المؤلفون: Barradas Bautista, Didier

المساهمون: University/Department: Universitat de Barcelona. Facultat de Medicina

Thesis Advisors: Fernández-Recio, Juan, Gelpí Buchaca, Josep Lluís

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Proteïnes, Proteínas, Proteins, Interacció cel·lular, Interacción celular, Cell interaction, Ciències de la Salut

وصف الملف: application/pdf

URL الوصول: http://hdl.handle.net/10803/401708

المؤلفون: Lensink, Marc F., Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A., Giulini, Marco, Honorato, Rodrigo V., van Noort, Charlotte, Teixeira, Joao M. C., Bonvin, Alexandre M. J. J., Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj S., Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A., Ichiishi, Eichiro, Rodriguez-Lumbreras, Luis A., Fernandez-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J., Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng-You, Roel-Touris, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles W., Jain, Anika J., Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob C., Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Negi, Surendra S., Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rui, Cheung, Melyssa, Guest, Johnathan D., Lee, Jessica, Pierce, Brian G., Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Yin, Rujie, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Bojarski, Krzysztof K., Lubecka, Emilia A., Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Gieldon, Artur, Liwo, Adam, Samsonov, Sergey A., Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K., Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovic, Kliment, Valancauskas, Lukas, Dapkunas, Justas, Venclovas, Ceslovas, Wallner, Björn, 1975, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qui, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Wodak, Shoshana J.

المصدر: Proteins. 91(12):1658-1683

مصطلحات موضوعية: AlphaFold, blind prediction, CAPRI, CASP, deep learning, protein assemblies, protein complexes, protein-protein interaction

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-200076
https://liu.diva-portal.org/smash/get/diva2:1827625/FULLTEXT01.pdf

المؤلفون: Gabor, Attila, Tognetti, Marco, Driessen, Alice, Tanevski, Jovan, Guo, Baosen, Cao, Wencai, Shen, He, Yu, Thomas, Chung, Verena, Bodenmiller, Bernd, Saez‐Rodriguez, Julio, Prusokas, Augustinas, Prusokas, Alidivinas, Retkute, Renata, Rajasekar, Anand, Raman, Karthik, Sudhakar, Malvika, Rengaswamy, Raghunathan, Shih, Edward SC, Kim, Min‐jeong, Cho, Changje, Kim, Dohyang, Oh, Hyeju, Hwang, Jinseub, Jongtae, Kim, Nam, Yeongeun, Yoon, Sanghoo, Kwon, Taeyong, Lee, Kyeongjun, Chaudhary, Sarika, Sharma, Nehal, Bande, Shreya, Cankut Cubuk, Gao Gao fan zhu, Gundogdu, Pelin, Dopazo, Joaquin, Rian, Kinza, Loucera, Carlos, Falco, Matias M, Garrido‐Rodriguez, Martin, Peña‐Chilet, Maria, Chen, Huiyuan, Turu, Gabor, Hunyadi, Laszlo, Misak, Adam, Zhou, Lisheng, Jiang, Xiaoqing, Zhang, Pieta, Rai, Aakansha, Kutum, Rintu, Rana, Sadhna, Srinivasan, Rajgopal, Pradhan, Swatantra, Li, James, Bajic, Vladimir, Van Neste, Christophe, Barradas‐bautista, Didier, Albarade, Somayah Abdullah, Nikolskiy, Igor, Sinkala, Musalula, Tran, Duc, Nguyen, Hung, Nguyen, Tin, Wu, Alexander, DeMeo, Benjamin, Hie, Brian, Singh, Rohit, Liu, Jiwei, Chen, Xueer, Saiz, Leonor, Vilar, Jose MG, Qiu, Peng, Gosain, Akash, Dhall, Anjali, Bajaj, Dinesh, Kaur, Harpreet, Bagaria, Krishna, Chauhan, Mayank, Sharma, Neelam, Raghava, Gajendra, Patiyal, Sumeet, Hao, Jianye, Peng, Jiajie, Ning, Shangyi, Ma, Yi, Wei, Zhongyu, Aalto, Atte, Goncalves, Jorge, Mombaerts, Laurent, Dai, Xinnan, Zheng, Jie, Mundra, Piyushkumar, Xu, Fan, Wang, Jie, Kant Singh, Krishna, Lee, Mingyu

المصدر: Molecular Systems Biology. 17(10)

