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PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction

Gabriel Cretin , Tatiana Galochkina , Alexandre de Brevern , Jean-Christophe Gelly
International Journal of Molecular Sciences, 2021, 22 (16), pp.8831. ⟨10.3390/ijms22168831⟩
Article dans une revue hal-03822577v1
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Protein Peeling 3D: new tools for analyzing protein structures.

Jean-Christophe Gelly , Alexandre de Brevern
Bioinformatics, 2011, 27 (1), pp.132-3. ⟨10.1093/bioinformatics/btq610⟩
Article dans une revue inserm-00568165v1
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iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach

Guilhem Faure , Agnel Praveen Joseph , Pierrick Craveur , Tarun Narwani , Narayanaswamy Srinivasan , et al.
Source Code for Biology and Medicine, 2019, 14 (1), ⟨10.1186/s13029-019-0075-3⟩
Article dans une revue inserm-02913723v1
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Detection and architecture of small heat shock protein monomers.

Pierre Poulain , Jean-Christophe Gelly , Delphine Flatters
PLoS ONE, 2010, 5 (4), pp.e9990. ⟨10.1371/journal.pone.0009990⟩
Article dans une revue inserm-00474076v1

An ambiguity principle for assigning protein structural domains

Guillaume Postic , Yassine Ghouzam , Romain Chebrek , Jean-Christophe Gelly
Science Advances , 2017, 3 (1), ⟨10.1126/sciadv.1600552⟩
Article dans une revue hal-03822852v1
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Recent advances on polyproline II.

Tarun Jairaj Narwani , Hubert Santuz , Nicolas Shinada , Akhila Melarkode Vattekatte , Yassine Ghouzam , et al.
Amino Acids, 2017, 49 (4), pp.705-713. ⟨10.1007/s00726-017-2385-6⟩
Article dans une revue inserm-01573940v1
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A structural entropy index to analyse local conformations in intrinsically disordered proteins

Akhila Melarkode Vattekatte , Tarun Jairaj Narwani , Aline Floch , Mirjana Maljković , Soubika Bisoo , et al.
Journal of Structural Biology, 2020, 210 (1), pp.107464. ⟨10.1016/j.jsb.2020.107464⟩
Article dans une revue inserm-02907335v1
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Bioinformatic analysis of the protein/DNA interface.

Bohdan Schneider , Jirí Cerny , Daniel Svozil , Petr Cech , Jean-Christophe Gelly , et al.
Nucleic Acids Research, 2014, 42 (5), pp.3381-94. ⟨10.1093/nar/gkt1273⟩
Article dans une revue inserm-00926088v1
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In silico prediction of protein flexibility with local structure approach

Tarun J. Narwani , Catherine Etchebest , Pierrick Craveur , Sylvain Léonard , Joseph Rebehmed , et al.
Biochimie, 2019, 165, pp.150-155. ⟨10.1016/j.biochi.2019.07.025⟩
Article dans une revue inserm-02266143v1

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

Yassine Ghouzam , Guillaume Postic , Pierre-Edouard Guerin , Alexandre de Brevern , Jean-Christophe Gelly
Scientific Reports, 2016, 6 (1), pp.28268. ⟨10.1038/srep28268⟩
Article dans une revue hal-03822893v1

OREMPRO web server: orientation and assessment of atomistic and coarse-grained structures of membrane proteins

Guillaume Postic , Yassine Ghouzam , Jean-Christophe Gelly
Bioinformatics, 2016, 32 (16), pp.2548-2550. ⟨10.1093/bioinformatics/btw208⟩
Article dans une revue hal-03822907v1

Membrane positioning for high- and low-resolution protein structures through a binary classification approach

Guillaume Postic , Yassine Ghouzam , Vincent Guiraud , Jean-Christophe Gelly
Protein Engineering, Design and Selection, 2016, 29 (3), pp.87-92. ⟨10.1093/protein/gzv063⟩
Article dans une revue hal-03822914v1
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Discrete analyses of protein dynamics

Akhila Melarkode Vattekatte , Tarun Jairaj Narwani , Pierrick Craveur , Nicolas K Shinada , Aline Floch , et al.
Journal of Biomolecular Structure and Dynamics, 2019, pp.1-15. ⟨10.1080/07391102.2019.1650112⟩
Article dans une revue inserm-02266159v1

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

Chris Papadopoulos , Isabelle Callebaut , Jean-Christophe Gelly , Isabelle Hatin , Olivier Namy , et al.
Genome Research, 2021, 31 (12), pp.2303-2315. ⟨10.1101/gr.275638.121⟩
Article dans une revue hal-03822836v1

MEDUSA: Prediction of Protein Flexibility from Sequence

Yann Vander Meersche , Gabriel Cretin , Alexandre de Brevern , Jean-Christophe Gelly , Tatiana Galochkina
Journal of Molecular Biology, 2021, 433 (11), pp.166882. ⟨10.1016/j.jmb.2021.166882⟩
Article dans une revue hal-03822593v1
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iPBA: a tool for protein structure comparison using sequence alignment strategies.

