New perspectives in cancer drug development: computational advances with an eye to design

Matteo Castelli, Stefano A. Serapian, Filippo Marchetti, Alice Triveri, Valentina Pirota, Luca Torielli, Simona Collina, Filippo Doria, Mauro Freccero and Giorgio Colombo

RSC Med. Chem., 2021, 12, 1491
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Oncogenic R248W mutation induced conformational perturbation of the p53 core domain and the structural protection by proteomimetic amyloid inhibitor ADH-6

Qian Liu, Yawei Yu and Guanghong Wei

Phys. Chem. Chem. Phys., 2024, 26, 20068
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Mechanistic insight into the destabilization of p53TD tetramer by cancer-related R337H mutation: a molecular dynamics study

Yawei Yu, Xuewei Dong, Yiming Tang, Le Li and Guanghong Wei

Phys. Chem. Chem. Phys., 2022, 24, 5199
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Kristine Degn, Ludovica Beltrame, Freja Dahl Hede, Valentina Sora, Vincenzo Nicolaci, Marina Vabistsevits, Kjeld Schmiegelow, Karin Wadt, Matteo Tiberti, Matteo Lambrughi and Elena Papaleo

Journal of Molecular Biology, 2022, 434, 167663
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A Small Molecule Reacts with the p53 Somatic Mutant Y220C to Rescue Wild-type Thermal Stability

Keelan Z. Guiley and Kevan M. Shokat

Cancer Discovery, 2023, 13, 56
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Dynamic Mechanisms of Neutral Amino Acid Exchanger ASCT2 Transporting Substrate Glutamine

Huamin Zhang, Mingyu Zhang, Huining Hou, Yingqing Chen, Weibing Sun and Qianqian Wang

J. Chem. Inf. Model., 2025, 65, 8238
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Water Leakage Pathway Leads to Internal Hydration of the p53 Core Domain

Igor D. M. Lima, Murilo M. Pedrote, Mayra A. Marques, Gileno dos S. de Sousa, Jerson L. Silva, Guilherme A. P. de Oliveira and Elio A. Cino

Biochemistry, 2023, 62, 35
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Computational strategies for protein conformational ensemble detection

Ali Rana Atilgan and Canan Atilgan

Current Opinion in Structural Biology, 2022, 72, 79
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Comparative study of innovative computational methods for identifying cryptic pockets

Yonggui Li, Lingling Song, Yawen Dong and Ge-Fei Hao

Drug Discovery Today, 2025, 30, 104430
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The Discovery of Cryptic Pockets Increases the Druggability of “Undruggable” Proteins

Mingyue Mou, Weicheng Yang, Guangyi Huang, Xiaoyan Yang, Xiao Zhang, Wasala Mudiyanselage Wishwajith Wickramabahu Kandegama, Charles R. Ashby, Gefei Hao and Yangyang Gao

Medicinal Research Reviews, 2025
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Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency

Marta Rigoli, Giovanni Spagnolli, Giulia Lorengo, Paola Monti, Raffaello Potestio, Emiliano Biasini and Alberto Inga

IJMS, 2022, 23, 7960
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Anticancer therapeutic strategies for targeting mutant p53-Y220C

Vitaly Chasov, Damir Davletshin, Elvina Gilyazova, Regina Mirgayazova, Anna Kudriaeva, Raniya Khadiullina, Youyong Yuan and Emil Bulatov

J Biomed Res, 2024, 38, 222
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Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes

Yue Wu, Siqin Cao, Yunrui Qiu and Xuhui Huang

The Journal of Chemical Physics, 2024, 160
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Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants

Artur Meller, Devin Kelly, Louis G. Smith and Gregory R. Bowman

Protein Science, 2024, 33
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AMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular Dynamics

Siqin Cao, Feliks Nüske, Bojun Liu, Micheline B. Soley and Xuhui Huang

J. Chem. Theory Comput., 2025, 21, 4855
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An integrated view of p53 dynamics, function, and reactivation

Özlem Demir, Emilia P Barros, Tavina L Offutt, Mia Rosenfeld and Rommie E Amaro

Current Opinion in Structural Biology, 2021, 67, 187
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Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain

Shruti Koulgi, Archana Achalere, Uddhavesh Sonavane and Rajendra Joshi

J. Chem. Inf. Model., 2022, 62, 6449
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How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations

Fanny Kozak and Dennis Kurzbach

Computational and Structural Biotechnology Journal, 2021, 19, 2097
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Manifold learning in atomistic simulations: a conceptual review

Jakub Rydzewski, Ming Chen and Omar Valsson

Mach. Learn.: Sci. Technol., 2023, 4, 031001
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Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space

Bojun Liu, Jordan G. Boysen, Ilona Christy Unarta, Xuefeng Du, Yixuan Li and Xuhui Huang

Nat Commun, 2025, 16
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Memory kernel minimization-based neural networks for discovering slow collective variables of biomolecular dynamics

Bojun Liu, Siqin Cao, Jordan G. Boysen, Mingyi Xue and Xuhui Huang

Nat Comput Sci, 2025, 5, 562
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Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs

Ruth Nussinov, Mingzhen Zhang, Ryan Maloney, Yonglan Liu, Chung-Jung Tsai and Hyunbum Jang

Journal of Molecular Biology, 2022, 434, 167569
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An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes

Yunrui Qiu, Michael S. O’Connor, Mingyi Xue, Bojun Liu and Xuhui Huang

J. Chem. Theory Comput., 2023, 19, 4728
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Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning

Kirill A. Konovalov, Ilona Christy Unarta, Siqin Cao, Eshani C. Goonetilleke and Xuhui Huang

JACS Au, 2021, 1, 1330
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Network Theory Analysis of Allosteric Drug-Rescue Mechanisms in the Tumor Suppressor Protein p53 Y220C Mutant

Benjamin S. Cowan and Kelly M. Thayer

IJMS, 2025, 26, 6884
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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation

Olof Stenström, Candide Champion, Marc Lehner, Guillaume Bouvignies, Sereina Riniker and Fabien Ferrage

Current Opinion in Structural Biology, 2022, 77, 102459
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Memory Unlocks the Future of Biomolecular Dynamics: Transformative Tools to Uncover Physical Insights Accurately and Efficiently

Anthony J. Dominic, Siqin Cao, Andrés Montoya-Castillo and Xuhui Huang

J. Am. Chem. Soc., 2023, 145, 9916
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Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM

Mohamed Marzouk Sobeh and Akio Kitao

J. Chem. Inf. Model., 2022, 62, 1294
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Understanding the conformational dynamics of PI3Kα due to helical domain mutations: insights from Markov state model analysis

Vinod Jani, Uddhavesh Sonavane and Sangeeta Sawant

Mol Divers, 2025
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Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies

Shashank Pant, Sepehr Dehghani-Ghahnaviyeh, Noah Trebesch, Ali Rasouli, Tianle Chen, Karan Kapoor, Po-Chao Wen and Emad Tajkhorshid

J. Phys. Chem. B, 2025, 129, 3703
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