A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions.

Gang Hu 0005 https://orcid.org/0000-0002-7134-3380 https://www.wikidata.org/entity/Q94562261 Nankai University, Tianjin, China Gang Hu Gang Hu 0001 Ping An Healthcare Technology, Beijing, China Gang Hu 0002 Xi'an University of Technology, Department of Applied Mathematics, China https://orcid.org/0000-0003-4916-3460 Gang Hu 0003 Yunnan University, China https://orcid.org/0000-0002-7867-8087 https://www.wikidata.org/entity/Q130847106 Gang Hu 0004 Huawei Technologies Company, Ltd., Chengdu, China https://orcid.org/0000-0001-9636-1158 Gang Hu 0006 https://orcid.org/0000-0002-8755-8829 https://www.wikidata.org/entity/Q61145069 Harbin Engineering University, Harbin, China Gang Hu 0007 https://orcid.org/0000-0001-6284-0812 Harbin Institute of Technology Shenzhen, Shenzhen, Guangdong, China Gang Hu 0008 https://orcid.org/0009-0002-9794-7964 Northwestern Polytechnical University, Xi'an, China Gang Hu 0009 https://orcid.org/0009-0008-0160-5892 https://www.wikidata.org/entity/Q130907640 Air Force Engineering University, China Gang Hu 0010 https://orcid.org/0000-0001-5890-772X University of Manchester, Manchester, UK Gang Hu 0011 https://orcid.org/0000-0001-7405-443X SUNY Buffalo State University, Buffalo, NY, USA Gang Hu 0012 https://orcid.org/0000-0003-0738-7490 Xi'an University of Technology, Xi'an, Shaanxi, China Gang Hu 0013 https://orcid.org/0000-0003-3758-1825 Central South University, Changsha, China Gang Hu 0014 https://orcid.org/0009-0009-4900-169X Beijing University of Posts and Telecommunications, Beijing, China Gang Hu 0015 https://orcid.org/0000-0001-6088-4707 Hong Kong Polytechnic University, Kowloon, Hong Kong, SAR, China Gang Hu 0016 https://orcid.org/0000-0001-9204-9140 https://www.wikidata.org/entity/Q91708644 Nankai University, Tianjin, China Gang Hu 0017 https://orcid.org/0009-0001-5043-5649 China Tobacco, Jinrongjie, China Gang Hu 0018 https://orcid.org/0000-0002-5356-0373 Air Force Engineering University, Xi'an, China Gang Hu 0019 https://orcid.org/0009-0007-6969-3764 Xidian University, Xi'an, China

Chunxiang Peng Wentao Ni Quancheng Liu Gang Hu 0005 Wei Zheng 0013 A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions. 2025 26 Briefings Bioinform. 5 https://doi.org/10.1093/bib/bbaf616 db/journals/bib/bib26.html#PengNLHZ25 streams/journals/bib

Yanping Zhao Kui Wang Gang Hu 0005 DIST: spatial transcriptomics enhancement using deep learning. 2023 March 24 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbad013 db/journals/bib/bib24.html#ZhaoWH23

Alessio Del Conte Adel Bouhraoua Mahta Mehdiabadi Damiano Clementel Alexander Miguel Monzon Alex S. Holehouse Daniel A. Griffith Ryan J. Emenecker Ashwini Patil Ronesh Sharma Tatsuhiko Tsunoda Alok Sharma Yi Jun Tang Bin Liu Claudio Mirabello Björn Wallner Burkhard Rost Dagmar Ilzhöfer Maria Littmann Michael Heinzinger Lea I M. Krautheimer Michael Bernhofer Liam J. McGuffin Isabelle Callebaut Tristan Bitard Feildel Jian Liu 0040 Jianlin Cheng Zhiye Guo Jinbo Xu Sheng Wang Nawar Malhis Jörg Gsponer Chol-Song Kim Kun-Sop Han Myong-Chol Ma Lukasz A. Kurgan Sina Ghadermarzi Akila Katuwawala Bi Zhao Zhenling Peng Zhonghua Wu Gang Hu 0005 Kui Wang Md. Tamjidul Hoque Md Wasi Ul Kabir Michele Vendruscolo Pietro Sormanni Min Li 0007 Fuhao Zhang Pengzhen Jia Yida Wang Michail Yu. Lobanov Oxana V. Galzitskaya Wim F. Vranken Adrián Díaz Thomas Litfin Yaoqi Zhou Jack Hanson Kuldip K. Paliwal Zsuzsanna Dosztányi Gábor Erdös 0002 Silvio C. E. Tosatto Damiano Piovesan CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. 62-69 2023 July 51 Nucleic Acids Res. W1 https://doi.org/10.1093/nar/gkad430 db/journals/nar/nar51.html#ConteBMCMHGEPSTSTLMWRILHKBMCFLCGXWM23

Xinyi Xu Xiaokang Yu Gang Hu 0005 Kui Wang Jingxiao Zhang Xiangjie Li Propensity score matching enables batch-effect-corrected imputation in single-cell RNA-seq analysis. 2022 23 Briefings Bioinform. 4 https://doi.org/10.1093/bib/bbac275 db/journals/bib/bib23.html#XuYHWZL22

Xinzhe Ni Bohao Geng Haoyu Zheng Jiawei Shi Gang Hu 0005 Jianzhao Gao Accurate Estimation of Single-Cell Differentiation Potency Based on Network Topology and Gene Ontology Information. 3255-3262 2022 19 IEEE ACM Trans. Comput. Biol. Bioinform. 6 https://doi.org/10.1109/TCBB.2021.3112951 db/journals/tcbb/tcbb19.html#NiGZSHG22