مصطلحات موضوعية: Cancer, Breast Cancer, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Breast Neoplasms, Female, Humans, Machine Learning, Proteins, Signal Transduction, cell signaling, crowdsourcing, mass cytometry, predictive modeling, single cell, Single Cell Signaling in Breast Cancer DREAM Consortium members, Biochemistry and Cell Biology, Other Biological Sciences, Bioinformatics

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/59c6b7df
https://escholarship.org/content/qt59c6b7df/qt59c6b7df.pdf

المؤلفون: Barradas-Bautista, Didier, Alvarado, Matías

مصطلحات موضوعية: Computer Science - Artificial Intelligence, Physics - Applied Physics, Physics - Data Analysis, Statistics and Probability

URL الوصول: http://arxiv.org/abs/1803.05983

المؤلفون: Schweke, Hugo, Xu, Qifang, Tauriello, Gerardo, Pantolini, Lorenzo, Schwede, Torsten, Cazals, Frédéric, Lhéritier, Alix, Fernandez-Recio, Juan, Rodríguez-Lumbreras, Luis Angel, Schueler-Furman, Ora, Varga, Julia K., Jiménez-García, Brian, Réau, Manon F., Bonvin, Alexandre M.J.J., Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Tubiana, Jérôme, Wolfson, Haim J., Oliva, Romina, Barradas-Bautista, Didier, Ricciardelli, Tiziana, Cavallo, Luigi, Venclovas, Česlovas, Olechnovič, Kliment, Guerois, Raphael, Andreani, Jessica, Martin, Juliette, Wang, Xiao, Terashi, Genki, Sarkar, Daipayan, Christoffer, Charles, Aderinwale, Tunde, Verburgt, Jacob, Kihara, Daisuke, Marchand, Anthony, Correia, Bruno E., Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Dey, Sucharita, Dunbrack, Roland L., Levy, Emmanuel D., Wodak, Shoshana J.

المساهمون: Sub NMR Spectroscopy, NMR Spectroscopy

مصطلحات موضوعية: crystal contacts, homodimers, potential energy, protein interactions, protein structure, Taverne, Biochemistry, Molecular Biology

وصف الملف: application/pdf

Relation: https://dspace.library.uu.nl/handle/1874/434203

الاتاحة: https://dspace.library.uu.nl/handle/1874/434203

المؤلفون: Barradas Bautista, Didier, Almajed, Ali, Oliva, Romina, Kalnis, Panos, Cavallo, Luigi

المساهمون: Kaust Visualization Lab, Core lab Division, King Abdullah University of Science and Technology (KAUST) , 23955-6900, Thuwal, Saudi Arabia, King Abdullah University of Science and Technology (KAUST) Kaust Extreme Computing Center, Computer, Electrical and Mathematical Science and Engineering Division, , 23955-6900, Thuwal, Saudi Arabia, King Abdullah University of Science and Technology (KAUST) Kaust Catalysis Center, Physical Sciences and Engineering Division, , 23955-6900, Thuwal, Saudi Arabia, Visualization, Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division, Extreme Computing Research Center, Chemical Science Program, KAUST Catalysis Center (KCC), Physical Science and Engineering (PSE) Division, KAUST Visualization Laboratory (KVL), University of Naples “Parthenope” Department of Sciences and Technologies, , I-80143, Naples, Italy

وصف الملف: application/pdf

Relation: Barradas-Bautista, D., Almajed, A., Oliva, R., Kalnis, P., & Cavallo, L. (2023). Improving classification of correct and incorrect protein-protein docking models by augmenting the training set. Bioinformatics Advances. https://doi.org/10.1093/bioadv/vbad012; Bioinformatics Advances; http://hdl.handle.net/10754/685235

الاتاحة: http://hdl.handle.net/10754/685235
https://doi.org/10.1093/bioadv/vbad012

المؤلفون: Jiménez-García, Brian, Roel-Touris, Jorge, Barradas Bautista, Didier

المساهمون: Kaust Visualization Lab, Core lab Division, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia., Visualization, KAUST Visualization Laboratory (KVL), Zymvol Biomodeling, Pau Claris 94 3B, 08010, Barcelona, Spain., Protein Design and Modeling Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028Barcelona, Spain.

