Search: WFRF:(Cohen MA) > (2020-2024) > Impact of AlphaFold...
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000 | 12410naa a2201657 4500 | |
001 | oai:DiVA.org:liu-200076 | |
003 | SwePub | |
008 | 240115s2023 | |||||||||||000 ||eng| | |
024 | 7 | a https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2000762 URI |
024 | 7 | a https://doi.org/10.1002/prot.266092 DOI |
040 | a (SwePub)liu | |
041 | a engb eng | |
042 | 9 SwePub | |
072 | 7 | a ref2 swepub-contenttype |
072 | 7 | a art2 swepub-publicationtype |
100 | 1 | a Lensink, Marc F.u Univ Lille, France4 aut |
245 | 1 0 | a Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment |
264 | c 2023 | |
264 | 1 | b WILEY,c 2023 |
338 | a print2 rdacarrier | |
500 | a Funding Agencies|Francis Crick Institute; Cancer Research UK [FC0001003]; UK Medical Research Council [FC001003]; Wellcome Trust [FC001003]; European Union Horizon 2020 [823830]; Netherlands e-Science Center [027.020.G13]; US National Institutes of Health [R01GM146340, R01GM093123]; Spanish Ministry of Science [501100011033, AEI/10.13039, PID2019-110167RB-I00]; National Institute of Health [R35 GM144083, RM1135136, R35GM118078, R01GM140098, R01GM123055, R01GM133840, R35-GM141881]; Advanced Research Computing at Hopkins (ARCH) core facility; National Natural Science Foundation of China [32161133002, 62072199]; European Molecular Biology Organization (EMBO) [ALTF 145-2021]; Government of Catalonia's Agency for Business Competitiveness (ACCIO); National Science Foundation [DMS 2054251, DBI2003635, IIS2211598, DBI2146026, MCB1925643, CMMI1825941, IIS1763246, DBI1759934, CCF-1943008, OAC1920103]; National Institute of General Medical Sciences [T32 GM132024]; NIH/NIGMS [R35GM136409, R35GM124952]; National Science Center of Poland (Narodowe Centrum Nauki) (NCN) [UMO2017/27/B/ST4/00926, UMO-2017/26/M/ ST4/00044, UMO2017/25/B/ST4/01026]; Research Council of Lithuania [: S-MIP-21-25]; Wallenberg AI, Autonomous System and Software Program (WASP); Knut and Alice Wallenberg Foundation (KAW); Swedish Research Council; Science Foundation of the National Key Laboratory of Science and Technology; Fundamental Research Funds for the Central Universities of China; [801342] | |
520 | a We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem. | |
650 | 7 | a NATURVETENSKAPx Data- och informationsvetenskapx Bioinformatik0 (SwePub)102032 hsv//swe |
650 | 7 | a NATURAL SCIENCESx Computer and Information Sciencesx Bioinformatics0 (SwePub)102032 hsv//eng |
653 | a AlphaFold; blind prediction; CAPRI; CASP; deep learning; protein assemblies; protein complexes; protein-protein interaction | |
700 | 1 | a Brysbaert, Guillaumeu Univ Lille, France4 aut |
700 | 1 | a Raouraoua, Nessimu Univ Lille, France4 aut |
700 | 1 | a Bates, Paul A.u Francis Crick Inst, England4 aut |
700 | 1 | a Giulini, Marcou Univ Utrecht, Netherlands4 aut |
700 | 1 | a Honorato, Rodrigo V.u Univ Utrecht, Netherlands4 aut |
700 | 1 | a van Noort, Charlotteu Univ Utrecht, Netherlands4 aut |
700 | 1 | a Teixeira, Joao M. C.u Univ Utrecht, Netherlands4 aut |
700 | 1 | a Bonvin, Alexandre M. J. J.u Univ Utrecht, Netherlands4 aut |
700 | 1 | a Kong, Renu Jiangsu Univ Technol, Peoples R China4 aut |
700 | 1 | a Shi, Hangu Jiangsu Univ Technol, Peoples R China4 aut |
700 | 1 | a Lu, Xufengu Jiangsu Univ Technol, Peoples R China4 aut |
700 | 1 | a Chang, Shanu Jiangsu Univ Technol, Peoples R China4 aut |
700 | 1 | a Liu, Jianu Univ Missouri, MO USA4 aut |
700 | 1 | a Guo, Zhiyeu Univ Missouri, MO USA4 aut |
