Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations by Yulan Liu, Yunong Xu, Yinuo Xu, Zhihao Zhao, Gui-Juan Cheng, Ruobing Ren, Ying-Chih Chiang

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Do NSm Virulence Factors in the <i>Bunyavirales</i> Viral Order Originate from Gn Gene Duplication? by Victor Lefebvre, Ravy Leon Foun Lin, Laura Cole, François-Loïc Cosset, Marie-Laure Fogeron, Anja Böckmann

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A Single <i>Aspergillus fumigatus</i> Gene Enables Ergothioneine Biosynthesis and Secretion by <i>Saccharomyces cerevisiae</i> by Sean Doyle, Daragh D. Cuskelly, Niall Conlon, David A. Fitzpatrick, Ciara B. Gilmartin, Sophia H. Dix, Gary W. Jones

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Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome by Briallen Lobb, Anson Shapter, Andrew C. Doxey, Jozef I. Nissimov

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Structural Evolution of Primate Glutamate Dehydrogenase 2 as Revealed by In Silico Predictions and Experimentally Determined Structures by Ionela Litso, Andreas Plaitakis, Vasiliki E. Fadouloglou, Mary Providaki, Michael Kokkinidis, Ioannis Zaganas

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PINNED: identifying characteristics of druggable human proteins using an interpretable neural network by Michael Cunningham, Danielle Pins, Zoltán Dezső, Maricel Torrent, Aparna Vasanthakumar, Abhishek Pandey

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In Silico Study of Superoxide Dismutase Gene Family in Potato and Effects of Elevated Temperature and Salicylic Acid on Gene Expression by Jelena Rudić, Milan B. Dragićević, Ivana Momčilović, Ana D. Simonović, Danijel Pantelić

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Anammox Bacterial <i>S</i>-Adenosyl-<span style="font-variant: small-caps">l</span>-Methionine Dependent Methyltransferase Crystal Structure and Its Interaction with Acyl Carrier P... by Tesshin Uegaki, Taisei Takei, Shuhei Yamaguchi, Keisuke Fujiyama, Yusuke Sato, Tomoya Hino, Shingo Nagano

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High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny by Nicole A. P. Lieberman, Thaddeus D. Armstrong, Benjamin Chung, Daniel Pfalmer, Christopher M. Hennelly, Austin Haynes, Emily Romeis, Qian-Qiu Wang, Qian-Qiu Wang, Rui-Li Zhang, Cai-Xia Kou, Cai-Xia Kou, Giulia Ciccarese, Ivano Dal Conte, Marco Cusini, Francesco Drago, Shu-ichi Nakayama, Kenichi Lee, Makoto Ohnishi, Kelika A. Konda, Kelika A. Konda, Silver K. Vargas, Silver K. Vargas, Maria Eguiluz, Carlos F. Caceres, Jeffrey D. Klausner, Oriol Mitja, Oriol Mitja, Anne Rompalo, Fiona Mulcahy, Edward W. Hook, Edward W. Hook, Edward W. Hook, Irving F. Hoffman, Irving F. Hoffman, Mitch M. Matoga, Mitch M. Matoga, Heping Zheng, Heping Zheng, Bin Yang, Bin Yang, Eduardo Lopez-Medina, Eduardo Lopez-Medina, Lady G. Ramirez, Lady G. Ramirez, Justin D. Radolf, Justin D. Radolf, Justin D. Radolf, Justin D. Radolf, Justin D. Radolf, Kelly L. Hawley, Kelly L. Hawley, Kelly L. Hawley, Kelly L. Hawley, Juan C. Salazar, Juan C. Salazar, Juan C. Salazar, Sheila A. Lukehart, Sheila A. Lukehart, Arlene C. Seña, Jonathan B. Parr, Lorenzo Giacani, Lorenzo Giacani, Alexander L. Greninger, Alexander L. Greninger

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Deconvolution of the MBP-Bri2 Interaction by a Yeast Two Hybrid System and Synergy of the AlphaFold2 and High Ambiguity Driven Protein-Protein Docking by Evgeniya V. Smirnova, Tatiana V. Rakitina, George A. Saratov, Anna A. Kudriaeva, Alexey A. Belogurov

“…Since the spatial structures for both MBP and Bri2 were not known, we used computational methods of structural biology including an artificial intelligence system AlphaFold2 and high ambiguity driven protein-protein docking (HADDOCK 2.1) to gain a mechanistic explanation of the found protein-protein interaction and elucidate a possible structure of the complex of MBP with Bri23R peptide. …”
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Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS by Yuya Hatano, Tomohiko Ishihara, Osamu Onodera

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SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models by Kobe Janssen, Ramon Duran-Romaña, Guy Bottu, Mainak Guharoy, Alexander Botzki, Frederic Rousseau, Joost Schymkowitz

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A computational study of the structure and function of human Zrt and Irt-like proteins metal transporters: An elevator-type transport mechanism predicted by AlphaFold2 by Andrea Pasquadibisceglie, Adriana Leccese, Fabio Polticelli, Fabio Polticelli

“…Different conformations of the representative hZIP transporters were obtained through a modified version of the AlphaFold2 algorithm. The inward and outward-facing conformations obtained suggest that the hZIP proteins function with an “elevator-type” mechanism.…”
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Comparing 2 crystal structures and 12 AlphaFold2-predicted human membrane glucose transporters and their water-soluble glutamine, threonine and tyrosine variants – CORRIGENDUM by Eva Smorodina, Fei Tao, Rui Qing, David Jin, Steve Yang, Shuguang Zhang

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Exploring AlphaFold2′s Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein by Haifan Zhao, Heng Zhang, Zhun She, Zengqiang Gao, Qi Wang, Zhi Geng, Yuhui Dong

Subjects: “…AlphaFold2…”
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Orthogonal analysis of variants in APOE gene using in-silico approaches reveals novel disrupting variants by Chang Li, Ian Hou, Mingjia Ma, Grace Wang, Yongsheng Bai, Yongsheng Bai, Xiaoming Liu

Subjects: “…AlphaFold…”
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CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome by Shiwei Wang, Haoyu Lin, Zhixian Huang, Yufeng He, Xiaobing Deng, Youjun Xu, Jianfeng Pei, Luhua Lai

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Conservation of Three-Dimensional Structure of Lepidoptera and Trichoptera L-Fibroins for 290 Million Years by Russell J. Stewart, Paul B. Frandsen, Steffen U. Pauls, Jacqueline Heckenhauer

Subjects: “…AlphaFold2…”
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AI-based protein models enhance the accuracy of experimentally determined protein crystal structures by Ki Hyun Nam, Ki Hyun Nam

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The Difference in Structural States between Canonical Proteins and Their Isoforms Established by Proteome-Wide Bioinformatics Analysis by Zarifa Osmanli, Theo Falgarone, Turkan Samadova, Gudrun Aldrian, Jeremy Leclercq, Ilham Shahmuradov, Andrey V. Kajava

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