وصف الملف: application/pdf; image/png

Relation: Jiménez-García, B., Roel-Touris, J., & Barradas-Bautista, D. (2023). The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad327; Nucleic acids research; http://hdl.handle.net/10754/691541

الاتاحة: http://hdl.handle.net/10754/691541
https://doi.org/10.1093/nar/gkad327

المؤلفون: Lensink, Marc, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul, Giulini, Marco, Honorato, Rodrigo Vargas, Noort, Charlotte van, Teixeira, João, Bonvin, Alexandre M.J.J., Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Carpio, Carlos Del, Ichiishi, Eichiro, Luis, Rodriguez-Lumbreras A, Fernández-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Shengyou, Roel, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles, Anika, Jain J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Surendra, Negi S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan, Lee, Jessica, Pierce, Brian, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Krzysztof, Bojarski K, Lubecka, Emilia, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Giełdoń, Artur, Liwo, Jozef, Samsonov, Sergey, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovič, Kliment, Valančauskas, Lukas, Dapkūnas, Justas, Venclovas, Ceslovas, Wallner, Björn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Shoshana, Wodak J

المساهمون: NMR Spectroscopy, Sub NMR Spectroscopy

وصف الملف: application/pdf

Relation: https://dspace.library.uu.nl/handle/1874/438081

الاتاحة: https://dspace.library.uu.nl/handle/1874/438081

المؤلفون: Moal, Iain H., Barradas-Bautista, Didier, Jimenez-Garcia, Brian, Torchala, Mieczyslaw, van der Velde, Arjan, Vreven, Thom, Weng, Zhiping, Bates, Paul A., Fernandez-Recio, Juan

المساهمون: Program in Bioinformatics and Integrative Biology

المصدر: Bioinformatics (Oxford, England) ; 33 ; 12 ; 1806-1813

مصطلحات موضوعية: IRaPPA, protein structure, information retrieval, Biochemistry, Bioinformatics, Biophysics, Computational Biology, Structural Biology

Relation: Link to Article in PubMed; https://doi.org/10.1093/bioinformatics/btx068; Bioinformatics (2017) 33 (12): 1806-1813. doi:10.1093/bioinformatics/btx068. Link to article on publisher's site; 1367-4803 (Linking); http://hdl.handle.net/20.500.14038/25817; https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1115&context=bioinformatics_pubs&unstamped=1; https://escholarship.umassmed.edu/bioinformatics_pubs/108; bioinformatics_pubs/108

الاتاحة: https://doi.org/10.1093/bioinformatics/btx068
https://hdl.handle.net/20.500.14038/25817
https://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=1115&context=bioinformatics_pubs&unstamped=1
https://escholarship.umassmed.edu/bioinformatics_pubs/108

المؤلفون: Lensink, Marc, Brysbaert, Guillaume, Mauri, Théo, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphael, Clarence, Tereza, Bates, Paul, Kong, Ren, Liu, Bin, Yang, Guangbo, Liu, Ming, Shi, Hang, Lu, Xufeng, Chang, Shan, Roy, Raj, Quadir, Farhan, Liu, Jian, Cheng, Jianlin, Antoniak, Anna, Czaplewski, Cezary, Giełdoń, Artur, Kogut, Mateusz, Lipska, Agnieszka, Liwo, Adam, Lubecka, Emilia, Maszota‐zieleniak, Martyna, Sieradzan, Adam, Ślusarz, Rafał, Wesołowski, Patryk, Zięba, Karolina, del Carpio Muñoz, Carlos, Ichiishi, Eiichiro, Harmalkar, Ameya, Gray, Jeffrey, Bonvin, Alexandre, Ambrosetti, Francesco, Vargas Honorato, Rodrigo, Jandova, Zuzana, Jiménez‐garcía, Brian, Koukos, Panagiotis, van Keulen, Siri, van Noort, Charlotte, Réau, Manon, Roel‐touris, Jorge, Kotelnikov, Sergei, Padhorny, Dzmitry, Porter, Kathryn, Alekseenko, Andrey, Ignatov, Mikhail, Desta, Israel, Ashizawa, Ryota, Sun, Zhuyezi, Ghani, Usman, Hashemi, Nasser, Vajda, Sandor, Kozakov, Dima, Rosell, Mireia, Rodríguez‐lumbreras, Luis, Fernandez‐recio, Juan, Karczynska, Agnieszka, Grudinin, Sergei, Yan, Yumeng, Li, Hao, Lin, Peicong, Huang, Sheng‐you, Christoffer, Charles, Terashi, Genki, Verburgt, Jacob, Sarkar, Daipayan, Aderinwale, Tunde, Wang, Xiao, Kihara, Daisuke, Nakamura, Tsukasa, Hanazono, Yuya, Gowthaman, Ragul, Guest, Johnathan, Yin, Rui, Taherzadeh, Ghazaleh, Pierce, Brian, Barradas‐bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Sun, Yuanfei, Zhu, Shaowen, Shen, Yang, Park, Taeyong, Woo, Hyeonuk, Yang, Jinsol, Kwon, Sohee, Won, Jonghun, Seok, Chaok, Kiyota, Yasuomi, Kobayashi, Shinpei, Harada, Yoshiki, Takeda‐shitaka, Mayuko, Kundrotas, Petras, Singh, Amar, Vakser, Ilya, Dapkūnas, Justas, Olechnovič, Kliment, Venclovas, Česlovas, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Wodak, Shoshana

