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3. Protein sequence-to-structure learning: Is this the end(-to-end revolution)?

Author

Laine, Elodie, Eismann, Stephan, Elofsson, Arne, and Grudinin, Sergei

Subjects
Quantitative Biology - Biomolecules, Computer Science - Machine Learning
Abstract

The potential of deep learning has been recognized in the protein structure prediction community for some time, and became indisputable after CASP13. In CASP14, deep learning has boosted the field to unanticipated levels reaching near-experimental accuracy. This success comes from advances transferred from other machine learning areas, as well as methods specifically designed to deal with protein sequences and structures, and their abstractions. Novel emerging approaches include (i) geometric learning, i.e. learning on representations such as graphs, 3D Voronoi tessellations, and point clouds; (ii) pre-trained protein language models leveraging attention; (iii) equivariant architectures preserving the symmetry of 3D space; (iv) use of large meta-genome databases; (v) combinations of protein representations; (vi) and finally truly end-to-end architectures, i.e. differentiable models starting from a sequence and returning a 3D structure. Here, we provide an overview and our opinion of the novel deep learning approaches developed in the last two years and widely used in CASP14.

Published
2021

8. Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import

Author

Nashed, Salomé, primary, El Barbry, Houssam, additional, Benchouaia, Médine, additional, Dijoux-Maréchal, Angélie, additional, Delaveau, Thierry, additional, Ruiz-Gutierrez, Nadia, additional, Gaulier, Lucie, additional, Tribouillard-Tanvier, Déborah, additional, Chevreux, Guillaume, additional, Le Crom, Stéphane, additional, Palancade, Benoit, additional, Devaux, Frédéric, additional, Laine, Elodie, additional, and Garcia, Mathilde, additional

Published
2023
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12. Supplementary Tables 1 - 7 and Figures 1 - 3 from Genetic Evidence of a Precisely Tuned Dysregulation in the Hypoxia Signaling Pathway during Oncogenesis

Author

Couvé, Sophie, primary, Ladroue, Charline, primary, Laine, Elodie, primary, Mahtouk, Karène, primary, Guégan, Justine, primary, Gad, Sophie, primary, Le Jeune, Hélène, primary, Le Gentil, Marion, primary, Nuel, Gregory, primary, Kim, William Y., primary, Lecomte, Bernard, primary, Pagès, Jean-Christophe, primary, Collin, Christine, primary, Lasne, Françoise, primary, Benusiglio, Patrick R., primary, Bressac-de Paillerets, Brigitte, primary, Feunteun, Jean, primary, Lazar, Vladimir, primary, Gimenez-Roqueplo, Anne-Paule, primary, Mazure, Nathalie M., primary, Dessen, Philippe, primary, Tchertanov, Luba, primary, Mole, David R., primary, Kaelin, William, primary, Ratcliffe, Peter, primary, Richard, Stéphane, primary, and Gardie, Betty, primary

Published
2023
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13. Data from Genetic Evidence of a Precisely Tuned Dysregulation in the Hypoxia Signaling Pathway during Oncogenesis

Author

Couvé, Sophie, primary, Ladroue, Charline, primary, Laine, Elodie, primary, Mahtouk, Karène, primary, Guégan, Justine, primary, Gad, Sophie, primary, Le Jeune, Hélène, primary, Le Gentil, Marion, primary, Nuel, Gregory, primary, Kim, William Y., primary, Lecomte, Bernard, primary, Pagès, Jean-Christophe, primary, Collin, Christine, primary, Lasne, Françoise, primary, Benusiglio, Patrick R., primary, Bressac-de Paillerets, Brigitte, primary, Feunteun, Jean, primary, Lazar, Vladimir, primary, Gimenez-Roqueplo, Anne-Paule, primary, Mazure, Nathalie M., primary, Dessen, Philippe, primary, Tchertanov, Luba, primary, Mole, David R., primary, Kaelin, William, primary, Ratcliffe, Peter, primary, Richard, Stéphane, primary, and Gardie, Betty, primary

Published
2023
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14. Supplementary Data from Genetic Evidence of a Precisely Tuned Dysregulation in the Hypoxia Signaling Pathway during Oncogenesis

Author

Couvé, Sophie, primary, Ladroue, Charline, primary, Laine, Elodie, primary, Mahtouk, Karène, primary, Guégan, Justine, primary, Gad, Sophie, primary, Le Jeune, Hélène, primary, Le Gentil, Marion, primary, Nuel, Gregory, primary, Kim, William Y., primary, Lecomte, Bernard, primary, Pagès, Jean-Christophe, primary, Collin, Christine, primary, Lasne, Françoise, primary, Benusiglio, Patrick R., primary, Bressac-de Paillerets, Brigitte, primary, Feunteun, Jean, primary, Lazar, Vladimir, primary, Gimenez-Roqueplo, Anne-Paule, primary, Mazure, Nathalie M., primary, Dessen, Philippe, primary, Tchertanov, Luba, primary, Mole, David R., primary, Kaelin, William, primary, Ratcliffe, Peter, primary, Richard, Stéphane, primary, and Gardie, Betty, primary

Published
2023
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19. Identification of Protein Interaction Partners from Shape Complementarity Molecular Cross-Docking

Author

Laine, Elodie, Carbone, Alessandra, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Petrosino, Alfredo, editor, Maddalena, Lucia, editor, and Pala, Pietro, editor

Published
2013
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21. Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import.

Author

Nashed, Salome, primary, El Barbry, Houssam, additional, Benchouaia, Medine, additional, Dijoux-Marechal, Angelie, additional, Ruiz Gutierrez, Nadia, additional, Gaulier, Lucie, additional, Chevreux, Guillaume, additional, Le Crom, Stephane, additional, Palancade, Benoit, additional, Devaux, Frederic, additional, Laine, Elodie, additional, and Garcia, Mathilde, additional

Published
2022
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24. Deep Local Analysis deconstructs protein–protein interfaces and accurately estimates binding affinity changes upon mutation.

