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Journal of Biomolecular Structure and Dynamics Volume 32, 2014 - Issue 4
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Articles

mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

Sylvain LéonardINSERM UMR-S 665, DSIMB, 6, rue Alexandre Cabanel, F-75739, Paris, France.;Sorbonne Paris Cité, Univ Paris Diderot, UMR_S 665, F-75739, Paris, France.;Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.;Laboratoire d’excellence, GR-Ex, F-75739, Paris, France.
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Agnel Praveen JosephINSERM UMR-S 665, DSIMB, 6, rue Alexandre Cabanel, F-75739, Paris, France.;Sorbonne Paris Cité, Univ Paris Diderot, UMR_S 665, F-75739, Paris, France.;Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.;Laboratoire d’excellence, GR-Ex, F-75739, Paris, France.
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Narayanaswamy SrinivasanMolecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
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Jean-Christophe GellyINSERM UMR-S 665, DSIMB, 6, rue Alexandre Cabanel, F-75739, Paris, France.;Sorbonne Paris Cité, Univ Paris Diderot, UMR_S 665, F-75739, Paris, France.;Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.;Laboratoire d’excellence, GR-Ex, F-75739, Paris, France.
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Alexandre G. de BrevernINSERM UMR-S 665, DSIMB, 6, rue Alexandre Cabanel, F-75739, Paris, France.;Sorbonne Paris Cité, Univ Paris Diderot, UMR_S 665, F-75739, Paris, France.;Institut National de la Transfusion Sanguine (INTS), F-75739, Paris, France.;Laboratoire d’excellence, GR-Ex, F-75739, Paris, France.Correspondence[email protected]
Pages 661-668 | Received 09 Jan 2013, Accepted 14 Mar 2013, Published online: 10 May 2013