المساهمون: Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute Hinxton (EMBL-EBI), EMBL Heidelberg, Biomolecular Modelling Laboratory London, The Francis Crick Institute London, Jiangsu University of Technology Changzhou, Department of Electrical Engineering and Computer Science Columbia (EECS), University of Missouri Columbia (Mizzou), University of Missouri System-University of Missouri System, Institute for Data Science and Informatics Columbia, University of Gdańsk (UG), Faculty of Electronics, Telecommunications and Informatics GUT Gdańsk (ETI), Gdańsk University of Technology (GUT), Medical University of Gdańsk, Graduate School of Medical Sciences Nagoya, Nagoya City University Nagoya, Japan, International University of Health and Welfare Hospital (IUHW Hospital), Department of Chemical and Biomolecular Engineering Baltimore, Johns Hopkins University (JHU), Bijvoet Center of Biomolecular Research Utrecht, Universiteit Utrecht / Utrecht University Utrecht, Stony Brook University SUNY (SBU), State University of New York (SUNY), Innopolis University, Boston University Boston (BU), Russian Academy of Sciences Moscow (RAS), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC-CNS), Universidad de La Rioja (UR), 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), Huazhong University of Science and Technology Wuhan (HUST), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Graduate School of Information Sciences Sendaï, Tohoku University Sendai, National Institutes for Quantum and Radiological Science and Technology (QST), University of Maryland Baltimore, King Abdullah University of Science and Technology Saudi Arabia (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, Texas A&M University Galveston, Seoul National University Seoul (SNU), Kitasato University, University of Kansas Lawrence (KU), Vilnius University Vilnius, University of Missouri System, VIB-VUB Center for Structural Biology Bruxelles, VIB Belgium, European Project: 675728,H2020,H2020-EINFRA-2015-1,BioExcel(2015), European Project: 823830,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures ,BioExcel-2(2019), European Project: 777536,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures,EOSC-hub(2018)

المصدر: ISSN: 0887-3585.

مصطلحات موضوعية: CAPRI, CASP, oligomeric state, blind prediction, protein-protein interaction, protein complexes, protein assemblies, template-based modeling, docking, protein docking, [SDV]Life Sciences [q-bio]

Relation: info:eu-repo/grantAgreement//675728/EU/Centre of Excellence for Biomolecular Research/BioExcel; info:eu-repo/grantAgreement//823830/EU/BioExcel Centre of Excellence for ComputationalBiomolecular Research/BioExcel-2; info:eu-repo/grantAgreement//777536/EU/Integrating and managing services for the European Open Science Cloud/EOSC-hub

الاتاحة: https://hal.science/hal-03448743
https://hal.science/hal-03448743v1/document
https://hal.science/hal-03448743v1/file/manuscript.pdf
https://doi.org/10.1002/prot.26222