Author

Behbahani, Yasser Mohseni, Laine, Elodie, and Carbone, Alessandra

Subjects
*PROTEIN structure prediction, *DEEP learning, *PEARSON correlation (Statistics), *PROTEIN structure, *SOURCE code
Abstract

Motivation The spectacular recent advances in protein and protein complex structure prediction hold promise for reconstructing interactomes at large-scale and residue resolution. Beyond determining the 3D arrangement of interacting partners, modeling approaches should be able to unravel the impact of sequence variations on the strength of the association. Results In this work, we report on Deep Local Analysis, a novel and efficient deep learning framework that relies on a strikingly simple deconstruction of protein interfaces into small locally oriented residue-centered cubes and on 3D convolutions recognizing patterns within cubes. Merely based on the two cubes associated with the wild-type and the mutant residues, DLA accurately estimates the binding affinity change for the associated complexes. It achieves a Pearson correlation coefficient of 0.735 on about 400 mutations on unseen complexes. Its generalization capability on blind datasets of complexes is higher than the state-of-the-art methods. We show that taking into account the evolutionary constraints on residues contributes to predictions. We also discuss the influence of conformational variability on performance. Beyond the predictive power on the effects of mutations, DLA is a general framework for transferring the knowledge gained from the available non-redundant set of complex protein structures to various tasks. For instance, given a single partially masked cube, it recovers the identity and physicochemical class of the central residue. Given an ensemble of cubes representing an interface, it predicts the function of the complex. Availability and implementation Source code and models are available at http://gitlab.lcqb.upmc.fr/DLA/DLA.git. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment

Author

Kryshtafovych, Andriy, Moult, John, Billings, Wendy, Della Corte, Dennis, Fidelis, Krzysztof, Kwon, Sohee, Olechnovič, Kliment, Seok, Chaok, Venclovas, Česlovas, Won, Jonghun, Adhikari, Badri, Adiyaman, Recep, Aguirre-Plans, Joaquim, Anishchenko, Ivan, Baek, Minkyung, Baker, David, Baldassarre, Frederico, Barger, Jacob, Bhattacharya, Sutanu, Bhattacharya, Debswapna, Bitton, Mor, Cao, Renzhi, Cheng, Jianlin, Christoffer, Charles, Czaplewski, Cezary, Elofsson, Arne, Faraggi, Eshel, Feig, Michael, Fernandez-Fuentes, Narcis, Grishin, Nick, Grudinin, Sergei, Guo, Zhiye, Hanazono, Yuya, Hassabis, Demis, Hedelius, Bryce, Heo, Lim, Hiranuma, Naozumi, Hunt, Cassandra, Igashov, Ilia, Ishida, Takashi, Jernigan, Robert, Jones, David, Jumper, John, Kadukova, Maria, Kandathil, Shaun, Keasar, Chen, Kihara, Daisuke, Kinch, Lisa, Kiyota, Yasuomi, Kloczkowski, Andrzje, Kohli, Pushmeet, Kogut, Mateusz, Laine, Elodie, Lilley, Cade, Liu, Jian, Liwo, Adam, Lubecka, Emilia, Mondal, Arup, Morris, Connor, Mcguffin, Liam, Molina, Alexis, Nakamura, Tsukasa, Oliva, Baldo, Perez, Alberto, Pozzati, Gabriele, Sarkar, Daipayan, Sato, Rin, Schwede, Torsten, Shrestha, Bikash, Sidi, Tomer, Studer, Gabriel, Shuvo, Md Hossain, Takeda-Shitaka, Mayuko, Takei, Yuma, Terashi, Genki, Tomii, Kentaro, Tsuchiya, Yuko, Tunyasuvunakool, Kathryn, Waliner, Björn, Wu, Tianqi, Xu, Jinbo, Yamamori, Yu, Zhang, Chengxin, Zhang, Yang, Zheng, Wei, University of California [Davis] (UC Davis), University of California (UC), Institute for Bioscience and Biotechnology Research [Rockville, MD, États-Unis] (IBBR), University of Maryland [College Park], University of Maryland System-University of Maryland System, Brigham Young University (BYU), Seoul National University [Seoul] (SNU), Vilnius University [Vilnius], University of Missouri [St. Louis], University of Missouri System, University of Reading (UOR), Universitat Pompeu Fabra [Barcelona] (UPF), Biorobotics Lab (University of Washington), University of Washington [Seattle], Royal Institute of Technology [Stockholm] (KTH ), Auburn University (AU), Ben-Gurion University of the Negev (BGU), Pacific Lutheran University [Tacoma] (PLU), University of Missouri [Columbia] (Mizzou), Purdue University [West Lafayette], University of Gdańsk (UG), Stockholm University, Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Michigan State University [East Lansing], Michigan State University System, Aberystwyth University, University of Texas Southwestern Medical Center [Dallas], Données, Apprentissage et Optimisation (DAO), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), National Institutes for Quantum and Radiological Science and Technology (QST), DeepMind [London], DeepMind Technologies, Moscow Institute of Physics and Technology [Moscow] (MIPT), Tokyo Institute of Technology [Tokyo] (TITECH), Iowa State University (ISU), University College of London [London] (UCL), Kitasato University, Ohio State University [Columbus] (OSU), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Florida [Gainesville] (UF), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Tohoku University [Sendai], University of Basel (Unibas), National Institute of Advanced Industrial Science and Technology (AIST), Linköping University (LIU), Toyota Technological Institute at Chicago [Chicago] (TTIC), University of Michigan [Ann Arbor], University of Michigan System, University of California, University of Maryland [Baltimore], Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), and Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )

Subjects
Models, Molecular, 2019-20 coronavirus outbreak, Research groups, Protein Conformation, Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Model accuracy, Genome, Viral, computer.software_genre, Biochemistry, SARS‐CoV‐2, Viroporin Proteins, Domain (software engineering), Viral Proteins, 03 medical and health sciences, Protein Domains, Structural Biology, EMA, Humans, CASP, Molecular Biology, Research Articles, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, COVID, 0303 health sciences, SARS-CoV-2, 030302 biochemistry & molecular biology, COVID-19, Protein structure prediction, Model quality, Critical assessment, Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Research Article
Abstract

International audience; Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

Published
2021

32. FUNCTIONAL PROTEIN SITES DECIPHEREDBY EVOLUTION AND STRUCTURAL DYNAMICS

Author

Laine, Elodie, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université , UPMC, Jacques Chomilier, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Laine, Elodie

