Review
Pharmacology & Pharmacy
Yuyu Feng, Yumeng Yan, Jiahua He, Huanyu Tao, Qilong Wu, Sheng-You Huang
Summary: Nucleic acid-ligand interactions play crucial roles in cellular processes and have attracted significant interest in drug discovery. However, traditional docking algorithms and scoring functions for protein-ligand interactions may not be applicable to nucleic acid-ligand docking due to the differences in their properties. This review discusses the current status, challenges, and limitations of docking algorithms and scoring functions for DNA/RNA-ligand interactions.
DRUG DISCOVERY TODAY
(2022)
Article
Optics
Fanfei Li, Jingcheng Hu, Shaohui Zhang, Yao Hu, Chenxu Xia, Qun Hao
Summary: This article from Optica Publishing Group introduces the advantages and contradictions of the laser 3D measurement technology FPP, and proposes a method to achieve high-speed and high-precision measurements. It also presents a correction method to eliminate measurement errors. The feasibility and effectiveness of this method are verified through experiments.
Article
Optics
Sen Xiang, Li Liu, Huiping Deng, Jin Wu, You Yang, Li Yu
Summary: The paper introduces phase light field (PLF) and re-formatted phase-epipolar-plane-images (phase EPIs) for depth estimation, and proposes a global cost minimization framework. The beetle antennae search (BAS) optimization algorithm is utilized to find the optimal line for depth estimation. The proposed method achieves significant acceleration compared to state-of-the-art methods while maintaining comparable depth quality.
Article
Chemistry, Applied
Xia Yu, Xinghong Cai, Shuang Li, Liyong Luo, Jie Wang, Min Wang, Liang Zeng
Summary: By utilizing various experimental techniques such as fluorescence spectroscopy and UV-vis absorption spectroscopy, the interaction mechanism between theaflavin-3,3'-digallate (TFDG) and bovine serum albumin (BSA) was studied, demonstrating that hydrophobic interactions and hydrogen bonds play a dominant role in their interaction. This research provides the possibility for further development of nanoparticles with superior biochemical properties and potential exploration of BSA as a transport carrier for TFDG.
Article
Biochemical Research Methods
Qilong Wu, Sheng-You Huang
Summary: Covalent inhibitors have attracted attention for their long residence time, high binding efficiency, and strong selectivity. The development of computational tools like HCovDock, an efficient docking algorithm for covalent protein-ligand interactions, is valuable for modeling and screening of covalent drugs. HCovDock outperforms seven other state-of-the-art covalent docking programs and exhibits a high success rate in reproducing experimentally observed structures and virtual screening.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Qilong Wu, Sheng-You Huang
Summary: Covalent inhibitors are highly valued for their long residence time, high binding efficiency, and strong selectivity. The development of computational tools like molecular docking, such as HCovDock, is important for modeling covalent protein-ligand interactions and screening potential drugs. HCovDock shows better performance than other state-of-the-art docking programs and has high success rates in reproducing experimentally observed structures.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Optics
Yu Xiao, Wenzhong Han, Xuejing Zhang, Ji Deng, Jian Li, Huifeng Kang, Zhoumo Zeng
Summary: This paper introduces a fast computational depth segmentation (FCDS) method which uses only five patterns for depth segmentation, improving segmentation speed, reducing computational complexity, and solving the problems of phase insensitivity and mis-segmentation.
JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION
(2021)
Article
Astronomy & Astrophysics
Ruben Krasnopolsky, Mario Ponce Martinez, Hsien Shang, Yao-Huan Tseng, Chien-Chang Yen
Summary: The study presents a novel direct numerical method for calculating gravitational potential and forces without the need for artificial boundary conditions. Numerical results show that the proposed method can achieve second order accuracy in computing both potential and forces.
ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES
(2021)
Article
Engineering, Electrical & Electronic
Quentin Gueuning, Christophe Craeye, Claude Oestges
Summary: A plane-wave spectrum method is introduced for efficiently calculating radiation integrals for tilted and separated source and observation plates. The method uses fast Laplace transforms with unequal spacing to expedite direct and inverse transforms between spatial and spectral domains.
IEEE TRANSACTIONS ON ANTENNAS AND PROPAGATION
(2022)
Article
Biochemistry & Molecular Biology
Mohammad Gholizadeh, Behzad Shareghi, Sadegh Farhadian
Summary: This study investigated the binding strength of Naringenin (NAG) to Alpha-Chymotrypsin (a-Chy) using multispectral methods and computational simulation techniques. The results showed that NAG reduced the intrinsic fluorescence of a-Chy through static quenching and induced a more flexible conformation. Thermal stability data and kinetic analysis supported these findings.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Yong Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant G. Honavar
Summary: Protein-protein interactions are crucial for biological function, and understanding their three-dimensional structures is essential. Computational docking is a useful alternative to experimental approaches for determining these structures, but the scoring problem still needs improvement. MetaScore is a machine-learning-based approach that uses protein-protein interfacial features to score docked conformations. It consistently outperforms traditional scoring functions and an ensemble method combining MetaScore with traditional functions achieves even better performance. Machine learning and ensemble methods can improve the accuracy of scoring protein-protein interactions.
