نتائج البحث - "Cournia, Zoe"

1

Academic Journal

Free energy landscape of the PI3Kα C-terminal activation

المؤلفون: Kotzampasi, Danai Maria, Papadourakis, Michail, Burke, John, Cournia, Zoe

مصطلحات موضوعية: PI3Kα, Cancer, Allostery, Molecular Dynamics, HDX-MS

Relation: https://doi.org/10.5281/zenodo.10610724; https://doi.org/10.5281/zenodo.13273642; oai:zenodo.org:13273642

الاتاحة: https://doi.org/10.5281/zenodo.13273642

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2

Academic Journal

Applications of Free-Energy Calculations to Biomolecular Processes. A Collection

المؤلفون: Cournia, Zoe, Chipot, Christophe

المساهمون: Academy of Athens, Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie - CNRS Chimie (INC-CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), University of Illinois at Urbana-Champaign Urbana (UIUC), University of Illinois System, University of Chicago

المصدر: ISSN: 1549-9596.

مصطلحات موضوعية: [CHIM.THER]Chemical Sciences/Medicinal Chemistry, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry

الاتاحة: https://hal.science/hal-04735622
https://hal.science/hal-04735622v1/document
https://hal.science/hal-04735622v1/file/Manuscript.pdf
https://doi.org/10.1021/acs.jcim.4c00349

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3

Academic Journal

Machine learning approaches in predicting allosteric sites

المؤلفون: Nerín-Fonz, Francho, Cournia, Zoe

المصدر: Current Opinion in Structural Biology, 85, 102774, (2024-02-13)

مصطلحات موضوعية: Allostery, Machine learning, Drug design, Protein binding sites

Relation: https://zenodo.org/communities/allodd-itn; https://doi.org/10.5281/zenodo.10658857; https://doi.org/10.5281/zenodo.10658858; oai:zenodo.org:10658858; https://doi.org/10.1016/j.sbi.2024.102774

الاتاحة: https://doi.org/10.5281/zenodo.10658858
https://doi.org/10.1016/j.sbi.2024.102774

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4

Academic Journal

Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators

المؤلفون: Diakogiannaki, Isidora, Papadourakis, Michail, Spyridaki, Vasileia, Cournia, Zoe, Koutselos, Andreas

المساهمون: H2020 Research Infrastructures, Bodossaki Foundation

المصدر: Journal of Chemical Information and Modeling ; volume 64, issue 13, page 5140-5150 ; ISSN 1549-9596 1549-960X

الاتاحة: http://dx.doi.org/10.1021/acs.jcim.3c01195
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01195

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5

Academic Journal

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

المؤلفون: Rizzi, Andrea, Jensen, Travis, Slochower, David R, Aldeghi, Matteo, Gapsys, Vytautas, Ntekoumes, Dimitris, Bosisio, Stefano, Papadourakis, Michail, Henriksen, Niel M, de Groot, Bert L, Cournia, Zoe, Dickson, Alex, Michel, Julien, Gilson, Michael K, Shirts, Michael R, Mobley, David L, Chodera, John D

المصدر: Journal of Computer-Aided Molecular Design. 34(5)

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/3x6032nq
https://escholarship.org/content/qt3x6032nq/qt3x6032nq.pdf

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6

Academic Journal

Alchemical Free Energy Calculations on Membrane-Associated Proteins

المؤلفون: Papadourakis, Michail, Sinenka, Hryhory, Matricon, Pierre, Hénin, Jérôme, Brannigan, Grace, Pérez-Benito, Laura, Pande, Vineet, van Vlijmen, Herman, de Graaf, Chris, Deflorian, Francesca, Tresadern, Gary, Cecchini, Marco, Cournia, Zoe

المصدر: Journal of Chemical Theory and Computation, 19(21), 7437–7458, (2023-10-30)

Relation: https://zenodo.org/communities/allodd-itn; https://doi.org/10.5281/zenodo.10066638; https://doi.org/10.5281/zenodo.10066639; oai:zenodo.org:10066639; https://doi.org/10.1021/acs.jctc.3c00365

الاتاحة: https://doi.org/10.5281/zenodo.10066639
https://doi.org/10.1021/acs.jctc.3c00365

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7

Academic Journal

A Perspective on the prospective use of AI in protein structure prediction ; Perspective sur l'utilisation prospective de l'IA dans la prédiction de la structure protéique

المؤلفون: Versini, Raphaelle, Sritharan, Sujith, Aykaç Fas, Burcu, Tubiana, Thibault, Aimeur, Sana Zineb, Henri, Julien, Erard, Marie, Nüsse, Oliver, Jessica, Andreani, Baaden, Marc, Fuchs, Patrick, Galochkina, Tatiana, Chatzigoulas, Alexios, Cournia, Zoe, Santuz, Hubert, Sacquin-Mora, Sophie, Taly, Antoine

المساهمون: Laboratoire de biochimie théorique Paris (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Physique (ICP), Institut de Chimie - CNRS Chimie (INC-CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris Sciences et Lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris Sciences et Lettres (PSL)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris Sciences et Lettres (PSL)-Institut de Chimie - CNRS Chimie (INC-CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS-PSL, Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine Paris (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre / Abymes Guadeloupe -Université des Antilles (UA)-Université Paris Cité (UPCité), National and Kapodistrian University of Athens (NKUA), ANR-19-CE11-0018,MITOFUSION,Structure, assemblage et propriétés biophysiques des mitofusines(2019), ANR-21-CE13-0016,DIVCON,Diviser et connecter: mise en place de la communication intercellulaire pendant la division cellulaire(2021), ANR-21-CE29-0013,SuperET,Production de superoxyde par transferts d'électrons transmembranaires(2021), ANR-21-CE45-0014,PIRATE,Pharmacophore Interactif grace à la Réalité AugmenTéE(2021), European Project: 956314,ALLODD

المصدر: ISSN: 1549-9596.