Subjects
évolution des protéines, dynamique des protéine, interactions protéiques, Protein interaction, [SDV]Life Sciences [q-bio], épissage alternatif, mutations, [SDV] Life Sciences [q-bio], alternative splicing, protein dynamics, mutation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], protein evolution, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Published
2020

37. Deep Local Analysis evaluates protein docking conformations with locally oriented cubes.

Author

Behbahani, Yasser Mohseni, Crouzet, Simon, Laine, Elodie, and Carbone, Alessandra

Subjects
PROTEIN conformation, SIGNAL recognition particle receptor, MOLECULAR docking, PROTEIN structure prediction, PROTEIN analysis, CUBES
Abstract

Motivation With the recent advances in protein 3D structure prediction, protein interactions are becoming more central than ever before. Here, we address the problem of determining how proteins interact with one another. More specifically, we investigate the possibility of discriminating near-native protein complex conformations from incorrect ones by exploiting local environments around interfacial residues. Results Deep Local Analysis (DLA)-Ranker is a deep learning framework applying 3D convolutions to a set of locally oriented cubes representing the protein interface. It explicitly considers the local geometry of the interfacial residues along with their neighboring atoms and the regions of the interface with different solvent accessibility. We assessed its performance on three docking benchmarks made of half a million acceptable and incorrect conformations. We show that DLA-Ranker successfully identifies near-native conformations from ensembles generated by molecular docking. It surpasses or competes with other deep learning-based scoring functions. We also showcase its usefulness to discover alternative interfaces. Availability and implementation http://gitlab.lcqb.upmc.fr/dla-ranker/DLA-Ranker.git Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Published
2022
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39. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Danko, David, primary, Bezdan, Daniela, additional, Afshin, Evan E., additional, Ahsanuddin, Sofia, additional, Bhattacharya, Chandrima, additional, Butler, Daniel J., additional, Chng, Kern Rei, additional, Donnellan, Daisy, additional, Hecht, Jochen, additional, Jackson, Katelyn, additional, Kuchin, Katerina, additional, Karasikov, Mikhail, additional, Lyons, Abigail, additional, Mak, Lauren, additional, Meleshko, Dmitry, additional, Mustafa, Harun, additional, Mutai, Beth, additional, Neches, Russell Y., additional, Ng, Amanda, additional, Nikolayeva, Olga, additional, Nikolayeva, Tatyana, additional, Png, Eileen, additional, Ryon, Krista A., additional, Sanchez, Jorge L., additional, Shaaban, Heba, additional, Sierra, Maria A., additional, Thomas, Dominique, additional, Young, Ben, additional, Abudayyeh, Omar O., additional, Alicea, Josue, additional, Bhattacharyya, Malay, additional, Blekhman, Ran, additional, Castro-Nallar, Eduardo, additional, Cañas, Ana M., additional, Chatziefthimiou, Aspassia D., additional, Crawford, Robert W., additional, De Filippis, Francesca, additional, Deng, Youping, additional, Desnues, Christelle, additional, Dias-Neto, Emmanuel, additional, Dybwad, Marius, additional, Elhaik, Eran, additional, Ercolini, Danilo, additional, Frolova, Alina, additional, Gankin, Dennis, additional, Gootenberg, Jonathan S., additional, Graf, Alexandra B., additional, Green, David C., additional, Hajirasouliha, Iman, additional, Hastings, Jaden J.A., additional, Hernandez, Mark, additional, Iraola, Gregorio, additional, Jang, Soojin, additional, Kahles, Andre, additional, Kelly, Frank J., additional, Knights, Kaymisha, additional, Kyrpides, Nikos C., additional, Łabaj, Paweł P., additional, Lee, Patrick K.H., additional, Leung, Marcus H.Y., additional, Ljungdahl, Per O., additional, Mason-Buck, Gabriella, additional, McGrath, Ken, additional, Meydan, Cem, additional, Mongodin, Emmanuel F., additional, Moraes, Milton Ozorio, additional, Nagarajan, Niranjan, additional, Nieto-Caballero, Marina, additional, Noushmehr, Houtan, additional, Oliveira, Manuela, additional, Ossowski, Stephan, additional, Osuolale, Olayinka O., additional, Özcan, Orhan, additional, Paez-Espino, David, additional, Rascovan, Nicolás, additional, Richard, Hugues, additional, Rätsch, Gunnar, additional, Schriml, Lynn M., additional, Semmler, Torsten, additional, Sezerman, Osman U., additional, Shi, Leming, additional, Shi, Tieliu, additional, Siam, Rania, additional, Song, Le Huu, additional, Suzuki, Haruo, additional, Court, Denise Syndercombe, additional, Tighe, Scott W., additional, Tong, Xinzhao, additional, Udekwu, Klas I., additional, Ugalde, Juan A., additional, Valentine, Brandon, additional, Vassilev, Dimitar I., additional, Vayndorf, Elena M., additional, Velavan, Thirumalaisamy P., additional, Wu, Jun, additional, Zambrano, María M., additional, Zhu, Jifeng, additional, Zhu, Sibo, additional, Mason, Christopher E., additional, Abdullah, Natasha, additional, Abraao, Marcos, additional, Adel, Ait-hamlat, additional, Afaq, Muhammad, additional, Al-Quaddoomi, Faisal S., additional, Alam, Ireen, additional, Albuquerque, Gabriela E., additional, Alexiev, Alex, additional, Ali, Kalyn, additional, Alvarado-Arnez, Lucia E., additional, Aly, Sarh, additional, Amachee, Jennifer, additional, Amorim, Maria G., additional, Ampadu, Majelia, additional, Amran, Muhammad