Article
Biochemical Research Methods
Leandro G. Radusky, Luis Serrano
Summary: In recent years, there has been an increase in the availability of protein structures, not only for new proteins but also for the same protein crystallized with different molecules or proteins. While protein design software has been successful, it can be sensitive to small conformational differences between structures of the same protein. To address this issue, the authors introduce pyFoldX, a Python library that allows the integrative analysis of structures of the same protein using FoldX. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module, and seamless integration with the Python programming language's data analysis ecosystem.
Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Aryaman Joshi, Shweata Maurya, Atharva Mahale, Soumya Lipsa Rath, Timir Tripathi, Aditya K. Padhi
Summary: This study performs a comparative analysis of the transmissibility and disease progression characteristics of different variants of SARS-CoV-2. The simulation findings suggest that the BA.1 variant dominates over others in terms of global prevalence. The results align well with experimental and epidemiological data.
Article
Multidisciplinary Sciences
Gabriele Orlando, Daniele Raimondi, Ramon Duran-Romana, Yves Moreau, Joost Schymkowitz, Frederic Rousseau
Summary: Structural bioinformatics lacks interfaces connecting with machine learning methods, hindering the application of modern neural network architectures. PyUUL is introduced as a library that translates biological structures into 3D tensors, enabling the application of state-of-the-art deep learning algorithms. The library also supports GPU and sparse calculation, and can be used to address typical bioinformatics problems.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Jing Xue, Yan Han, Hamid Baniasadi, Weizhong Zeng, Jimin Pei, Nick Grishin, Junmei Wang, Benjamin P. Tu, Youxing Jiang
Summary: TMEM120A, also known as TACAN, is a novel membrane protein highly conserved in vertebrates and has been proposed to function as an enzyme for fatty acid metabolism, rather than a mechanosensitive channel, based on the cryo-EM structure analysis presented in this study.
Article
Multidisciplinary Sciences
Georgios E. Premetis, Angeliki Stathi, Anastassios C. Papageorgiou, Nikolaos E. Labrou
Summary: Multidrug-resistant (MDR) bacteria, especially Enterococcus faecium, pose a significant threat to public health. In this study, a potential peptidoglycan-degrading enzyme (PDE), EfAmi1, was identified in the E. faecium genome. EfAmi1 showed strong lytic and antimicrobial activities against clinically isolated bacterial pathogens. The crystal structure of the N-terminal amidase-2 domain in EfAmi1 was determined, revealing its potential as a promising new antimicrobial agent in the post-antibiotic era.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Lisha Ye, Peikun Wu, Zhenling Peng, Jianzhao Gao, Jian Liu, Jianyi Yang
Summary: Protein model quality assessment is crucial in structure prediction, and QDistance is a new approach using inter-residue distances to estimate both global and local qualities. By comparing with reference models and incorporating predicted distances, QDistance proves to be competitive and robust in predicting protein structure quality.
Article
Biochemical Research Methods
Damla Ovek, Ameer Taweel, Zeynep Abali, Ece Tezsezen, Yunus Emre Koroglu, Chung-Jung Tsai, Ruth Nussinov, Ozlem Keskin, Attila Gursoy
Summary: This web-based server provides navigation and visualization of possible interactions between SARS-CoV-2 and human host proteins. It catalogues all interactions, using an innovative interface mimicry strategy, allowing users to explore and view these interactions.
Article
Biochemistry & Molecular Biology
Nikolai N. Sluchanko, Eugene G. Maksimov, Yury B. Slonimskiy, Larisa A. Varfolomeeva, Antonina Y. Bukhanko, Nikita A. Egorkin, Georgy Tsoraev, Maria G. Khrenova, Baosheng Ge, Song Qin, Konstantin M. Boyko, Vladimir O. Popov
Summary: This study presents the first crystal structures of OCP2 from cyanobacteria with different morphoecophysiological characteristics and provides a comprehensive comparison of their structure, spectroscopy, and function with OCP1, OCP3, and all-OCP ancestor. The structures enable the correlation of spectroscopic signatures with the effective number of hydrogen and the discovery of chalcogen bonds anchoring the ketocarotenoid in OCP, as well as the rotation of the echinenone's beta-ionone ring in the CTD. The structural data also helped rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Laiyi Fu, Yingxin Cao, Jie Wu, Qinke Peng, Qing Nie, Xiaohui Xie
Summary: UFold is a deep learning-based method for RNA secondary structure prediction, which uses a novel image-like representation of RNA sequences to achieve accurate predictions in a short time, outperforming previous methods on within-family datasets and showing similar performance on distinct RNA families.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Yoochan Myung, Douglas E. Pires, David B. Ascher
Summary: The study developed a machine learning method CSM-AB capable of predicting antibody-antigen binding affinity and accurately ranking near-native poses, showing promising results for the development of new immunotherapies.
Article
Biochemistry & Molecular Biology
Brian Jimenez-Garcia, Jorge Roel-Touris, Didier Barradas-Bautista
Summary: The LightDock Server is a web server for integrative modeling of macromolecular interactions, offering ease of use and improved user experience.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yi Zhang, Yong-ping Xu, Ju-kui Nie, Hong Chen, Genji Qin, Bo Wang, Xiao-Dong Su
Summary: The crystal structures of TCP domains in complex with different dsDNA reveal their unique DNA-binding motif and three-site recognition mode. The TCP domains show broad specificity for DNA sequences even shorter than the consensus binding sites, adding complexity to the regulatory network of plant TCP transcription factors.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yining Wang, Pengfei Li, Sajjan Rajpoot, Uzma Saqib, Peifa Yu, Yunlong Li, Yang Li, Zhongren Ma, Mirza S. Baig, Qiuwei Pan
Summary: This study found that remdesivir and favipiravir have the potential to inhibit HCoV-NL63 infection, with remdesivir showing higher affinity in cell culture models. Combining these drugs with interferon-alpha resulted in synergistic effects, suggesting their repurposing for treating HCoV-NL63 infection.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Liisa Holm, Aleksi Laiho, Petri Toronen, Marco Salgado
Summary: Structural comparison can detect remote homology missed by sequence comparison. The DALI web server offers structural analysis tools such as database searches, interactive visualization, and 3D structure alignment. In this study, we used DALI to mine the AlphaFold Database and discovered 100 previously unreported remote homologous relationships. The findings provided insights into protein families and allowed for the generation of functional hypotheses for further exploration in structural biology studies.