المؤلفون: Lensink, Marc F., Brysbaert, Guillaume, Mauri, Théo, Nadzirin, Nurul, Velankar, Sameer, Chaleil, Raphael A.G., Clarence, Tereza, Bates, Paul A., Kong, Ren, Liu, Bin, Yang, Guangbo, Liu, Ming, Shi, Hang, Lu, Xufeng, Chang, Shan, Roy, Raj S., Quadir, Farhan, Liu, Jian, Cheng, Jianlin, Antoniak, Anna, Czaplewski, Cezary, Giełdoń, Artur, Kogut, Mateusz, Lipska, Agnieszka G., Liwo, Adam, Lubecka, Emilia A., Maszota-Zieleniak, Martyna, Sieradzan, Adam K., Ślusarz, Rafał, Wesołowski, Patryk A., Zięba, Karolina, Del Carpio Muñoz, Carlos A., Ichiishi, Eiichiro, Harmalkar, Ameya, Gray, Jeffrey J., Bonvin, Alexandre M.J.J., Ambrosetti, Francesco, Vargas Honorato, Rodrigo, Jandova, Zuzana, Jiménez-García, Brian, Koukos, Panagiotis I., Van Keulen, Siri, Van Noort, Charlotte W., Réau, Manon, Roel-Touris, Jorge, Kotelnikov, Sergei, Padhorny, Dzmitry, Porter, Kathryn A., Alekseenko, Andrey, Ignatov, Mikhail, Desta, Israel, Ashizawa, Ryota, Sun, Zhuyezi, Ghani, Usman, Hashemi, Nasser, Vajda, Sandor, Kozakov, Dima, Rosell, Mireia, Rodríguez-Lumbreras, Luis A., Fernandez-Recio, Juan, Karczynska, Agnieszka, Grudinin, Sergei, Yan, Yumeng, Li, Hao, Lin, Peicong, Huang, Sheng You, Christoffer, Charles, Terashi, Genki, Verburgt, Jacob, Sarkar, Daipayan, Aderinwale, Tunde, Wang, Xiao, Kihara, Daisuke, Nakamura, Tsukasa, Hanazono, Yuya, Gowthaman, Ragul, Guest, Johnathan D., Yin, Rui, Taherzadeh, Ghazaleh, Pierce, Brian G., Barradas-Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina, Sun, Yuanfei, Zhu, Shaowen, Shen, Yang, Park, Taeyong, Woo, Hyeonuk, Yang, Jinsol, Kwon, Sohee, Won, Jonghun, Seok, Chaok, Kiyota, Yasuomi, Kobayashi, Shinpei, Harada, Yoshiki, Takeda-Shitaka, Mayuko, Kundrotas, Petras J., Singh, Amar, Vakser, Ilya A., Dapkūnas, Justas, Olechnovič, Kliment, Venclovas, Česlovas, Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Wodak, Shoshana J.

المساهمون: Sub NMR Spectroscopy, Sub Overig UiLOTS, Sub Mathematics Education, NMR Spectroscopy

مصطلحات موضوعية: blind prediction, CAPRI, CASP, docking, oligomeric state, protein assemblies, protein complexes, protein docking, protein–protein interaction, template-based modeling, Taverne, Structural Biology, Biochemistry, Molecular Biology

وصف الملف: application/pdf

Relation: https://dspace.library.uu.nl/handle/1874/418962

الاتاحة: https://dspace.library.uu.nl/handle/1874/418962

المؤلفون: Barradas Bautista, Didier, Cao, Zhen, Vangone, Anna, Oliva, Romina, Cavallo, Luigi

المساهمون: KAUST Catalysis Center (KCC), Chemical Science Program, Physical Science and Engineering (PSE) Division, Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Munich,Large Molecule Research, Nonnenwald 2, 82377, Penzberg, Germany, Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy

وصف الملف: application/pdf

Relation: Barradas-Bautista, D., Cao, Z., Vangone, A., Oliva, R., & Cavallo, L. (2021). A Random Forest Classifier for Protein-Protein Docking Models. Bioinformatics Advances. doi:10.1093/bioadv/vbab042; Bioinformatics Advances; http://hdl.handle.net/10754/669803

الاتاحة: http://hdl.handle.net/10754/669803
https://doi.org/10.1093/bioadv/vbab042
https://doi.org/10.1101/2021.06.23.449420

المؤلفون: Barradas Bautista, Didier, Cao, Zhen, Cavallo, Luigi, Oliva, Romina

المساهمون: KAUST Catalysis Center (KCC), Physical Science and Engineering (PSE) Division, Chemical Science Program, Department of Sciences and Technologies, University of Naples “Parthenope”, Centro Direzionale - Isola C4, 80143, Naples, Italy.