Al-Fath, additional, An, Nala, additional, Andrew, Watson, additional, Andrianjakarivony, Harilanto, additional, Angelov, Michael, additional, Antelo, Verónica, additional, Aquino, Catharine, additional, Aranguren, Álvaro, additional, Araujo, Luiza F., additional, Vasquez Arevalo, Hitler Francois, additional, Arevalo, Jenny, additional, Arnan, Carme, additional, Alvarado Arnez, Lucia Elena, additional, Arredondo, Fernanda, additional, Arthur, Matthew, additional, Asenjo, Freddy, additional, Aung, Thomas Saw, additional, Auvinet, Juliette, additional, Aventin, Nuria, additional, Ayaz, Sadaf, additional, Baburyan, Silva, additional, Bakere, Abd-Manaaf, additional, Bakhl, Katrin, additional, Bartelli, Thais F., additional, Batdelger, Erdenetsetseg, additional, Baudon, François, additional, Becher, Kevin, additional, Bello, Carla, additional, Benchouaia, Médine, additional, Benisty, Hannah, additional, Benoiston, Anne-Sophie, additional, Benson, Joseph, additional, Benítez, Diego, additional, Bernardes, Juliana, additional, Bertrand, Denis, additional, Beurmann, Silvia, additional, Bitard-Feildel, Tristan, additional, Bittner, Lucie, additional, Black, Christina, additional, Blanc, Guillaume, additional, Blyther, Brittany, additional, Bode, Toni, additional, Boeri, Julia, additional, Boldgiv, Bazartseren, additional, Bolzli, Kevin, additional, Bordigoni, Alexia, additional, Borrelli, Ciro, additional, Bouchard, Sonia, additional, Bouly, Jean-Pierre, additional, Boyd, Alicia, additional, Branco, Gabriela P., additional, Breschi, Alessandra, additional, Brindefalk, Björn, additional, Brion, Christian, additional, Briones, Alan, additional, Buczansla, Paulina, additional, Burke, Catherine M., additional, Burrell, Aszia, additional, Butova, Alina, additional, Buttar, Irvind, additional, Bynoe, Jalia, additional, Bönigk, Sven, additional, Bøifot, Kari O., additional, Caballero, Hiram, additional, Cai, Xiao Wen, additional, Calderon, Dayana, additional, Cantillo, Angela, additional, Carbajo, Miguel, additional, Carbone, Alessandra, additional, Cardenas, Anais, additional, Carrillo, Katerine, additional, Casalot, Laurie, additional, Castro, Sofia, additional, Castro, Ana V., additional, Castro, Astred, additional, Castro, Ana Valeria B., additional, Cawthorne, Simone, additional, Cedillo, Jonathan, additional, Chaker, Salama, additional, Chalangal, Jasna, additional, Chan, Allison, additional, Chasapi, Anastasia I., additional, Chatziefthimiou, Starr, additional, Chaudhuri, Sreya Ray, additional, Chavan, Akash Keluth, additional, Chavez, Francisco, additional, Chem, Gregory, additional, Chen, Xiaoqing, additional, Chen, Michelle, additional, Chen, Jenn-Wei, additional, Chernomoretz, Ariel, additional, Chettouh, Allaeddine, additional, Cheung, Daisy, additional, Chicas, Diana, additional, Chiu, Shirley, additional, Choudhry, Hira, additional, Chrispin, Carl, additional, Ciaramella, Kianna, additional, Cifuentes, Erika, additional, Cohen, Jake, additional, Coil, David A., additional, Collin, Sylvie, additional, Conger, Colleen, additional, Conte, Romain, additional, Corsi, Flavia, additional, Cossio, Cecilia N., additional, Costa, Ana F., additional, Cuebas, Delisia, additional, D’Alessandro, Bruno, additional, Dahlhausen, Katherine E., additional, Darling, Aaron E., additional, Das, Pujita, additional, Davenport, Lucinda B., additional, David, Laurent, additional, Davidson, Natalie R., additional, Dayama, Gargi, additional, Delmas, Stéphane, additional, Deng, Chris K., additional, Dequeker, Chloé, additional, Desert, Alexandre, additional, Devi, Monika, additional, Dezem, Felipe S., additional, Dias, Clara N., additional, Donahoe, Timothy Ryan, additional, Dorado, Sonia, additional, Dorsey, LaShonda, additional, Dotsenko, Valeriia, additional, Du, Steven, additional, Dutan, Alexandra, additional, Eady, Naya, additional, Eisen, Jonathan A., additional, Elaskandrany, Miar, additional, Epping, Lennard, additional, Escalera-Antezana, Juan P., additional, Ettinger, Cassie L., additional, Faiz, Iqra, additional, Fan, Luice, additional, Farhat, Nadine, additional, Faure, Emile, additional, Fauzi, Fazlina, additional, Feigin, Charlie, additional, Felice, Skye, additional, Ferreira, Laís Pereira, additional, Figueroa, Gabriel, additional, Fleiss, Aubin, additional, Flores, Denisse, additional, Velasco Flores, Jhovana L., additional, Fonseca, Marcos A.S., additional, Foox, Jonathan, additional, Forero, Juan Carlos, additional, Francis, Aaishah, additional, French, Kelly, additional, Fresia, Pablo, additional, Friedman, Jacob, additional, Fuentes, Jaime J., additional, Galipon, Josephine, additional, Garcia, Mathilde, additional, Garcia, Laura, additional, García, Catalina, additional, Geiger, Annie, additional, Gerner, Samuel M., additional, Ghose, Sonia L., additional, Giang, Dao Phuong, additional, Giménez, Matías, additional, Giovannelli, Donato, additional, Githae, Dedan, additional, Gkotzis, Spyridon, additional, Godoy, Liliana, additional, Goldman, Samantha, additional, Gonnet, Gaston H., additional, Gonzalez, Juana, additional, Gonzalez, Andrea, additional, Gonzalez-Poblete, Camila, additional, Gray, Andrew, additional, Gregory, Tranette, additional, Greselle, Charlotte, additional, Guasco, Sophie, additional, Guerra, Juan, additional, Gurianova, Nika, additional, Haehr, Wolfgang, additional, Halary, Sebastien, additional, Hartkopf, Felix, additional, Hawkins-Zafarnia, Arya, additional, Hazrin-Chong, Nur