Jean-Christophe Gelly , Agnel Praveen Joseph , Narayanaswamy Srinivasan , Alexandre de Brevern
Nucleic Acids Research, 2011, 39 (Web Server issue), pp.W18-23. ⟨10.1093/nar/gkr333⟩
Article dans une revue inserm-00646241v1
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mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet.

Sylvain Léonard , Agnel Praveen Joseph , Narayanaswamy Srinivasan , Jean-Christophe Gelly , Alexandre de Brevern
Journal of Biomolecular Structure and Dynamics, 2014, 32 (4), pp.661-8. ⟨10.1080/07391102.2013.787026⟩
Article dans une revue inserm-00926338v1
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Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.

Jean-Christophe Gelly , Alexandre de Brevern , Serge A. Hazout
Bioinformatics, 2006, 22 (2), pp.129-33. ⟨10.1093/bioinformatics/bti773⟩
Article dans une revue inserm-00133725v1
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Identification of a new regulation pathway of EGFR and E-cadherin dynamics

Véronique Proux-Gillardeaux , Tamara Advedissian , Charlotte Perin , Jean-Christophe Gelly , Mireille Viguier , et al.
Scientific Reports, 2021, 11, pp.22705. ⟨10.1038/s41598-021-02042-3⟩
Article dans une revue hal-03098373v1
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Selective constraint on human pre-mRNA splicing by protein structural properties.

Jean-Christophe Gelly , Hsuan-Yu Lin , Alexandre de Brevern , Trees-Juen Chuang , Feng-Chi Chen
Genome Biology and Evolution, 2012, 4 (9), pp.966-75. ⟨10.1093/gbe/evs071⟩
Article dans une revue inserm-00750397v1
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A short survey on protein blocks.

Agnel Joseph , Garima Agarwal , Swapnil Mahajan , Jean-Christophe Gelly , Lakshmipuram S. Swapna , et al.
Biophysical Reviews, 2010, 2 (3), pp.137-147. ⟨10.1007/s12551-010-0036-1⟩
Article dans une revue inserm-00512823v1
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Data set of intrinsically disordered proteins analysed at a local protein conformation level

Akhila Melarkode Vattekatte , Tarun Jairaj Narwani , Aline Floch , Mirjana Maljković , Soubika Bisoo , et al.
Data in Brief, 2020, 29, pp.105383. ⟨10.1016/j.dib.2020.105383⟩
Article dans une revue inserm-02907359v1

Insights into Comparative Modeling of VHH Domains

Akhila Melarkode Vattekatte , Frédéric Cadet , Jean-Christophe Gelly , Alexandre de Brevern
International Journal of Molecular Sciences, 2021, 22 (18), pp.9771. ⟨10.3390/ijms22189771⟩
Article dans une revue hal-03537422v1
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Assignment of PolyProline II Conformation and Analysis of Sequence - Structure Relationship.

Yohann Mansiaux , Agnel Praveen Joseph , Jean-Christophe Gelly , Alexandre de Brevern
PLoS ONE, 2011, 6 (3), pp.e18401. ⟨10.1371/journal.pone.0018401⟩
Article dans une revue inserm-00586725v1
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PredyFlexy: flexibility and local structure prediction from sequence.

Alexandre de Brevern , Aurélie Bornot , Pierrick Craveur , Catherine Etchebest , Jean-Christophe Gelly
Nucleic Acids Research, 2012, 40 (Web Server issue), pp.W317-22. ⟨10.1093/nar/gks482⟩
Article dans une revue inserm-00750270v1
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A bioinformatic web server to cut protein structures in terms of Protein Units.

Jean-Christophe Gelly , Alexandre de Brevern
Jaclyn E. Morris. Computer Science Research and the Internet, Nova Book Press, pp.169-183, 2011
Chapitre d'ouvrage inserm-00646177v1
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Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction

Akhila Melarkode Vattekatte , Nicolas Ken Shinada , Tarun J Narwani , Floriane Noël , Olivier Bertrand , et al.
PeerJ, 2020, 8, pp.e8408. ⟨10.7717/peerj.8408⟩
Article dans une revue inserm-02907323v1
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Protein Peeling 2: a web server to convert protein structures into series of protein units.

Jean-Christophe Gelly , Catherine Etchebest , Serge A. Hazout , Alexandre de Brevern
Nucleic Acids Research, 2006, 34 (Web Server issue), pp.W75-8. ⟨10.1093/nar/gkl292⟩
Article dans une revue inserm-00133731v1

SWORD2: hierarchical analysis of protein 3D structures

Gabriel Cretin , Tatiana Galochkina , Yann Vander Meersche , Alexandre G de Brevern , Guillaume Postic , et al.
Nucleic Acids Research, 2022, 50 (W1), pp.W732--W738. ⟨10.1093/nar/gkac370⟩
Article dans une revue hal-03738483v1