical University of Denmark (DTU)), Bob van de Water (Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University)

المصدر: ALTEX ; issn:1868-596X

مصطلحات موضوعية: in vitro, mitochondrial toxicity, neurotoxicity, PBK-modelling, uncertainty analysis

وصف الملف: application/pdf

Relation: hdl:11353/10.1604356; https://phaidra.univie.ac.at/o:1604356

الاتاحة: https://doi.org/10.14573/altex.2103051
https://phaidra.univie.ac.at/o:1604356

المؤلفون: Manuel Pastor (10670238), José Carlos Gómez-Tamayo (10670241), Ferran Sanz (89706)

مصطلحات موضوعية: Artificial Intelligence and Image Processing, Computer Software, Modeling framework, Modeling tools, Reproducibility, Model management, Workflow, QSAR, Model integration, Web-interfaces, In-silico toxicology

Relation: https://figshare.com/articles/journal_contribution/Additional_file_2_of_Flame_an_open_source_framework_for_model_development_hosting_and_usage_in_production_environments/14450922

الاتاحة: https://doi.org/10.6084/m9.figshare.14450922.v1

المؤلفون: Theodora Katsila, Styliani A. Chasapi, Jose Carlos Gomez Tamayo, Constantina Chalikiopoulou, Eleni Siapi, Giorgos Moros, Panagiotis Zoumpoulakis, Georgios A. Spyroulias, Dimitrios Kardamakis

المصدر: Cancers; Volume 13; Issue 12; Pages: 2877

مصطلحات موضوعية: amifostine, 3D cellular angiogenesis assay, metabolomics, drug repurposing, radioprotection, anti-angiogenesis

وصف الملف: application/pdf

Relation: https://dx.doi.org/10.3390/cancers13122877

الاتاحة: https://doi.org/10.3390/cancers13122877

المؤلفون: José Carlos Gómez Tamayo, Mireia Olivella, Santiago Ríos, Marlous Hoogstraat, Angel Gonzalez, Eduardo Mayol, Xavier Deupi, Mercedes Campillo, Arnau Cordomí

المصدر: PLoS ONE, Vol 13, Iss 7, p e0199843 (2018)

مصطلحات موضوعية: Medicine, Science

Relation: http://europepmc.org/articles/PMC6059404?pdf=render; https://doaj.org/toc/1932-6203; https://doaj.org/article/4d2df72786e54bdaa66f5f592626f074

الاتاحة: https://doi.org/10.1371/journal.pone.0199843
https://doaj.org/article/4d2df72786e54bdaa66f5f592626f074

المؤلفون: Constantina Chalikiopoulou, José Carlos Gómez-Tamayo, Theodora Katsila

المصدر: Mass Spectrometry for Metabolomics ISBN: 9781071626986

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::0e24fba1166021877576c727e2af5f19
https://doi.org/10.1007/978-1-0716-2699-3_7

المؤلفون: Constantina, Chalikiopoulou, José Carlos, Gómez-Tamayo, Theodora, Katsila

المصدر: Methods in molecular biology (Clifton, N.J.). 2571

مصطلحات موضوعية: Biomedical Research, Phenotype, Research Design, Humans, Metabolomics, Biomarkers

URL الوصول: https://explore.openaire.eu/search/publication?articleId=pmid________::861a7a45275bf9848d726b30b978b00c
https://pubmed.ncbi.nlm.nih.gov/36152151

المؤلفون: Manuel Pastor, José Carlos Gómez-Tamayo, Javier Saiz, B.A. Trenor-Gomis, J. Llopis-Lorente, K. Kopanska

المصدر: Toxicology Letters. 350:S64-S65

مصطلحات موضوعية: Estimation, Drug, business.industry, In silico, media_common.quotation_subject, Medicine, General Medicine, Computational biology, Toxicology, business, media_common

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::e1f739b0332e2d7ad4adbb2ad2d60281
https://doi.org/10.1016/s0378-4274(21)00399-4

المؤلفون: José Carlos Gómez-Tamayo, Iker Reina, Mercedes Campillo, Mireia Olivella, Adrián García-Recio, Arnau Cordomí

المصدر: NAR Genomics and Bioinformatics
Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona

مصطلحات موضوعية: AcademicSubjects/SCI01140, Genetics, 0303 health sciences, Web server, AcademicSubjects/SCI01060, Application Notes, AcademicSubjects/SCI00030, 030302 biochemistry & molecular biology, Transmembrane Region, Biology, AcademicSubjects/SCI01180, computer.software_genre, Pathogenesis, 03 medical and health sciences, Membrane protein, Missense mutation, AcademicSubjects/SCI00980, computer, 030304 developmental biology