Hazlin, additional, Helfrich, Eric, additional, Hell, Eva, additional, Henry, Tamera, additional, Hernandez, Samuel, additional, Hernandez, Pilar Lopez, additional, Hess-Homeier, David, additional, Hittle, Lauren E., additional, Hoan, Nghiem Xuan, additional, Holik, Aliaksei, additional, Homma, Chiaki, additional, Hoxie, Irene, additional, Huber, Michael, additional, Humphries, Elizabeth, additional, Hyland, Stephanie, additional, Hässig, Andrea, additional, Häusler, Roland, additional, Hüsser, Nathalie, additional, Petit, Robert A., additional, Iderzorig, Badamnyambuu, additional, Igarashi, Mizuki, additional, Iqbal, Shaikh B., additional, Ishikawa, Shino, additional, Ishizuka, Sakura, additional, Islam, Sharah, additional, Islam, Riham, additional, Ito, Kohei, additional, Ito, Sota, additional, Ito, Takayuki, additional, Ivankovic, Tomislav, additional, Iwashiro, Tomoki, additional, Jackson, Sarah, additional, Jacobs, JoAnn, additional, James, Marisano, additional, Jaubert, Marianne, additional, Jerier, Marie-Laure, additional, Jiminez, Esmeralda, additional, Jinfessa, Ayantu, additional, De Jong, Ymke, additional, Joo, Hyun Woo, additional, Jospin, Guilllaume, additional, Kajita, Takema, additional, Ahmad Kassim, Affifah Saadah, additional, Kato, Nao, additional, Kaur, Amrit, additional, Kaur, Inderjit, additional, de Souza Gomes Kehdy, Fernanda, additional, Khadka, Vedbar S., additional, Khan, Shaira, additional, Khavari, Mahshid, additional, Ki, Michelle, additional, Kim, Gina, additional, Kim, Hyung Jun, additional, Kim, Sangwan, additional, King, Ryan J., additional, KoLoMonaco, Giuseppe, additional, Koag, Ellen, additional, Kobko-Litskevitch, Nadezhda, additional, Korshevniuk, Maryna, additional, Kozhar, Michael, additional, Krebs, Jonas, additional, Kubota, Nanami, additional, Kuklin, Andrii, additional, Kumar, Sheelta S., additional, Kwong, Rachel, additional, Kwong, Lawrence, additional, Lafontaine, Ingrid, additional, Lago, Juliana, additional, Lai, Tsoi Ying, additional, Laine, Elodie, additional, Laiola, Manolo, additional, Lakhneko, Olha, additional, Lamba, Isha, additional, de Lamotte, Gerardo, additional, Lannes, Romain, additional, De Lazzari, Eleonora, additional, Leahy, Madeline, additional, Lee, Hyunjung, additional, Lee, Yunmi, additional, Lee, Lucy, additional, Lemaire, Vincent, additional, Leong, Emily, additional, Lewandowska, Dagmara, additional, Li, Chenhao, additional, Liang, Weijun, additional, Lin, Moses, additional, Lisboa, Priscilla, additional, Litskevitch, Anna, additional, Liu, Eric Minwei, additional, Liu, Tracy, additional, Livia, Mayra Arauco, additional, Lo, Yui Him, additional, Losim, Sonia, additional, Loubens, Manon, additional, Lu, Jennifer, additional, Lykhenko, Olexandr, additional, Lysakova, Simona, additional, Mahmoud, Salah, additional, Majid, Sara Abdul, additional, Makogon, Natalka, additional, Maldonado, Denisse, additional, Mallari, Krizzy, additional, Malta, Tathiane M., additional, Mamun, Maliha, additional, Manoir, Dimitri, additional, Marchandon, German, additional, Marciniak, Natalia, additional, Marinovic, Sonia, additional, Marques, Brunna, additional, Mathews, Nicole, additional, Matsuzaki, Yuri, additional, Matthys, Vincent, additional, May, Madelyn, additional, McComb, Elias, additional, Meagher, Annabelle, additional, Melamed, Adiell, additional, Menary, Wayne, additional, Mendez, Katterinne N., additional, Mendez, Ambar, additional, Mendy, Irène Mauricette, additional, Meng, Irene, additional, Menon, Ajay, additional, Menor, Mark, additional, Meoded, Roy, additional, Merino, Nancy, additional, Miah, Karishma, additional, Mignotte, Mathilde, additional, Miketic, Tanja, additional, Miranda, Wilson, additional, Mitsios, Athena, additional, Miura, Ryusei, additional, Miyake, Kunihiko, additional, Moccia, Maria D., additional, Mohan, Natasha, additional, Mohsin, Mohammed, additional, Moitra, Karobi, additional, Moldes, Mauricio, additional, Molina, Laura, additional, Molinet, Jennifer, additional, Molomjamts, Orgil-Erdene, additional, Moniruzzaman, Eftar, additional, Moon, Sookwon, additional, de Oliveira Moraes, Isabelle, additional, Moreno, Mario, additional, Mosella, Maritza S., additional, Moser, Josef W., additional, Mozsary, Christopher, additional, Muehlbauer, Amanda L., additional, Muner, Oasima, additional, Munia, Muntaha, additional, Munim, Naimah, additional, Muscat, Maureen, additional, Mustac, Tatjana, additional, Muñoz, Cristina, additional, Nadalin, Francesca, additional, Naeem, Areeg, additional, Nagy-Szakal, Dorottya, additional, Nakagawa, Mayuko, additional, Narce, Ashanti, additional, Nasu, Masaki, additional, Navarrete, Irene González, additional, Naveed, Hiba, additional, Nazario, Bryan, additional, Nedunuri, Narasimha Rao, additional, Neff, Thomas, additional, Nesimi, Aida, additional, Ng, Wan Chiew, additional, Ng, Synti, additional, Nguyen, Gloria, additional, Ngwa, Elsy, additional, Nicolas, Agier, additional, Nicolas, Pierre, additional, Nika, Abdollahi, additional, Noorzi, Hosna, additional, Nosrati, Avigdor, additional, Nunes, Diana N., additional, O’Brien, Kathryn, additional, O’Hara, Niamh B., additional, Oken, Gabriella, additional, Olawoyin, Rantimi A., additional, Oliete, Javier Quilez, additional, Olmeda, Kiara, additional, Oluwadare, Tolulope, additional, Oluwadare, Itunu A., additional, Ordioni, Nils, additional, Orpilla, Jenessa, additional, Orrego, Jacqueline, additional, Ortega, Melissa, additional, Osma, Princess, additional, Osuolale, Israel