Using AlphaFold Predictions in Viral Research

Daria Gutnik, Peter Evseev, Konstantin Miroshnikov and Mikhail Shneider

CIMB, 2023, 45, 3705
DOI: 10.3390/cimb45040240

The Active Site of the Enzyme 10-Formyl-THFDH in the Honey Bee Apis mellifera—A Key Player in Formic Acid Detoxification

Moritz Mating, Ye Zou, Soroush Sharbati and Ralf Einspanier

IJMS, 2022, 24, 354
DOI: 10.3390/ijms24010354

Target engagement in bacterial and protozoan pathogens: in vitro and cellular assays for drug discovery

Priscila Z. Ramos, Carolina M.C. Catta-Preta and Rafael M. Couñago

Current Opinion in Structural Biology, 2026, 96, 103194
DOI: 10.1016/j.sbi.2025.103194

Advancing time-resolved structural biology: latest strategies in cryo-EM and X-ray crystallography

Amir Banari, Amit K. Samanta, Anna Munke, Tim Laugks, Saša Bajt, Kay Grünewald, Thomas C. Marlovits, Jochen Küpper, Filipe R.N.C. Maia, Henry N. Chapman, Dominik Oberthür and Carolin Seuring

Nat Methods, 2025, 22, 1420
DOI: 10.1038/s41592-025-02659-6

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

Ruth Nussinov, Mingzhen Zhang, Yonglan Liu and Hyunbum Jang

Drug Discovery Today, 2023, 28, 103551
DOI: 10.1016/j.drudis.2023.103551

Unlocking the secrets of SARS-CoV-2 nsp3 by combining experiments with AlphaFold2 domain prediction

Maximilian Edich, Yunyun Gao, David C Briggs and Andrea Thorn

Life Sci. Alliance, 2026, 9, e202503247
DOI: 10.26508/lsa.202503247

Generating Protein Structures for Pathway Discovery Using Deep Learning

Konstantia Georgouli, Robert R. Stephany, Jeremy O. B. Tempkin, Claudio Santiago, Fikret Aydin, Mark A. Heimann, Loïc Pottier, Xiaohua Zhang, Timothy S. Carpenter, Tim Hsu, Dwight V. Nissley, Frederick H. Streitz, Felice C. Lightstone, Helgi I. Ingolfsson and Peer-Timo Bremer

J. Chem. Theory Comput., 2024, 20, 8795
DOI: 10.1021/acs.jctc.4c00816

Learning molecular machines by machine learning

Rumeysa Hilal Çelik, Hacı Aslan Onur İşcil, Ecem Bulut and Saliha Ece Acuner

Eurasian Journal of Science Engineering and Technology, 2025, 6, 100
DOI: 10.55696/ejset.1620495

Generative artificial intelligence performs rudimentary structural biology modeling

Alexander M. Ille, Christopher Markosian, Stephen K. Burley, Michael B. Mathews, Renata Pasqualini and Wadih Arap

Sci Rep, 2024, 14
DOI: 10.1038/s41598-024-69021-2

Protein crystallization strategies in structure-based drug design

Margareta Ek, Linda Öster, Helena Käck and Tove Sjögren

Expert Opinion on Drug Discovery, 2026, 21, 201
DOI: 10.1080/17460441.2025.2605355

Embedding AI in the Protein Crystallography Workflow

Richard J. Gildea, Christian M. Orr, Neil G. Paterson and David R. Hall

Synchrotron Radiation News, 2022, 35, 51
DOI: 10.1080/08940886.2022.2114723

A Perspective on the Prospective Use of AI in Protein Structure Prediction

Raphaelle Versini, Sujith Sritharan, Burcu Aykac Fas, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, Oliver Nüsse, Jessica Andreani, Marc Baaden, Patrick Fuchs, Tatiana Galochkina, Alexios Chatzigoulas, Zoe Cournia, Hubert Santuz, Sophie Sacquin-Mora and Antoine Taly

J. Chem. Inf. Model., 2024, 64, 26
DOI: 10.1021/acs.jcim.3c01361

AQuaRef: machine learning accelerated quantum refinement of protein structures

Roman Zubatyuk, Malgorzata Biczysko, Kavindri Ranasinghe, Nigel W. Moriarty, Hatice Gokcan, Holger Kruse, Billy K. Poon, Paul D. Adams, Mark P. Waller, Adrian E. Roitberg, Olexandr Isayev and Pavel V. Afonine

Nat Commun, 2025, 16
DOI: 10.1038/s41467-025-64313-1

Exploring AlphaFold2′s Performance on Predicting Amino Acid Side-Chain Conformations and Its Utility in Crystal Structure Determination of B318L Protein

Haifan Zhao, Heng Zhang, Zhun She, Zengqiang Gao, Qi Wang, Zhi Geng and Yuhui Dong

IJMS, 2023, 24, 2740
DOI: 10.3390/ijms24032740

Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation

Wen Ma, Shengjun You, Michael Regnier and J. Andrew McCammon

Proc. Natl. Acad. Sci. U.S.A., 2023, 120
DOI: 10.1073/pnas.2215836120

AlphaFold2 and its applications in the fields of biology and medicine

Zhenyu Yang, Xiaoxi Zeng, Yi Zhao and Runsheng Chen

Sig Transduct Target Ther, 2023, 8
DOI: 10.1038/s41392-023-01381-z