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::99c771ef35a8936a7092db87e64a0a6a
https://doi.org/10.1093/nargab/lqab008

المؤلفون: Frank Bringezu, José Carlos Gómez-Tamayo, Manuel Pastor

المصدر: Computational Toxicology

مصطلحات موضوعية: Computer science, Health, Toxicology and Mutagenesis, Cellular homeostasis, 010501 environmental sciences, Mitochondrion, Toxicology, Machine learning, computer.software_genre, 01 natural sciences, 03 medical and health sciences, Classifier (linguistics), medicine, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, Training set, Mitochondrial toxicity, business.industry, medicine.disease, 3. Good health, Computer Science Applications, Ensemble prediction model, Ensemble prediction, Gradient boosting, Artificial intelligence, business, computer, Function (biology), Intracellular organelles, Random forest

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a18d7e3afbb3e64fc4c6df858212c722
http://hdl.handle.net/10230/52488

المؤلفون: Oscar Mendez Lucio (10722798), José Carlos Gómez-Tamayo (10670241), Mazen Ahmad (10672772), Ehecatl Antonio del Rio-Chanona (10672770), Jörg Kurt Wegner (8780135)

مصطلحات موضوعية: Cheminformatics, Computational Chemistry, Biologically Active Molecules, Biomolecular Modelling and Design, Artificial inteligence, Docking approaches, Neural Networks (NN), structure based drug design, geometric deep learning

Relation: https://figshare.com/articles/dataset/CASF-2016_dataset_prepared_with_Schrodinger_for_DeepDock_evaluation/16598621

الاتاحة: https://doi.org/10.6084/m9.figshare.16598621.v1

المؤلفون: Oscar Mendez Lucio (10722798), José Carlos Gómez-Tamayo (10670241), Mazen Ahmad (10672772), Ehecatl Antonio del Rio-Chanona (10672770), Jörg Kurt Wegner (8780135)

مصطلحات موضوعية: Cheminformatics, Computational Chemistry, Biologically Active Molecules, Biomolecular Modelling and Design, artificial intelligence, Docking approaches, Neural Networks (NN), structure based drug design, geometric deep learning

Relation: https://figshare.com/articles/dataset/DeepDock_training_dataset_curated_with_Schrodinger/16598648

الاتاحة: https://doi.org/10.6084/m9.figshare.16598648.v1

المؤلفون: Johanna K. S. Tiemann, George Khelashvili, Brian Medel-Lacruz, Ramon Guixà-González, Alejandro Varela-Rial, José Carlos Gómez-Tamayo, Marta Filizola, Dorota Latek, Gianni De Fabritiis, David Aranda-García, Juan Manuel Ramírez-Anguita, Santiago Ríos, Davide Provasi, David E. Gloriam, Jana Selent, Minos-Timotheos Matsoukas, Toni Giorgino, Ferran Sanz, Jon Kapla, Silvana Vasile, Slawomir Filipek, Xavier Deupi, Adrián Morales-Pastor, Przemyslaw Miszta, Àngel Puyol González, Mireia Jiménez-Rosés, Harel Weinstein, Peter Kolb, Agnieszka Sztyler, Nathalie Worp, Maria Marti-Solano, Arnau Cordomí, Ulrich Zachariae, Ismael Rodríguez-Espigares, Pierre Matricon, Ivan R. Torrecillas, Tomasz Maciej Stepniewski, Eduardo Mayol, Gáspár Pándy-Szekeres, Peter W. Hildebrand, Mireia Olivella, Mariona Torrens-Fontanals, Hugo Gutiérrez-de-Terán, Laura Pérez-Benito, Jens Carlsson, Willem Jespers, Jessica Sallander

المصدر: Nature Methods. 17:861-862

مصطلحات موضوعية: Published Erratum, Protein database, Cell Biology, Computational biology, Biology, Molecular Biology, Biochemistry, Membrane biophysics, Biotechnology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::3068198597dedfe387324ef53f9b005b
https://doi.org/10.1038/s41592-020-0928-3

المؤلفون: Adrián Garcia-Recio, José Carlos Gómez-Tamayo, Iker Reina, Mercedes Campillo, Arnau Cordomí, Mireia Olivella

مصطلحات موضوعية: Pathogenesis, Web server, Membrane protein, Mutation (genetic algorithm), Mutation database, Missense mutation, Computational biology, Transmembrane Region, Biology, computer.software_genre, computer, DNA sequencing

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1f6ff2f56cb40b8197b3167233ca19ca