O., additional, Osuolale, Oluwatosin M., additional, Ota, Mitsuki, additional, Oteri, Francesco, additional, Oto, Yuya, additional, Ounit, Rachid, additional, Ouzounis, Christos A., additional, Pakrashi, Subhamitra, additional, Paras, Rachel, additional, Pardo-Este, Coral, additional, Park, Young-Ja, additional, Pastuszek, Paulina, additional, Patel, Suraj, additional, Pathmanathan, Jananan, additional, Patrignani, Andrea, additional, Perez, Manuel, additional, Peros, Ante, additional, Persaud, Sabrina, additional, Peters, Anisia, additional, Phillips, Adam, additional, Pineda, Lisbeth, additional, Pizzi, Melissa P., additional, Plaku, Alma, additional, Plaku, Alketa, additional, Pompa-Hogan, Brianna, additional, Portilla, María Gabriela, additional, Posada, Leonardo, additional, Priestman, Max, additional, Prithiviraj, Bharath, additional, Priya, Sambhawa, additional, Pugdeethosal, Phanthira, additional, Pugh, Catherine E., additional, Pulatov, Benjamin, additional, Pupiec, Angelika, additional, Pyrshev, Kyrylo, additional, Qing, Tao, additional, Rahiel, Saher, additional, Rahmatulloev, Savlatjon, additional, Rajendran, Kannan, additional, Ramcharan, Aneisa, additional, Ramirez-Rojas, Adan, additional, Rana, Shahryar, additional, Ratnanandan, Prashanthi, additional, Read, Timothy D., additional, Rehrauer, Hubert, additional, Richer, Renee, additional, Rivera, Alexis, additional, Rivera, Michelle, additional, Robertiello, Alessandro, additional, Robinson, Courtney, additional, Rodríguez, Paula, additional, Rojas, Nayra Aguilar, additional, Roldán, Paul, additional, Rosario, Anyelic, additional, Roth, Sandra, additional, Ruiz, Maria, additional, Boja Ruiz, Stephen Eduard, additional, Russell, Kaitlan, additional, Rybak, Mariia, additional, Sabedot, Thais S., additional, Sabina, Mahfuza, additional, Saito, Ikuto, additional, Saito, Yoshitaka, additional, Malca Salas, Gustavo Adolfo, additional, Salazar, Cecilia, additional, San, Kaung Myat, additional, Sanchez, Jorge, additional, Sanchir, Khaliun, additional, Sankar, Ryan, additional, de Souza Santos, Paulo Thiago, additional, Saravi, Zulena, additional, Sasaki, Kai, additional, Sato, Yuma, additional, Sato, Masaki, additional, Sato, Seisuke, additional, Sato, Ryo, additional, Sato, Kaisei, additional, Sayara, Nowshin, additional, Schaaf, Steffen, additional, Schacher, Oli, additional, Schinke, Anna-Lena M., additional, Schlapbach, Ralph, additional, Schori, Christian, additional, Schriml, Jason R., additional, Segato, Felipe, additional, Sepulveda, Felipe, additional, Serpa, Marianna S., additional, De Sessions, Paola F., additional, Severyn, Juan C., additional, Shakil, Maheen, additional, Shalaby, Sarah, additional, Shari, Aliyah, additional, Shim, Hyenah, additional, Shirahata, Hikaru, additional, Shiwa, Yuh, additional, Da Silva, Ophélie, additional, Silva, Jordana M., additional, Simon, Gwenola, additional, Singh, Shaleni K., additional, Sluzek, Kasia, additional, Smith, Rebecca, additional, So, Eunice, additional, Andreu Somavilla, Núria, additional, Sonohara, Yuya, additional, Rufino de Sousa, Nuno, additional, Souza, Camila, additional, Sperry, Jason, additional, Sprinsky, Nicolas, additional, Stark, Stefan G., additional, La Storia, Antonietta, additional, Suganuma, Kiyoshi, additional, Suliman, Hamood, additional, Sullivan, Jill, additional, Supie, Arif Asyraf Md, additional, Suzuki, Chisato, additional, Takagi, Sora, additional, Takahara, Fumie, additional, Takahashi, Naoya, additional, Takahashi, Kou, additional, Takeda, Tomoki, additional, Takenaka, Isabella K., additional, Tanaka, Soma, additional, Tang, Anyi, additional, Man Tang, Yuk, additional, Tarcitano, Emilio, additional, Tassinari, Andrea, additional, Taye, Mahdi, additional, Terrero, Alexis, additional, Thambiraja, Eunice, additional, Thiébaut, Antonin, additional, Thomas, Sade, additional, Thomas, Andrew M., additional, Togashi, Yuto, additional, Togashi, Takumi, additional, Tomaselli, Anna, additional, Tomita, Masaru, additional, Tomita, Itsuki, additional, Toth, Oliver, additional, Toussaint, Nora C., additional, Tran, Jennifer M., additional, Truong, Catalina, additional, Tsonev, Stefan I., additional, Tsuda, Kazutoshi, additional, Tsurumaki, Takafumi, additional, Tuz, Michelle, additional, Tymoshenko, Yelyzaveta, additional, Urgiles, Carmen, additional, Usui, Mariko, additional, Vacant, Sophie, additional, Vann, Laura E., additional, Velter, Fabienne, additional, Ventorino, Valeria, additional, Vera-Wolf, Patricia, additional, Vicedomini, Riccardo, additional, Suarez-Villamil, Michael A., additional, Vincent, Sierra, additional, Vivancos-Koopman, Renee, additional, Wan, Andrew, additional, Wang, Cindy, additional, Warashina, Tomoro, additional, Watanabe, Ayuki, additional, Weekes, Samuel, additional, Werner, Johannes, additional, Westfall, David, additional, Wieler, Lothar H., additional, Williams, Michelle, additional, Wolf, Silver A., additional, Wong, Brian, additional, Wong, Yan Ling, additional, Wong, Tyler, additional, Wright, Rasheena, additional, Wunderlin, Tina, additional, Yamanaka, Ryota, additional, Yang, Jingcheng, additional, Yano, Hirokazu, additional, Yeh, George C., additional, Yemets, Olena, additional, Yeskova, Tetiana, additional, Yoshikawa, Shusei, additional, Zafar, Laraib, additional, Zhang, Yang, additional, Zhang, Shu, additional, Zhang, Amy, additional, Zheng, Yuanting, additional, and Zubenko, Stas, additional