وصف الملف: application/pdf

Relation: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03600-8; Barradas-Bautista, D., Cao, Z., Cavallo, L., & Oliva, R. (2020). The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses. BMC Bioinformatics, 21(S8). doi:10.1186/s12859-020-03600-8; S8; BMC Bioinformatics; http://hdl.handle.net/10754/665269; 21

الاتاحة: http://hdl.handle.net/10754/665269
https://doi.org/10.1186/s12859-020-03600-8

المؤلفون: Barradas Bautista, Didier

المساهمون: KAUST Catalysis Center (KCC), Physical Science and Engineering (PSE) Division

مصطلحات موضوعية: Machine learning, Deep learning, Random Forest, Malaria, DREAM Challenge

وصف الملف: application/pdf

Relation: https://zenodo.org/record/4018883; Barradas-Bautista, D. (2020). Random Forest and Deep Learning Performance on the Malaria DREAM Sub Challenge One. Zenodo. https://doi.org/10.5281/ZENODO.4018883; http://hdl.handle.net/10754/668555

الاتاحة: http://hdl.handle.net/10754/668555
https://doi.org/10.5281/zenodo.4018883

المؤلفون: Barradas-Bautista, Didier, Rosell, Mireia, Pallara, Chiara, Fernández-Recio, Juan

المساهمون: Barcelona Supercomputing Center

مصطلحات موضوعية: Àrees temàtiques de la UPC::Ciències de la salut, Protein-protein interactions, Biomedical and health research, Protein–protein interactions, Complex structure, Computational docking, Interface prediction, Hot-spot residues, Drug discovery, Edgetic effect, Pathological mutations, Proteïnes--Investigació

وصف الملف: 46 p.

Relation: https://www.sciencedirect.com/science/article/pii/S1876162317300433; info:eu-repo/grantAgreement/MINECO/PE2013-2016/BIO2016-79960-R; Barradas-Bautista, D. [et al.]. Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems. A: Advances in Protein Chemistry and Structural Biology. "Protein-Protein Interactions in Human Disease, Part A". Academic Press, 2018, p. 203-249.; http://hdl.handle.net/2117/115854

الاتاحة: http://hdl.handle.net/2117/115854
https://doi.org/10.1016/bs.apcsb.2017.06.003

المؤلفون: Lensink, Marc F, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A, Giulini, Marco, Honorato, Rodrigo V, van Noort, Charlotte, Teixeira, Joao M C, Bonvin, Alexandre M J J, Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj S, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A, Ichiishi, Eichiro, Rodriguez-Lumbreras, Luis A, Fernandez-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng-You, Roel-Touris, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles W, Jain, Anika J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob C, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Negi, Surendra S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan D, Lee, Jessica, Pierce, Brian G, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Bojarski, Krzysztof K, Lubecka, Emilia A, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Gieldon, Artur, Liwo, Adam, Samsonov, Sergey A, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovic, Kliment, Valancauskas, Lukas, Dapkunas, Justas, Venclovas, Ceslovas, Wallner, Bjorn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qui, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Wodak, Shoshana J

المصدر: Proteins: Structure, Function and Genetics vol.91 (2023) nr.12 p.1658-1683 [ISSN 0887-3585]

مصطلحات الفهرس: AlphaFold, CAPRI, CASP, blind prediction, deep learning, protein assemblies, protein complexes, protein-protein interaction, Article

URL: https://research-portal.uu.nl/en/publications/de688c10-88fd-42c2-bddb-e99e9ab98a51
https://dspace.library.uu.nl/bitstream/handle/1874/434472/Proteins_-_2023_-_Lensink_-_Impact_of_AlphaFold_on_structure_prediction_of_protein_complexes_The_CASP15_CAPRI_experiment.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/434472/Proteins_-_2023_-_Lensink_-_Impact_of_AlphaFold_on_structure_prediction_of_protein_complexes_The_CASP15_CAPRI_experiment.pdf?sequence=1

المؤلفون: Sub NMR Spectroscopy, NMR Spectroscopy, Lensink, Marc F, Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A, Giulini, Marco, Honorato, Rodrigo V, van Noort, Charlotte, Teixeira, Joao M C, Bonvin, Alexandre M J J, Kong, Ren, Shi, Hang, Lu, Xufeng, Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj S, Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A, Ichiishi, Eichiro, Rodriguez-Lumbreras, Luis A, Fernandez-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J, Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng-You, Roel-Touris, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles W, Jain, Anika J, Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob C, Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Negi, Surendra S, Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rujie, Cheung, Melyssa, Guest, Johnathan D, Lee, Jessica, Pierce, Brian G, Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Bojarski, Krzysztof K, Lubecka, Emilia A, Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Gieldon, Artur, Liwo, Adam, Samsonov, Sergey A, Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K, Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovic, Kliment, Valancauskas, Lukas, Dapkunas, Justas, Venclovas, Ceslovas, Wallner, Bjorn, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qui, Liming, Xu, Xianjin, Zou, Xiaoqin, Velankar, Sameer, Wodak, Shoshana J