المؤلفون: Ismael Rodríguez-Espigares, Mariona Torrens-Fontanals, Johanna K.S. Tiemann, David Aranda-García, Juan Manuel Ramírez-Anguita, Tomasz Maciej Stepniewski, Nathalie Worp, Alejandro Varela-Rial, Adrián Morales-Pastor, Brian Medel Lacruz, Gáspár Pándy-Szekeres, Eduardo Mayol, Toni Giorgino, Jens Carlsson, Xavier Deupi, Slawomir Filipek, Marta Filizola, José Carlos Gómez-Tamayo, Angel Gonzalez, Hugo Gutierrez-de-Teran, Mireia Jimenez, Willem Jespers, Jon Kapla, George Khelashvili, Peter Kolb, Dorota Latek, Maria Marti-Solano, Pierre Matricon, Minos-Timotheos Matsoukas, Przemyslaw Miszta, Mireia Olivella, Laura Perez-Benito, Davide Provasi, Santiago Ríos, Iván Rodríguez-Torrecillas, Jessica Sallander, Agnieszka Sztyler, Nagarajan Vaidehi, Silvana Vasile, Harel Weinstein, Ulrich Zachariae, Peter W. Hildebrand, Gianni De Fabritiis, Ferran Sanz, David E. Gloriam, Arnau Cordomi, Ramon Guixà-González, Jana Selent

المصدر: Nature Methods
bioRxiv

مصطلحات موضوعية: Flexibility (engineering), 0303 health sciences, Protein family, Computer science, media_common.quotation_subject, Context (language use), Data science, Visualization, 03 medical and health sciences, Molecular dynamics, 0302 clinical medicine, Resource (project management), Function (engineering), 030217 neurology & neurosurgery, 030304 developmental biology, media_common, G protein-coupled receptor

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d1c905a0f93c55dbafbbb30b26336a8

المؤلفون: Minos-Timotheos Matsoukas, David E. Gloriam, Ismael Rodríguez-Espigares, Agnieszka Sztyler, Davide Provasi, Arnau Cordomí, Peter Kolb, David Aranda-García, Toni Giorgino, Ferran Sanz, Mariona Torrens-Fontanals, Peter W. Hildebrand, Maria Marti-Solano, Mireia Olivella, Alejandro Varela-Rial, Gianni De Fabritiis, José Carlos Gómez-Tamayo, Laura Pérez-Benito, Tomasz Maciej Stepniewski, Eduardo Mayol, Silvana Vasile, Slawomir Filipek, Ulrich Zachariae, Jens Carlsson, Dorota Latek, Harel Weinstein, Gáspár Pándy-Szekeres, Przemyslaw Miszta, Willem Jespers, Nathalie Worp, Mireia Jiménez-Rosés, Juan Manuel Ramírez-Anguita, Marta Filizola, George Khelashvili, Angel Gonzalez, Brian Medel Lacruz, Pierre Matricon, Iván Rodríguez-Torrecillas, Xavier Deupi, Adrián Morales-Pastor, Jessica Sallander, Hugo Gutiérrez-de-Terán, Johanna K. S. Tiemann, Jana Selent, Jon Kapla, Ramon Guixà-González, Santiago Ríos

المصدر: Nature Methods
Nature methods (Online) 17 (2020): 777–787. doi:10.1038/s41592-020-0884-y
info:cnr-pdr/source/autori:Rodríguez-Espigares, Ismael; Torrens-Fontanals, Mariona; Tiemann, Johanna K.S.; Aranda-García, David; Ramírez-Anguita, Juan Manuel; Stepniewski, Tomasz Maciej; Worp, Nathalie; Varela-Rial, Alejandro; Morales-Pastor, Adrián; Medel-Lacruz, Brian; Pándy-Szekeres, Gáspár; Mayol, Eduardo; Giorgino, Toni; Carlsson, Jens; Deupi, Xavier; Filipek, Slawomir; Filizola, Marta; Gómez-Tamayo, José Carlos; Gonzalez, Angel; Gutiérrez-de-Terán, Hugo; Jiménez-Rosés, Mireia; Jespers, Willem; Kapla, Jon; Khelashvili, George; Kolb, Peter; Latek, Dorota; Marti-Solano, Maria; Matricon, Pierre; Matsoukas, Minos Timotheos; Miszta, Przemyslaw; Olivella, Mireia; Perez-Benito, Laura; Provasi, Davide; Ríos, Santiago; R. Torrecillas, Iván; Sallander, Jessica; Sztyler, Agnieszka; Vasile, Silvana; Weinstein, Harel; Zachariae, Ulrich; Hildebrand, Peter W.; De Fabritiis, Gianni; Sanz, Ferran; Gloriam, David E.; Cordomi, Arnau; Guixà-González, Ramon; Selent, Jana/titolo:GPCRmd uncovers the dynamics of the 3D-GPCRome/doi:10.1038%2Fs41592-020-0884-y/rivista:Nature methods (Online)/anno:2020/pagina_da:777/pagina_a:787/intervallo_pagine:777–787/volume:17