Published
2021
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48. ProfileView: multiple probabilistic models resolve protein families functional diversity

Author

Vicedomini, Riccardo, Bouly, Jean Pierre, Laine, Elodie, Falciatore, Angela, and Carbone, Alessandra

Abstract

Sequence functional classification has become a fundamental bottleneck to the understanding of the myriad of protein sequences accumulating in our databases due to the recent progress in genomics and metagenomics. The large diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of living organisms and for biotechnological applications. ProfileView is a novel computational method designed to functionally classify sets of homologous sequences. Its architecture strongly relies on the structure of biological data, and answers to the challenge of automatically partitioning datasets of protein sequences in pertinent subfamilies based on meaningful conservation patterns. It constructs a library of probabilistic models accurately representing the functional variability of protein families, and extracts biologically interpretable information from the classification process. It applies to protein families that are not necessarily large, nor conserved, whose homologs might be very divergent and for which functions should be discovered or characterised more precisely. As a proof of concept, we apply ProfileView to the Cryptochrome/Photolyase family (CPF) and to the WW domain family, two widespread classes of proteins showing a large variety of functions and high sequence divergence. Decades of experimental studies on these families, functionally characterizing sequences and highlighting constitutive motifs, allow us to validate the two functional organisations obtained with the ProfileView approach. In addition, the method allows to identify a distinct functional group for the CPF, likely corresponding to novel photoreceptors. Thus, ProfileView appears as a powerful tool to classify protein sequences by function, screen sequences towards the design of accurate functional testing experiments and, possibly, discover new functions of natural sequences. Software and data availability http://www.lcqb.upmc.fr/profileview/ A restrained access is momentarily set. Once the article is accepted, all information will be freely accessible.

Published
2019
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49. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Author

Agence Nationale de la Recherche (France), Cancer Research UK, European Commission, Medical Research Council (UK), National Institutes of Health (US), National Natural Science Foundation of China, National Research Foundation of Korea, National Science Foundation (US), Ministerio de Economía y Competitividad (España), Università degli Studi di Napoli PARTHENOPE, Wellcome Trust, Lensink, Marc F., Brysbaert, Guillaume, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphaël A. G., Gerguri, Tereza, Bates, Paul A., Laine, Elodie, Carbone, Alessandra, Grudinin, Sergei, Kong, Ren, Weng, Zhiping, Guest, Johnathan D., Gowthaman, Ragul, Pierce, Brian G., Xu, Xianjin, Duan, Rui, Qiu, Liming, Hou, Jie, Merideth, Benjamin Ryan, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Koukos, Panagiotis I., Roel-Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Schaarschmidt, Jörg, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li, Jiménez-García, Brian, Noort, Charlotte W. van, Honorato, Rodrigo V., Bonvin, A. M. J. J., Wodak, Shoshana J., Liu, Ran-Ran, Xu, Xi-Ming, Shi, Hang, Chang, Shan, Eisenstein, Miriam, Karczynska, Agnieszka, Czaplewski, Cezary, Emilia Lubecka, Emilia, Lipska, Agnieszka, Krupa, Paweł, Mozolewska, Magdalena, Golon, Łukasz, Samsonov, Sergey, Liwo, Adam, Crivelli, Silvia, Pagès, Guillaume, Karasikov, Mikhaill, Kadukova, Maria, Yan, Yumeng, Huang, Sheng-You, Rosell, Mireia, Rodríguez-Lumbreras, Luis A., Romero-Durana, Miguel, Díaz-Bueno, Lucía, Fernández-Recio, Juan, Christoffer, Charles, Terashi, Genki, Shin, Woong-Hee, Aderinwale, Tunde, Venkata Subraman, Sai Raghavendra Maddhuri, Kihara, Daisuke, Kozakov, Dima, Vajda, Sandor, Porter, Kathryn, Padhorny, Dzmitry, Desta, Israel, Beglov, Dmitri, Ignatov, Mikhail, Kotelnikov, Sergey, Moal, Iain H., Ritchie, David W., Chauvot de Beauchêne, Isaure, Maigret, Bernard, Devignes, Marie-Dominique, Ruiz Echartea, Maria E., Barradas-Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Cao, Yue, Shen, Yang, Baek, Minkyung, Park, Taeyong, Woo, Hyeonuk, Seok, Chaok, Braitbard, Merav, Bitton, Lirane, Scheidman-Duhovny, Dina, Dapkunas, Justas, Olechnovic, Kliment, Venclovas, Česlovas, Kundrotas, Petras J., Belkin, Saveliy, Chakravarty, Devlina, Badal, Varsha D., Vakser, Ilya A., Vreven, Thom, Vangaveti, Sweta, Borrman, Tyler, Agence Nationale de la Recherche (France), Cancer Research UK, European Commission, Medical Research Council (UK), National Institutes of Health (US), National Natural Science Foundation of China, National Research Foundation of Korea, National Science Foundation (US), Ministerio de Economía y Competitividad (España), Università degli Studi di Napoli PARTHENOPE, Wellcome Trust, Lensink, Marc F., Brysbaert, Guillaume, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphaël A. G., Gerguri, Tereza, Bates, Paul A., Laine, Elodie, Carbone, Alessandra, Grudinin, Sergei, Kong, Ren, Weng, Zhiping, Guest, Johnathan D., Gowthaman, Ragul, Pierce, Brian G., Xu, Xianjin, Duan, Rui, Qiu, Liming, Hou, Jie, Merideth, Benjamin Ryan, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Koukos, Panagiotis I., Roel-Touris, Jorge, Ambrosetti, Francesco, Geng, Cunliang, Schaarschmidt, Jörg, Trellet, Mikael E., Melquiond, Adrien S. J., Xue, Li, Jiménez-García, Brian, Noort, Charlotte W. van, Honorato, Rodrigo V., Bonvin, A. M. J. J., Wodak, Shoshana J., Liu, Ran-Ran, Xu, Xi-Ming, Shi, Hang, Chang, Shan, Eisenstein, Miriam, Karczynska, Agnieszka, Czaplewski, Cezary, Emilia Lubecka, Emilia, Lipska, Agnieszka, Krupa, Paweł, Mozolewska, Magdalena, Golon, Łukasz, Samsonov, Sergey, Liwo, Adam, Crivelli, Silvia, Pagès, Guillaume, Karasikov, Mikhaill, Kadukova, Maria, Yan, Yumeng, Huang, Sheng-You, Rosell, Mireia, Rodríguez-Lumbreras, Luis A., Romero-Durana, Miguel, Díaz-Bueno, Lucía, Fernández-Recio, Juan, Christoffer, Charles, Terashi, Genki, Shin, Woong-Hee, Aderinwale, Tunde, Venkata Subraman, Sai Raghavendra Maddhuri, Kihara, Daisuke, Kozakov, Dima, Vajda, Sandor, Porter, Kathryn, Padhorny, Dzmitry, Desta, Israel, Beglov, Dmitri, Ignatov, Mikhail, Kotelnikov, Sergey, Moal, Iain H., Ritchie, David W., Chauvot de Beauchêne, Isaure, Maigret, Bernard, Devignes, Marie-Dominique, Ruiz Echartea, Maria E., Barradas-Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Cao, Yue, Shen, Yang, Baek, Minkyung, Park, Taeyong, Woo, Hyeonuk, Seok, Chaok, Braitbard, Merav, Bitton, Lirane, Scheidman-Duhovny, Dina, Dapkunas, Justas, Olechnovic, Kliment, Venclovas, Česlovas, Kundrotas, Petras J., Belkin, Saveliy, Chakravarty, Devlina, Badal, Varsha D., Vakser, Ilya A., Vreven, Thom, Vangaveti, Sweta, and Borrman, Tyler