URL: https://doi.org/10.1002/prot.26609
http://hdl.handle.net/1874/434472
https://dspace.library.uu.nl/handle/1874/434472
http://www.scopus.com/inward/record.url?scp=85175465612&partnerID=8YFLogxK
0887-3585
Proteins: Structure, Function and Genetics
91
12
1658
1683

المؤلفون: Sub NMR Spectroscopy, NMR Spectroscopy, Schweke, Hugo, Xu, Qifang, Tauriello, Gerardo, Pantolini, Lorenzo, Schwede, Torsten, Cazals, Frédéric, Lhéritier, Alix, Fernandez-Recio, Juan, Rodríguez-Lumbreras, Luis Angel, Schueler-Furman, Ora, Varga, Julia K., Jiménez-García, Brian, Réau, Manon F., Bonvin, Alexandre M.J.J., Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Tubiana, Jérôme, Wolfson, Haim J., Oliva, Romina, Barradas-Bautista, Didier, Ricciardelli, Tiziana, Cavallo, Luigi, Venclovas, Česlovas, Olechnovič, Kliment, Guerois, Raphael, Andreani, Jessica, Martin, Juliette, Wang, Xiao, Terashi, Genki, Sarkar, Daipayan, Christoffer, Charles, Aderinwale, Tunde, Verburgt, Jacob, Kihara, Daisuke, Marchand, Anthony, Correia, Bruno E., Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Dey, Sucharita, Dunbrack, Roland L., Levy, Emmanuel D., Wodak, Shoshana J.

URL: https://doi.org/10.1002/pmic.202200323
http://hdl.handle.net/1874/434203
http://www.scopus.com/inward/record.url?scp=85162927714&partnerID=8YFLogxK
1615-9853
Proteomics
23
17
2200323

المؤلفون: Francis Crick Institute, Cancer Research UK, Medical Research Council (UK), Wellcome Trust, European Commission, National Science Foundation (US), National Institutes of Health (US), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Johns Hopkins University, National Natural Science Foundation of China, EMBO, Generalitat de Catalunya, Purdue University, National Science Centre (Poland), University of Warsaw, Research Council of Lithuania, Knut and Alice Wallenberg Foundation, Swedish Research Council, Lensink, Marc F., Brysbaert, Guillaume, Raouraoua, Nessim, Bates, Paul A., Giulini, Marco, Honorato, Rodrigo V., van Noort, Charlotte, Teixeira, Joao M. C., Bonvin, Alexandre M. J. J., Kong, Ren, Shi, Hang, Samsonov, Sergey A., Slusarz, Rafal, Zieba, Karolina, Sieradzan, Adam K., Czaplewski, Cezary, Kobayashi, Shinpei, Miyakawa, Yuta, Kiyota, Yasuomi, Takeda-Shitaka, Mayuko, Olechnovic, Kliment, Wallner, Bjorn, Valancauskas, Lukas, Dapkunas, Justas, Venclovas, Ceslovas, Yang, Lin, Hou, Chengyu, He, Xiaodong, Guo, Shuai, Jiang, Shenda, Ma, Xiaoliang, Duan, Rui, Qui, Liming, Xu, Xianjin, Lu, Xufeng, Zou, Xiaoqin, Velankar, Sameer, Wodak, Shoshana J., Chang, Shan, Liu, Jian, Guo, Zhiye, Chen, Xiao, Morehead, Alex, Roy, Raj S., Wu, Tianqi, Giri, Nabin, Quadir, Farhan, Chen, Chen, Cheng, Jianlin, Del Carpio, Carlos A., Ichiishi, Eichiro, Rodríguez-Lumbreras, Luis A., Fernández-Recio, Juan, Harmalkar, Ameya, Chu, Lee-Shin, Canner, Sam, Smanta, Rituparna, Gray, Jeffrey J., Li, Hao, Lin, Peicong, He, Jiahua, Tao, Huanyu, Huang, Sheng-You, Roel-Touris, Jorge, Jimenez-Garcia, Brian, Christoffer, Charles W., Jain, Anika J., Kagaya, Yuki, Kannan, Harini, Nakamura, Tsukasa, Terashi, Genki, Verburgt, Jacob C., Zhang, Yuanyuan, Zhang, Zicong, Fujuta, Hayato, Sekijima, Masakazu, Kihara, Daisuke, Khan, Omeir, Kotelnikov, Sergei, Ghani, Usman, Padhorny, Dzmitry, Beglov, Dmitri, Vajda, Sandor, Kozakov, Dima, Negi, Surendra S., Ricciardelli, Tiziana, Barradas-Bautista, Didier, Cao, Zhen, Chawla, Mohit, Cavallo, Luigi, Oliva, Romina, Yin, Rui, Cheung, Melyssa, Guest, Johnathan D., Lee, Jessica, Pierce, Brian G., Shor, Ben, Cohen, Tomer, Halfon, Matan, Schneidman-Duhovny, Dina, Zhu, Shaowen, Yin, Rujie, Sun, Yuanfei, Shen, Yang, Maszota-Zieleniak, Martyna, Bojarski, Krzysztof K., Lubecka, Emilia A., Marcisz, Mateusz, Danielsson, Annemarie, Dziadek, Lukasz, Gaardlos, Margrethe, Gieldon, Artur, Liwo, Adam