مصطلحات موضوعية: Models, Molecular, 0303 health sciences, model, business.industry, Computer science, Extramural, Protein Conformation, Protein database, Cell Biology, Molecular Dynamics Simulation, simulation, Biochemistry, Data science, molecular dynamics, Visualization, Receptors, G-Protein-Coupled, 03 medical and health sciences, Software, GPCR, Metabolome, business, Molecular Biology, 030304 developmental biology, Biotechnology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0cb6367e2808eb6eb81235f76f7853ad

المؤلفون: Eduardo Mayol, Daniel Fourmy, Leonardo Pardo, José Carlos Gómez-Tamayo, Mireia Olivella, Arnau Cordomí

المصدر: Protein Science. 25:1517-1524

مصطلحات موضوعية: 0301 basic medicine, chemistry.chemical_classification, Stereochemistry, Peripheral membrane protein, chemistry.chemical_element, Crystal structure, 010402 general chemistry, Sulfur containing, 01 natural sciences, Biochemistry, Sulfur, 0104 chemical sciences, Amino acid, 03 medical and health sciences, symbols.namesake, 030104 developmental biology, chemistry, Membrane protein, symbols, Side chain, van der Waals force, Molecular Biology

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_________::e2bd8ba86b5f14fb3d3939e324c2e4bf
https://doi.org/10.1002/pro.2955

المؤلفون: Katy Barreto-Valer, Leonardo Pardo, Jesús Jiménez-Barbero, Gianluigi Caltabiano, Ana Ardá, Gregorio Valencia, Veronica Gonzalez-Nunez, Mònica Rosa, Gemma Arsequell, Raquel E. Rodríguez, José Carlos Gómez-Tamayo

المصدر: ACS Medicinal Chemistry Letters. 6:872-876

مصطلحات موضوعية: inorganic chemicals, Steric effects, chemistry.chemical_classification, Halogen bond, Stereochemistry, Chemistry, Organic Chemistry, Halogenation, Peptide binding, Peptide, Biochemistry, Combinatorial chemistry, Drug Discovery, Halogen, Opioid peptide, G protein-coupled receptor

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ad7d68537b8a33f0e0597f729201706d
https://doi.org/10.1021/acsmedchemlett.5b00126

المؤلفون: Leonardo Pardo, Angel Gonzalez, José Carlos Gómez-Tamayo, Jean-Christophe Nebel, Cristina Izquierdo

المصدر: Dipòsit Digital de Documents de la UAB
Universitat Autònoma de Barcelona
PLoS Computational Biology
PLoS Computational Biology, Vol 14, Iss 1, p e1005945 (2018)

مصطلحات موضوعية: 0301 basic medicine, Sensory Receptors, Social Sciences, Cell Cycle Proteins, Molecular Dynamics, Ligands, Biochemistry, Receptors, G-Protein-Coupled, Database and Informatics Methods, chemistry.chemical_compound, Computational Chemistry, 0302 clinical medicine, Polyamines, Psychology, Amines, Receptor, lcsh:QH301-705.5, Zebrafish, Phylogeny, chemistry.chemical_classification, Ecology, Behavior, Animal, Organic Compounds, Eukaryota, Nuclear Proteins, Animal Models, Cell cycle proteins, Computer simulation, Amino acid, Molecular Docking Simulation, Smell, Chemistry, medicine.anatomical_structure, Experimental Organism Systems, Computational Theory and Mathematics, Osteichthyes, Modeling and Simulation, Physical Sciences, Vertebrates, Sensory Perception, Sequence Analysis, Research Article, Signal Transduction, Protein Binding, Multiple Alignment Calculation, Transmembrane Receptors, Bioinformatics, Diamines, Research and Analysis Methods, Biologia computacional, 03 medical and health sciences, Cellular and Molecular Neuroscience, Olfacte -- Animals, Biomolècules, Model Organisms, Olfactory Mucosa, Sequence Motif Analysis, Cadaverine, Computational Techniques, Genetics, medicine, Putrescine, Humans, Animals, Computer Simulation, Homology modeling, Molecular Biology, Ecology, Evolution, Behavior and Systematics, G protein-coupled receptor, Aspartic Acid, Organic Chemistry, Organisms, Chemical Compounds, Biology and Life Sciences, Proteins, Computational Biology, Cell Biology, Split-Decomposition Method, Fish, 030104 developmental biology, lcsh:Biology (General), chemistry, Docking (molecular), G Protein Coupled Receptors, Sequence Alignment, Olfactory epithelium, 030217 neurology & neurosurgery, Neuroscience

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::812a045a1b583198d3e56cdd2e152d1c
https://ddd.uab.cat/record/187855