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Aravindan Arun Nadaradjane, Julien Diharce, Joseph Rebehmed, Frédéric Cadet, Fabrice Gardebien, Jean-Christophe Gelly, Catherine Etchebest & Alexandre G. de Brevern. (2023) Quality assessment of VHH models. Journal of Biomolecular Structure and Dynamics 41:22, pages 13287-13301.
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Tarun Jairaj Narwani, Pierrick Craveur, Nicolas K. Shinada, Aline Floch, Hubert Santuz, Akhila Melarkode Vattekatte, Narayanaswamy Srinivasan, Joseph Rebehmed, Jean-Christophe Gelly, Catherine Etchebest & Alexandre G. de Brevern. (2020) Discrete analyses of protein dynamics. Journal of Biomolecular Structure and Dynamics 38:10, pages 2988-3002.
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Agata Kranjc, Tarun Jairaj Narwani, Sophie S. Abby & Alexandre G. de Brevern. (2023) Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations. International Journal of Molecular Sciences 24:17, pages 13280.
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Diego Javier Zea, Elin Teppa & Cristina Marino-Buslje. 2023. Homology Modeling. Homology Modeling 83 100 .
Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed & Alexandre G. de Brevern. (2022) Shaking the β-Bulges. IEEE/ACM Transactions on Computational Biology and Bioinformatics 19:1, pages 14-18.
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Janan Sykes, Barbara R. Holland & Michael A. Charleston. (2020) Benchmarking Methods of Protein Structure Alignment. Journal of Molecular Evolution 88:7, pages 575-597.
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Alexandre G. de Brevern. (2020) Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. Biomolecules 10:7, pages 1080.
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Muthuvel Prasath Karuppasamy, Suresh Venkateswaran & Parthasarathy Subbiah. (2020) PDB-2-PBv3.0: An updated protein block database. Journal of Bioinformatics and Computational Biology 18:02, pages 2050009.
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Melarkode Vattekatte Akhila, Tarun Jairaj Narwani, Aline Floch, Mirjana Maljković, Soubika Bisoo, Nicolas K. Shinada, Agata Kranjc, Jean-Christophe Gelly, Narayanaswamy Srinivasan, Nenad Mitić & Alexandre G. de Brevern. (2020) A structural entropy index to analyse local conformations in intrinsically disordered proteins. Journal of Structural Biology 210:1, pages 107464.
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Alexei N. Nekrasov, Ludmila G. Alekseeva, Rudolf А. Pogosyan, Dmitry A. Dolgikh, M.P. Kirpichnikov, Alexandre G. de Brevern & Anastasia A. Anashkina. (2019) A minimum set of stable blocks for rational design of polypeptide chains. Biochimie 160, pages 88-92.
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Alexandre G. de Brevern, Aline Floch, Aurélie Barrault, Jennifer Martret, Gwellaouen Bodivit, Rachid Djoudi, France Pirenne & Christophe Tournamille. (2018) Alloimmunization risk associated with amino acid 223 substitution in the RhD protein: analysis in the light of molecular modeling. Transfusion 58:11, pages 2683-2692.
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Runze Dong, Zhenling Peng, Yang Zhang & Jianyi Yang. (2018) mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics 34:10, pages 1719-1725.
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Maroua Ben Amira, Robin Mom, David Lopez, Hatem Chaar, Ali Khouaja, Valérie Pujade-Renaud, Boris Fumanal, Aurélie Gousset-Dupont, Gisèle Bronner, Philippe Label, Jean-Louis Julien, Mohamed Ali Triki, Daniel Auguin & Jean-Stéphane Venisse. (2018) MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees. PLOS ONE 13:3, pages e0193760.
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Jonathan Barnoud, Hubert Santuz, Pierrick Craveur, Agnel Praveen Joseph, Vincent Jallu, Alexandre G. de Brevern & Pierre Poulain. (2017) PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks. PeerJ 5, pages e4013.
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Leslie Regad, Jean-Baptiste Chéron, Dhoha Triki, Caroline Senac, Delphine Flatters & Anne-Claude Camproux. (2017) Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight. PLOS ONE 12:8, pages e0182972.
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Lina Rozano, Muhammad Redha Abdullah Zawawi, Muhamad Aizuddin Ahmad & Indu Bala Jaganath. (2017) Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl Peptidase-IV Inhibitor . Advances in Bioinformatics 2017, pages 1-16.
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Floriane Noël, Alain Malpertuy & Alexandre G. de Brevern. (2016) Global analysis of VHHs framework regions with a structural alphabet. Biochimie 131, pages 11-19.
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Alessandro Pandini & Arianna Fornili. (2016) Using Local States To Drive the Sampling of Global Conformations in Proteins. Journal of Chemical Theory and Computation 12:3, pages 1368-1379.
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Pierrick Craveur, Agnel P. Joseph, Jeremy Esque, Tarun J. Narwani, Floriane Noël, Nicolas Shinada, Matthieu Goguet, Sylvain Leonard, Pierre Poulain, Olivier Bertrand, Guilhem Faure, Joseph Rebehmed, Amine Ghozlane, Lakshmipuram S. Swapna, Ramachandra M. Bhaskara, Jonathan Barnoud, Stéphane Téletchéa, Vincent Jallu, Jiri Cerny, Bohdan Schneider, Catherine Etchebest, Narayanaswamy Srinivasan, Jean-Christophe Gelly & Alexandre G. de Brevern. (2015) Protein flexibility in the light of structural alphabets. Frontiers in Molecular Biosciences 2.
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Gautam B. SinghGautam B. Singh. 2015. Fundamentals of Bioinformatics and Computational Biology. Fundamentals of Bioinformatics and Computational Biology 127 142 .
Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe & Adam Godzik. (2014) POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Research 42:W1, pages W240-W245.
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Eugenio Mattei, Gabriele Ausiello, Fabrizio Ferrè & Manuela Helmer-Citterich. (2014) A novel approach to represent and compare RNA secondary structures. Nucleic Acids Research 42:10, pages 6146-6157.
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