مصطلحات الفهرس: AlphaFold, CAPRI, CASP, Blind prediction, Deep learning, Protein assemblies, Protein complexes, Protein-protein interaction, artículo

URL: http://hdl.handle.net/10261/347795
https://api.elsevier.com/content/abstract/scopus_id/85175465612
https://doi.org/10.1002/prot.26609
Publisher's version
The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1002/prot.26609
https://doi.org/10.1002/prot.26609
Sí
info:eu-repo/grantAgreement/EC/H2020/823830
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-110167RB-I00/ES/NUEVA METODOLOGIA DE DOCKING ENTRE PROTEINAS PARA LA INTERPRETACION DE VARIANTES GENETICAS DE RELEVANCIA PARA LA SALUD HUMANA
info:eu-repo/grantAgreement/EC/H2020/801342

المؤلفون: National Institutes of Health (US), National Science Foundation (US), Netherlands eScience Center, Netherlands Organization for Scientific Research, European Commission, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Generalitat de Catalunya, European Research Council, Israel Science Foundation, Israel Academy of Sciences and Humanities, Schweke, Hugo, Xu, Qifang, Tauriello, Gerardo, Pantolini, Lorenzo, Schwede, Torsten, Cazals, Frédéric, Lhéritier, Alix, Fernández-Recio, Juan, Rodríguez-Lumbreras, Luis A., Schueler-Furman, Ora, Varga, Julia K., Jiménez-García, Brian, Réau, Manon F., Bonvin, Alexandre M. J. J., Savojardo, Castrense, Martelli, Pier-Luigi, Casadio, Rita, Tubiana, Jérôme, Wolfson, Haim J., Oliva, Romina, Barradas-Bautista, Didier, Ricciardelli, Tiziana, Cavallo, Luigi, Venclovas, Česlovas, Olechnovič, Kliment, Guerois, Raphael, Andreani, Jessica, Martin, Juliette, Wang, Xiao, Terashi, Genki, Sarkar, Daipayan, Christoffer, Charles, Aderinwale, Tunde, Verburgt, Jacob, Kihara, Daisuke, Marchand, Anthony, Correia, Bruno E., Duan, Rui, Qiu, Liming, Xu, Xianjin, Zhang, Shuang, Zou, Xiaoqin, Dey, Sucharita, Dunbrack, Roland L., Levy, Emmanuel D., Wodak, Shoshana J.

مصطلحات الفهرس: Crystal contacts, Homodimers, Potential energy, Protein interactions, Protein structure, artículo

URL: http://hdl.handle.net/10261/347702
https://api.elsevier.com/content/abstract/scopus_id/85162927714
https://doi.org/10.1002/pmic.202200323
The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1002/pmic.202200323
https://doi.org/10.1002/pmic.202200323
Sí
info:eu-repo/grantAgreement/EC/H2020/823830
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-110167RB-I00/ES/NUEVA METODOLOGIA DE DOCKING ENTRE PROTEINAS PARA LA INTERPRETACION DE VARIANTES GENETICAS DE RELEVANCIA PARA LA SALUD HUMANA
info:eu-repo/grantAgreement/EC/H2020/801342
info:eu-repo/grantAgreement/EC/H2020/819318
info:eu-repo/grantAgreement/EC/H2020/860517