Abstract

We present the results for CAPRI Round 46, the third joint CASP‐CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo‐oligomers and 6 heterocomplexes. Eight of the homo‐oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher‐order assemblies. These were more difficult to model, as their prediction mainly involved “ab‐initio” docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance “gap” was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template‐based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.

Published
2019

50. Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Author

Lensink, Marc F., primary, Brysbaert, Guillaume, additional, Nadzirin, Nurul, additional, Velankar, Sameer, additional, Chaleil, Raphaël A. G., additional, Gerguri, Tereza, additional, Bates, Paul A., additional, Laine, Elodie, additional, Carbone, Alessandra, additional, Grudinin, Sergei, additional, Kong, Ren, additional, Liu, Ran‐Ran, additional, Xu, Xi‐Ming, additional, Shi, Hang, additional, Chang, Shan, additional, Eisenstein, Miriam, additional, Karczynska, Agnieszka, additional, Czaplewski, Cezary, additional, Lubecka, Emilia, additional, Lipska, Agnieszka, additional, Krupa, Paweł, additional, Mozolewska, Magdalena, additional, Golon, Łukasz, additional, Samsonov, Sergey, additional, Liwo, Adam, additional, Crivelli, Silvia, additional, Pagès, Guillaume, additional, Karasikov, Mikhail, additional, Kadukova, Maria, additional, Yan, Yumeng, additional, Huang, Sheng‐You, additional, Rosell, Mireia, additional, Rodríguez‐Lumbreras, Luis A., additional, Romero‐Durana, Miguel, additional, Díaz‐Bueno, Lucía, additional, Fernandez‐Recio, Juan, additional, Christoffer, Charles, additional, Terashi, Genki, additional, Shin, Woong‐Hee, additional, Aderinwale, Tunde, additional, Maddhuri Venkata Subraman, Sai Raghavendra, additional, Kihara, Daisuke, additional, Kozakov, Dima, additional, Vajda, Sandor, additional, Porter, Kathryn, additional, Padhorny, Dzmitry, additional, Desta, Israel, additional, Beglov, Dmitri, additional, Ignatov, Mikhail, additional, Kotelnikov, Sergey, additional, Moal, Iain H., additional, Ritchie, David W., additional, Chauvot de Beauchêne, Isaure, additional, Maigret, Bernard, additional, Devignes, Marie‐Dominique, additional, Ruiz Echartea, Maria E., additional, Barradas‐Bautista, Didier, additional, Cao, Zhen, additional, Cavallo, Luigi, additional, Oliva, Romina, additional, Cao, Yue, additional, Shen, Yang, additional, Baek, Minkyung, additional, Park, Taeyong, additional, Woo, Hyeonuk, additional, Seok, Chaok, additional, Braitbard, Merav, additional, Bitton, Lirane, additional, Scheidman‐Duhovny, Dina, additional, Dapkūnas, Justas, additional, Olechnovič, Kliment, additional, Venclovas, Česlovas, additional, Kundrotas, Petras J., additional, Belkin, Saveliy, additional, Chakravarty, Devlina, additional, Badal, Varsha D., additional, Vakser, Ilya A., additional, Vreven, Thom, additional, Vangaveti, Sweta, additional, Borrman, Tyler, additional, Weng, Zhiping, additional, Guest, Johnathan D., additional, Gowthaman, Ragul, additional, Pierce, Brian G., additional, Xu, Xianjin, additional, Duan, Rui, additional, Qiu, Liming, additional, Hou, Jie, additional, Ryan Merideth, Benjamin, additional, Ma, Zhiwei, additional, Cheng, Jianlin, additional, Zou, Xiaoqin, additional, Koukos, Panagiotis I., additional, Roel‐Touris, Jorge, additional, Ambrosetti, Francesco, additional, Geng, Cunliang, additional, Schaarschmidt, Jörg, additional, Trellet, Mikael E., additional, Melquiond, Adrien S. J., additional, Xue, Li, additional, Jiménez‐García, Brian, additional, van Noort, Charlotte W., additional, Honorato, Rodrigo V., additional, Bonvin, Alexandre M. J. J., additional, and Wodak, Shoshana J., additional

Published
2019
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