700 | 1 | a Chen, Xiaou Univ Missouri, MO USA4 aut |
700 | 1 | a Morehead, Alexu Univ Missouri, MO USA4 aut |
700 | 1 | a Roy, Raj S.u Univ Missouri, MO USA4 aut |
700 | 1 | a Wu, Tianqiu Univ Missouri, MO USA4 aut |
700 | 1 | a Giri, Nabinu Univ Missouri, MO USA4 aut |
700 | 1 | a Quadir, Farhanu Univ Missouri, MO USA4 aut |
700 | 1 | a Chen, Chenu Univ Missouri, MO USA4 aut |
700 | 1 | a Cheng, Jianlinu Univ Missouri, MO USA4 aut |
700 | 1 | a Del Carpio, Carlos A.u Fukushimuta Hosp, Japan4 aut |
700 | 1 | a Ichiishi, Eichirou Int Univ Hlth & Welf IUHV Hosp, Japan4 aut |
700 | 1 | a Rodriguez-Lumbreras, Luis A.u CSIC Univ Rioja Gobierno La Rioja, Spain; Barcelona Supercomp Ctr BSC, Spain4 aut |
700 | 1 | a Fernandez-Recio, Juanu CSIC Univ Rioja Gobierno La Rioja, Spain; Barcelona Supercomp Ctr BSC, Spain4 aut |
700 | 1 | a Harmalkar, Ameyau Johns Hopkins Univ, MD USA4 aut |
700 | 1 | a Chu, Lee-Shinu Johns Hopkins Univ, MD USA4 aut |
700 | 1 | a Canner, Samu Johns Hopkins Univ, MD USA4 aut |
700 | 1 | a Smanta, Rituparnau Johns Hopkins Univ, MD USA4 aut |
700 | 1 | a Gray, Jeffrey J.u Johns Hopkins Univ, MD USA; Johns Hopkins Univ, MD USA4 aut |
700 | 1 | a Li, Haou Huazhong Univ Sci & Technol, Peoples R China4 aut |
700 | 1 | a Lin, Peicongu Huazhong Univ Sci & Technol, Peoples R China4 aut |
700 | 1 | a He, Jiahuau Huazhong Univ Sci & Technol, Peoples R China4 aut |
700 | 1 | a Tao, Huanyuu Huazhong Univ Sci & Technol, Peoples R China4 aut |
700 | 1 | a Huang, Sheng-Youu Huazhong Univ Sci & Technol, Peoples R China4 aut |
700 | 1 | a Roel-Touris, Jorgeu Mol Biol Inst Barcelona IBMB CSIC, Spain4 aut |
700 | 1 | a Jimenez-Garcia, Brianu Zymvol Biomodeling, Spain4 aut |
700 | 1 | a Christoffer, Charles W.u Purdue Univ, IN USA4 aut |
700 | 1 | a Jain, Anika J.u Purdue Univ, IN USA4 aut |
700 | 1 | a Kagaya, Yukiu Purdue Univ, IN USA4 aut |
700 | 1 | a Kannan, Hariniu Purdue Univ, IN USA; Indian Inst Technol Madras, India4 aut |
700 | 1 | a Nakamura, Tsukasau Purdue Univ, IN USA4 aut |
700 | 1 | a Terashi, Genkiu Purdue Univ, IN USA4 aut |
700 | 1 | a Verburgt, Jacob C.u Purdue Univ, IN USA4 aut |
700 | 1 | a Zhang, Yuanyuanu Purdue Univ, IN USA4 aut |
700 | 1 | a Zhang, Zicongu Purdue Univ, IN USA4 aut |
700 | 1 | a Fujuta, Hayatou Indian Inst Technol Madras, India4 aut |
700 | 1 | a Sekijima, Masakazuu Tokyo Inst Technol, Japan4 aut |
700 | 1 | a Kihara, Daisukeu Purdue Univ, IN USA4 aut |
700 | 1 | a Khan, Omeiru Boston Univ, MA USA4 aut |
700 | 1 | a Kotelnikov, Sergeiu SUNY Stony Brook, NY USA4 aut |
700 | 1 | a Ghani, Usmanu Boston Univ, MA USA4 aut |
700 | 1 | a Padhorny, Dzmitryu SUNY Stony Brook, NY USA4 aut |
700 | 1 | a Beglov, Dmitriu Boston Univ, MA USA4 aut |
700 | 1 | a Vajda, Sandoru Boston Univ, MA USA4 aut |
700 | 1 | a Kozakov, Dimau SUNY Stony Brook, NY USA4 aut |
700 | 1 | a Negi, Surendra S.u Univ Texas Med Branch, TX USA4 aut |
700 | 1 | a Ricciardelli, Tizianau King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut |
700 | 1 | a Barradas-Bautista, Didieru King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut |
700 | 1 | a Cao, Zhenu King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut |
700 | 1 | a Chawla, Mohitu King Abdullah Univ Sci & Technol KAUST, Saudi Arabia4 aut |
700 | 1 | a Cavallo, Luigiu King Abdullah Univ Sci & Technol KAUST, Saudi Arabia; Univ Salerno, Italy4 aut |
700 | 1 | a Oliva, Rominau Univ Naples Parthenope, Italy4 aut |
700 | 1 | a Yin, Ruiu Univ Maryland, MD USA4 aut |
700 | 1 | a Cheung, Melyssau Univ Maryland, MD USA; Univ Maryland, MD USA4 aut |
