Search Results - Li C. Xue

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  1. 1
    HomPPI: a class of sequence homology based protein-protein interface prediction methods

    HomPPI: a class of sequence homology based protein-protein interface prediction methods by Li C. Xue, Drena Dobbs, Vasant Honavar

    Published 2011
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  2. 2
    Computational prediction of protein interfaces: A review of data driven methods

    Computational prediction of protein interfaces: A review of data driven methods by Li C. Xue, Drena Dobbs, Alexandre M. J. J. Bonvin, Vasant Honavar

    Published 2015
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  3. 3
    DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces

    DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces by Manon Réau, Nicolas Renaud, Li C. Xue, Alexandre M. J. J. Bonvin

    Published 2022
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  4. 4
    Finding the ΔΔ<i>G</i> spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

    Finding the ΔΔ<i>G</i> spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it? by Cunliang Geng, Li C. Xue, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin

    Published 2019
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  5. 5
    RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins

    RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins by Rasna R. Walia, Li C. Xue, Katherine Wilkins, Yasser EL‐Manzalawy, Drena Dobbs, Vasant Honavar

    Published 2014
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  6. 6
    PRODIGY: a web server for predicting the binding affinity of protein–protein complexes

    PRODIGY: a web server for predicting the binding affinity of protein–protein complexes by Li C. Xue, João Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone

    Published 2016
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  7. 7
    iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations

    iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations by Cunliang Geng, Anna Vangone, Gert E. Folkers, Li C. Xue, Alexandre M. J. J. Bonvin

    Published 2018
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  8. 8
    DeepRank: a deep learning framework for data mining 3D protein-protein interfaces

    DeepRank: a deep learning framework for data mining 3D protein-protein interfaces by Nicolas Renaud, Cunliang Geng, Sonja Georgievska, Francesco Ambrosetti, Lars Ridder, Dario F. Marzella, Manon Réau, Alexandre M. J. J. Bonvin, Li C. Xue

    Published 2021
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  9. 9
    PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes

    PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes by Dario F. Marzella, Farzaneh M. Parizi, Derek van Tilborg, Nicolas Renaud, Daan Sybrandi, Rafaella Buzatu, Daniel T. Rademaker, Peter A.C. ‘t Hoen, Li C. Xue

    Published 2022
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  10. 10
    Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

    Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment by Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen‐You Huang, Dina Schneidman‐Duhovny, Andrej Šali, Joan Segura, Narcís Fernández‐Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Émilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan‐Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie‐Dominique Devignes, Anisah W. Ghoorah, Mieczyslaw Torchala, Raphaël A. G. Chaleil, Paul A. Bates, Efrat Ben‐Zeev, Miriam Eisenstein, Surendra S. Negi, Zhiping Weng, Thom Vreven, Brian G. Pierce, Tyler Borrman, Jinchao Yu, Françoise Ochsenbein, Raphaël Guérois, Anna Vangone, João Rodrigues, Gydo van Zundert, Mehdi Nellen, Li C. Xue, Ezgi Karaca, Adrien S. J. Melquiond, Koen M. Visscher, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyungrae Kim, Amit Roy, Xusi Han, Juan Esquivel‐Rodríguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero‐Durana, Brian Jiménez‐García, Iain H. Moal, Juan Fernández‐Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sándor Vajda, Scott E. Mottarella, David R. Hall, Dmitri Beglov, Artem B. Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J. Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva

    Published 2016
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  11. 11
    Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

    Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment by Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil, Tereza Gerguri, Paul A. Bates, Élodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran‐Ran Liu, Ximing Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczyńska, Cezary Czaplewski, Emilia A. Lubecka, Agnieszka G. Lipska, Paweł Krupa, Magdalena A. Mozolewska, Łukasz Golon, Sergey A. Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng‐You Huang, Mireia Rosell, Luis Ángel Rodríguez-Lumbreras, Miguel Romero‐Durana, Lucía Díaz, Juan Fernández‐Recio, Charles Christoffer, Genki Terashi, Woong‐Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sándor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H. Moal, David W. Ritchie, Isaure Chauvot de Beauchêne, Bernard Maigret, Marie‐Dominique Devignes, Maria Elisa Ruiz Echartea, Didier Barradas‐Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman‐Duhovny, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Petras J. Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D. Badal, Ilya A. Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Zhiping Weng, Johnathan D. Guest, Ragul Gowthaman, Brian G. Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikaël Trellet, Adrien S. J. Melquiond, Li C. Xue

    Published 2019
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