Article
Biochemistry & Molecular Biology
Edoardo Milanetti, Mattia Miotto, Lorenzo Di Rienzo, Michele Monti, Giorgio Gosti, Giancarlo Ruocco
Summary: The method efficiently assesses protein-protein interactions to form complexes by measuring geometrical shape complementarity. It successfully identifies real binding regions and shows potential for blind recognition of binding sites. The efficiency in finding the right binding region depends on surface roughness and expansion order.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Luis Angel Rodriguez-Lumbreras, Brian Jimenez-Garcia, Silvia Gimenez-Santamarina, Juan Fernandez-Recio
Summary: Protein-DNA interactions play essential roles in cellular processes, but there is a limited number of protein-DNA complex structures in current databases and a lack of computational methods for modeling their structures. In this study, a web server called pyDockDNA is presented, which can successfully predict protein-DNA complex structures with reasonable accuracy.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Engineering, Electrical & Electronic
Fang-Jia Yan, Bing-Zhao Li
Summary: This paper addresses a key challenge in graph signal processing by proposing the windowed graph fractional Fourier transform (WGFRFT) and a fast algorithm for it. The robustness and superiority of the algorithm are verified through simulations, demonstrating its practicality in graph clustering applications.
DIGITAL SIGNAL PROCESSING
(2021)
Article
Biochemical Research Methods
Maria Kadukova, Karina Dos Santos Machado, Pablo Chacon, Sergei Grudinin
Summary: This study introduces a novel coarse-grained potential based on a 3D joint probability distribution function that depends only on the pairwise orientation and position between protein backbone and ligand atoms. Despite its simplicity, this approach demonstrates competitive results in docking and screening tasks compared to state-of-the-art scoring functions.
Article
Chemistry, Medicinal
Pei Zhou, Botong Li, Yumeng Yan, Bowen Jin, Libang Wang, Sheng-You Huang
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2018)
Article
Biochemistry & Molecular Biology
Yumeng Yan, Zeyu Wen, Di Zhang, Sheng-You Huang
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Yumeng Yan, Huanyu Tao, Sheng-You Huang
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Marc F. Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Gerguri, Paul A. Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran-Ran Liu, Xi-Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Pawel Krupa, Magdalena Mozolewska, Lukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pages, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng-You Huang, Mireia Rosell, Luis A. Rodriguez-Lumbreras, Miguel Romero-Durana, Lucia Diaz-Bueno, Juan Fernandez-Recio, Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H. Moal, David W. Ritchie, Isaure Chauvot de Beauchene, Bernard Maigret, Marie-Dominique Devignes, Maria E. 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 Dapkunas, Kliment Olechnovic, Ceslovas 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, Panos I. Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jorg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li Xue, Brian Jimenez-Garcia, Charlotte W. van Noort, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin, Shoshana J. Wodak
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2019)
Article
Biochemistry & Molecular Biology
Yumeng Yan, Jiahua He, Yuyu Feng, Peicong Lin, Huanyu Tao, Sheng-You Huang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Yumeng Yan, Huanyu Tao, Jiahua He, Sheng-You Huang
Article
Virology
Jiahua He, Huanyu Tao, Yumeng Yan, Sheng-You Huang, Yi Xiao
Article
Biochemical Research Methods
Yumeng Yan, Sheng-You Huang
Summary: DeepHomo, a deep learning model for predicting inter-protein residue-residue contacts, integrates various information sources and achieves high precision, outperforming existing methods on both experimentally determined structures and simulated targets.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Marc F. Lensink, Guillaume Brysbaert, Theo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Clarence, Paul A. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S. Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Gieldon, Mateusz Kogut, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Martyna Maszota-Zieleniak, Adam K. Sieradzan, Rafal Slusarz, Patryk A. Wesolowski, Karolina Zieba, Carlos A. Del Carpio Munoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, Alexandre M. J. J. Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jimenez-Garcia, Panagiotis I. Koukos, Siri Van Keulen, Charlotte W. Van Noort, Manon Reau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A. Rodriguez-Lumbreras, Juan Fernandez-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G. Pierce, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, Petras J. Kundrotas, Amar Singh, Ilya A. Vakser, Justas Dapkunas, Kliment Olechnovic, Ceslovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J. Wodak
Summary: The results of the CAPRI Round 50 showed that 25 groups participated in submitting models for 12 targets, with a good level of accuracy overall.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Fuqing Hu, Da Song, Yumeng Yan, Changsheng Huang, Chentao Shen, Jingqin Lan, Yaqi Chen, Anyi Liu, Qi Wu, Li Sun, Feng Xu, Fayong Hu, Lisheng Chen, Xuelai Luo, Yongdong Feng, Shengyou Huang, Junbo Hu, Guihua Wang
Summary: IL-6 activates autophagy in colorectal cancer through the interaction between JAK2 and autophagy regulator BECN1, leading to chemotherapeutic resistance. BECN1 Y333 phosphorylation is crucial for BECN1 activation and IL-6-induced autophagy by regulating PI3KC3 complex formation. Combination treatment targeting the IL-6/JAK2/BECN1 signaling pathway may be a potential strategy for CRC therapy.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Medicinal
Hao Li, Yumeng Yan, Xuejun Zhao, Sheng-You Huang
Summary: Protein-protein interactions are crucial in biological processes. This study proposes a hybrid scoring function for predicting protein-protein complex structures, which significantly improves the docking performance and achieves the best performance in binding mode predictions among state-of-the-art docking programs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Computer Science, Artificial Intelligence
Yumeng Yan, Sheng-You Huang
BIG DATA MINING AND ANALYTICS
(2019)
Proceedings Paper
Computer Science, Artificial Intelligence
Yumeng Yan, Sheng-You Huang
INTELLIGENT COMPUTING THEORIES AND APPLICATION, PT I
(2018)
Article
Biochemical Research Methods
Yumeng Yan, Sheng-You Huang