700 | 1 | a Guest, Johnathan D.u Univ Maryland, MD USA; Univ Maryland, MD USA4 aut |
700 | 1 | a Lee, Jessicau Univ Maryland, MD USA; Univ Maryland, MD USA4 aut |
700 | 1 | a Pierce, Brian G.u Univ Maryland, MD USA4 aut |
700 | 1 | a Shor, Benu Hebrew Univ Jerusalem, Israel4 aut |
700 | 1 | a Cohen, Tomeru Hebrew Univ Jerusalem, Israel4 aut |
700 | 1 | a Halfon, Matanu Hebrew Univ Jerusalem, Israel4 aut |
700 | 1 | a Schneidman-Duhovny, Dinau Hebrew Univ Jerusalem, Israel4 aut |
700 | 1 | a Zhu, Shaowenu Hebrew Univ Jerusalem, Israel; Texas M Univ, TX USA4 aut |
700 | 1 | a Yin, Rujieu Texas M Univ, TX USA4 aut |
700 | 1 | a Sun, Yuanfeiu Texas M Univ, TX USA4 aut |
700 | 1 | a Shen, Yangu Texas M Univ, TX USA; Texas A&M Univ, TX USA; Texas A&M Univ, TX USA; Texas A&M Univ, TX USA4 aut |
700 | 1 | a Maszota-Zieleniak, Martynau Univ Gdansk, Poland4 aut |
700 | 1 | a Bojarski, Krzysztof K.u Univ Gdansk, Poland; Techn Univ Gdansk, Poland4 aut |
700 | 1 | a Lubecka, Emilia A.u Techn Univ Gdansk, Poland4 aut |
700 | 1 | a Marcisz, Mateuszu Univ Gdansk, Poland4 aut |
700 | 1 | a Danielsson, Annemarieu Univ Gdansk, Poland4 aut |
700 | 1 | a Dziadek, Lukaszu Univ Gdansk, Poland4 aut |
700 | 1 | a Gaardlos, Margretheu Univ Gdansk, Poland4 aut |
700 | 1 | a Gieldon, Arturu Univ Gdansk, Poland4 aut |
700 | 1 | a Liwo, Adamu Univ Gdansk, Poland4 aut |
700 | 1 | a Samsonov, Sergey A.u Univ Gdansk, Poland4 aut |
700 | 1 | a Slusarz, Rafalu Univ Gdansk, Poland4 aut |
700 | 1 | a Zieba, Karolinau Univ Gdansk, Poland4 aut |
700 | 1 | a Sieradzan, Adam K.u Univ Gdansk, Poland4 aut |
700 | 1 | a Czaplewski, Cezaryu Univ Gdansk, Poland4 aut |
700 | 1 | a Kobayashi, Shinpeiu Kitasato Univ, Japan4 aut |
700 | 1 | a Miyakawa, Yutau Kitasato Univ, Japan4 aut |
700 | 1 | a Kiyota, Yasuomiu Kitasato Univ, Japan4 aut |
700 | 1 | a Takeda-Shitaka, Mayukou Kitasato Univ, Japan4 aut |
700 | 1 | a Olechnovic, Klimentu Vilnius Univ, Lithuania4 aut |
700 | 1 | a Valancauskas, Lukasu Vilnius Univ, Lithuania4 aut |
700 | 1 | a Dapkunas, Justasu Vilnius Univ, Lithuania4 aut |
700 | 1 | a Venclovas, Ceslovasu Vilnius Univ, Lithuania4 aut |
700 | 1 | a Wallner, Björn,d 1975-u Linköpings universitet,Bioinformatik,Tekniska fakulteten4 aut0 (Swepub:liu)bjowa51 |
700 | 1 | a Yang, Linu Harbin Inst Technol, Peoples R China; Univ Sydney, Australia4 aut |
700 | 1 | a Hou, Chengyuu Harbin Inst Technol, Peoples R China4 aut |
700 | 1 | a He, Xiaodongu Harbin Inst Technol, Peoples R China; Shenzhen STRONG Adv Mat Res Inst Col Ltd, Peoples R China4 aut |
700 | 1 | a Guo, Shuaiu Harbin Inst Technol, Peoples R China4 aut |
700 | 1 | a Jiang, Shendau Harbin Inst Technol, Peoples R China4 aut |
700 | 1 | a Ma, Xiaoliangu Harbin Inst Technol, Peoples R China4 aut |
700 | 1 | a Duan, Ruiu Univ Missouri, MO USA4 aut |
700 | 1 | a Qui, Limingu Univ Missouri, MO USA4 aut |
700 | 1 | a Xu, Xianjinu Univ Missouri, MO USA4 aut |
700 | 1 | a Zou, Xiaoqinu Univ Missouri, MO USA; Univ Missouri, MO USA; Univ Missouri, MO USA; Univ Missouri, MO USA4 aut |
700 | 1 | a Velankar, Sameeru European Bioinformat Inst EMBL EBI, England4 aut |
700 | 1 | a Wodak, Shoshana J.u VUB Ctr Struct Biol VIB, Belgium4 aut |
710 | 2 | a Univ Lille, Franceb Francis Crick Inst, England4 org |
773 | 0 | t Proteinsd : WILEYx 0887-3585x 1097-0134 |
856 | 4 8 | u https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-200076 |
856 | 4 8 | u https://doi.org/10.1002/prot.26609 |
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