مصطلحات موضوعية: Alphafold2, Structure prediction, Machin Learning, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry

Relation: info:eu-repo/grantAgreement//956314/EU/Allostery in Drug Discovery/ALLODD

الاتاحة: https://hal.science/hal-04306436
https://hal.science/hal-04306436v1/document
https://hal.science/hal-04306436v1/file/JCIM_Perspective_prospective%20%281%29.pdf
https://doi.org/10.1021/acs.jcim.3c01361

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8

Academic Journal

Predicting protein-membrane interfaces using molecular simulations and ensemble machine learning

المؤلفون: Cournia, Zoe

المصدر: Biophysical Journal ; volume 122, issue 3, page 325a ; ISSN 0006-3495

الاتاحة: http://dx.doi.org/10.1016/j.bpj.2022.11.1819
https://api.elsevier.com/content/article/PII:S0006349522027357?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S0006349522027357?httpAccept=text/plain

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9

Academic Journal

Martini 3 force field parameters for protein lipidation post-translational modifications

المؤلفون: Koukos, Panagiotis I., Dehghani-Ghahnaviyeh, Sepehr, Velez-Vega, Camilo, Manchester, John, Tieleman, D. Peter, Duca, José S., Souza, Paulo C. T., Cournia, Zoe

المصدر: Journal of Chemical Theory and Computation, (2023-11-28)

Relation: https://doi.org/10.5281/zenodo.7849262; https://doi.org/10.5281/zenodo.10213934; oai:zenodo.org:10213934

الاتاحة: https://doi.org/10.5281/zenodo.10213934

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10

Academic Journal

Trajectory data for the publication 'Investigating the bioactive conformation of Angiotensin II using Markov State Modeling revisited with web-scale clustering'

المؤلفون: Cournia, Zoe, Christorou, Emmanouil, Leontiadou, Haris, Noé, Frank, Samios, Jannis, Emiris, Ioannis Z.

Relation: https://doi.org/10.5281/zenodo.5887612; https://doi.org/10.5281/zenodo.5887613; oai:zenodo.org:5887613

الاتاحة: https://doi.org/10.5281/zenodo.5887613

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11

Academic Journal

The orchestrated signaling by PI3Kα and PTEN at the membrane interface

المؤلفون: Kotzampasi, Danai Maria, Premeti, Kyriaki, Papafotika, Alexandra, Syropoulou, Vasiliki, Christoforidis, Savvas, Cournia, Zoe, Leondaritis, George

المصدر: Computational and Structural Biotechnology Journal, 20, 5607-5621, (2022-10-06)

مصطلحات موضوعية: PI3Ka, PTEN, Allostery, Membrane trafficking, Phosphoinositides, Membrane-binding

Relation: https://zenodo.org/communities/allodd-itn; https://doi.org/10.5281/zenodo.8425942; https://doi.org/10.5281/zenodo.8425943; oai:zenodo.org:8425943; https://doi.org/10.1016/j.csbj.2022.10.007

الاتاحة: https://doi.org/10.5281/zenodo.8425943
https://doi.org/10.1016/j.csbj.2022.10.007

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12

Academic Journal

Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering

المؤلفون: Christoforou, Emmanouil, Leontiadou, Hari, Noé, Frank, Samios, Jannis, Emiris, Ioannis Z., Cournia, Zoe

المساهمون: National and Kapodistrian University of Athens (NKUA), AlgebRe, geOmetrie, Modelisation et AlgoriTHmes (AROMATH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-National and Kapodistrian University of Athens (NKUA), Biomedical Research Foundation of the Academy of Athens (BRFAA), Freie Universität Berlin, Athena Research and Innovation Centre (ARC)

المصدر: ISSN: 1549-9618.

مصطلحات موضوعية: structural bioinformatics, simulation, molecular dynamics, clustering, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology

الاتاحة: https://hal.science/hal-03895590
https://hal.science/hal-03895590v1/document
https://hal.science/hal-03895590v1/file/EmirisChristoforouCourniaEtal2022open.pdf
https://doi.org/10.1021/acs.jctc.1c00881

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13

Academic Journal

Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning

المؤلفون: Chatzigoulas, Alexios, Cournia, Zoe

المساهمون: State Scholarships Foundation, Hellenic Foundation for Research and Innovation, National Infrastructures for Research and Technology

المصدر: Briefings in Bioinformatics ; volume 23, issue 2 ; ISSN 1467-5463 1477-4054

الاتاحة: http://dx.doi.org/10.1093/bib/bbab518
https://academic.oup.com/bib/article-pdf/23/2/bbab518/42804915/bbab518.pdf

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14

Academic Journal

DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design

المؤلفون: Chatzigoulas, Alexios, Cournia, Zoe

المساهمون: Cowen, Lenore, State Scholarships Foundation, Hellenic Foundation for Research and Innovation, Europe – NI4OS Europe”, Greek Research & Technology Network

المصدر: Bioinformatics ; volume 38, issue 24, page 5449-5451 ; ISSN 1367-4803 1367-4811

الاتاحة: https://doi.org/10.1093/bioinformatics/btac680
https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac680/47702942/btac680.pdf
https://academic.oup.com/bioinformatics/article-pdf/38/24/5449/47886926/btac680.pdf

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