Gang Hu 0005 Zhonghua Wu Christopher J. Oldfield Chen Wang Lukasz A. Kurgan Quality assessment for the putative intrinsic disorder in proteins. 1692-1700 2019 35 Bioinform. 10 https://doi.org/10.1093/bioinformatics/bty881 https://www.wikidata.org/entity/Q57452799 db/journals/bioinformatics/bioinformatics35.html#HuWOWK19

Yu Hu 0014 Jennie Lin Jian Hu Gang Hu 0005 Kui Wang Hanrui Zhang 0004 Muredach P. Reilly Mingyao Li PennDiff: detecting differential alternative splicing and transcription by RNA sequencing. 2384-2391 2018 34 Bioinform. 14 https://doi.org/10.1093/bioinformatics/bty097 https://www.wikidata.org/entity/Q50104538 db/journals/bioinformatics/bioinformatics34.html#HuLHHWZRL18

Tong Wang Wei Zheng 0013 Qiqige Wuyun Zhenfeng Wu Jishou Ruan Gang Hu 0005 Jianzhao Gao PrAS: Prediction of amidation sites using multiple feature extraction. 57-62 2017 66 Comput. Biol. Chem. https://doi.org/10.1016/j.compbiolchem.2016.11.004 https://www.wikidata.org/entity/Q50539649 db/journals/candc/candc66.html#WangZWWRHG17

Zhonghua Wu Gang Hu 0005 Kui Wang Lukasz A. Kurgan Exploratory Analysis of Quality Assessment of Putative Intrinsic Disorder in Proteins. 722-732 2017 ICAISC (1) https://doi.org/10.1007/978-3-319-59063-9_65 conf/icaisc/2017-1 db/conf/icaisc/icaisc2017-1.html#WuHWK17

Chen Wang Gang Hu 0005 Kui Wang Michal Brylinski Lei Xie Lukasz A. Kurgan PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. 579-586 2016 32 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btv597 https://www.wikidata.org/entity/Q40389931 db/journals/bioinformatics/bioinformatics32.html#WangHWBXK16

Gang Hu 0005 Kui Wang Jody Groenendyk Khaled H. Barakat Marcin J. Mizianty Jishou Ruan Marek Michalak Lukasz A. Kurgan Human structural proteome-wide characterization of Cyclosporine A targets. 3561-3566 2014 30 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btu581 https://www.wikidata.org/entity/Q42185186 db/journals/bioinformatics/bioinformatics30.html#HuWGBMRMK14

Shuangjian Zhang Jun Du Liang Zhang Cheng Zeng Qiao Liu Tao Zhang 0062 Gang Hu 0005 Circular Cone: A novel approach for protein ligand shape matching using modified PCA. 168-175 2012 108 Comput. Methods Programs Biomed. 1 https://doi.org/10.1016/j.cmpb.2012.02.011 https://www.wikidata.org/entity/Q51393037 db/journals/cmpb/cmpb108.html#ZhangDZZLZH12

Gang Hu 0005 Shiyi Shen Kui Wang On the evolution rate in mammalian mitochondrial genomes. 137-142 2011 35 Comput. Biol. Chem. 3 https://doi.org/10.1016/j.compbiolchem.2011.04.001 https://www.wikidata.org/entity/Q51554313 db/journals/candc/candc35.html#HuSW11

Khaled H. Barakat Michael Bernhofer Adel Bouhraoua Michal Brylinski Isabelle Callebaut Jianlin Cheng Damiano Clementel Alessio Del Conte Adrián Díaz Zsuzsanna Dosztányi Jun Du Ryan J. Emenecker Gábor Erdös 0002 Tristan Bitard Feildel Oxana V. Galzitskaya Jianzhao Gao Bohao Geng Sina Ghadermarzi Daniel A. Griffith Jody Groenendyk Jörg Gsponer Zhiye Guo Kun-Sop Han Jack Hanson Michael Heinzinger Alex HolehouseAlex S. Holehouse Tamjidul HoqueMd. Tamjidul Hoque Jian Hu Yu Hu 0014 Dagmar Ilzhöfer Pengzhen Jia Md Wasi Ul Kabir Akila Katuwawala Chol-Song Kim Lea I M. Krautheimer Lukasz A. Kurgan Min Li 0007 Mingyao Li Xiangjie Li Jennie Lin Thomas Litfin Maria Littmann Bin Liu Jian Liu 0040 Qiao Liu Quancheng Liu Michail Yu. Lobanov Myong-Chol Ma Nawar Malhis Liam J. McGuffin Mahta Mehdiabadi Marek Michalak Claudio Mirabello Marcin J. Mizianty Alexander Miguel Monzon Wentao Ni Xinzhe Ni Christopher J. Oldfield Kuldip K. Paliwal Ashwini Patil Chunxiang Peng Zhen-Ling PengZhenling Peng Damiano Piovesan Muredach P. Reilly Burkhard Rost Jishou Ruan Alok Sharma Ronesh Sharma Shiyi Shen Jiawei Shi Pietro Sormanni Yi Jun Tang Silvio C. E. Tosatto Tatsuhiko Tsunoda Michele Vendruscolo Wim F. Vranken Björn Wallner Chen Wang Kui Wang Sheng Wang Tong Wang Yida Wang Zhenfeng Wu Zhonghua Wu Qiqige Wuyun Lei Xie Jinbo Xu Xinyi Xu Xiaokang Yu Cheng Zeng Fuhao Zhang Hanrui Zhang 0004 Jingxiao Zhang Liang Zhang Shuangjian Zhang Tao Zhang 0062 Bi Zhao Yanping Zhao Haoyu Zheng Wei Zheng 0013 Yaoqi Zhou