AlphaFold2: A Role for Disordered Protein/Region Prediction?

Cited by (174)

Items 101–174 of 174

1. Development and tissue specific expression of RAPGEF1 (C3G) transcripts having exons encoding disordered segments with predicted regulatory function
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2. Exploring voltage-gated sodium channel conformations and protein–protein interactions using AlphaFold2
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3. The Myotubularin Related Proteins and the Untapped Interaction Potential of Their Disordered C‐Terminal Regions
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4. Phage-associated Cas12p nucleases require binding to bacterial thioredoxin for activation and cleavage of target DNA
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5. Miniaturizing and modifying natural proteins with Raygun
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6. Accurate and Fast Prediction of Intrinsic Disorder Using flDPnn
   Kui Wang, Gang Hu, Zhonghua Wu, Lukasz Kurgan · 2024 · Methods in molecular biology
7. The evolution and exploration of intrinsically disordered and phase-separated protein states
   Chi Fung Willis Chow, Ágnes Tóth-Petróczy · 2024 · Elsevier eBooks
8. Making use of machine learning
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9. Large protein databases reveal structural complementarity and functional locality
   Paweł Szczerbiak, Lukasz M. Szydlowski, Witold Wydmański, P. Douglas Renfrew, Julia Koehler Leman, Tomasz Kościółek · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
10. QuPepFold: A python package for hybrid quantum-classical protein folding simulations with CVaR-optimized VQE
    Akshay Uttarkar, Vidya Niranjan, Amit Saxena, Vinay Kumar · 2026 · PLoS ONE
11. Recent advances in the integration of protein mechanics and machine learning
    Yen‐Lin Chen, Shu‐Wei Chang · 2024 · Extreme Mechanics Letters
12. Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction
    Cong Wang, Bin Zhang · 2025 · Journal of Chemical Theory and Computation
13. Repetitive proteins that undergo large conformational changes evade structural prediction algorithms
    Marina P. Chang, Tianyi Jin, Alana P. Gudinas, Daniel Fernández, Alfredo Alexander‐Katz, Tsutomu Matsui, Danielle J. Mai · 2025 · The Journal of Chemical Physics
14. Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases
    Kui Wang, Gang Hu, Jing Yu, Lukasz Kurgan · 2026 · Cellular and Molecular Life Sciences
15. AlphaFold-based peptide structure prediction: Opportunities, limitations, and future directions
    Buke Zhang, Junjie Zhu, Hai-Feng Chen, Lu‐Ning Liu · 2026 · Biotechnology Advances
16. Decoding Protein Dynamics in Cells Using Chemical Cross‐Linking and Hierarchical Analysis**
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17. Complementarity of the residue-level protein function and structure predictions in human proteins
    Bálint Biró, Bi Zhao, Lukasz Kurgan · 2022 · Computational and Structural Biotechnology Journal
18. The intrinsically disordered protein glue of myelin: Linking AlphaFold2 predictions to experimental data
    Oda C. Krokengen, Arne Raasakka, Petri Kursula · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
19. SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection
    Dimitriya Hristoforova Garvanska, R. Elias Alvarado, Filip Oskar Mundt, Emma Nilsson, Josephine Kerzel Duel, Fabian Coscia, Richard Lindqvist, Kumari G. Lokugamage, Bryan A. Johnson, Jessica A. Plante et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
20. AI ‐Based Protein Structure Predictions and Their Implications in Drug Discovery
    Tahsin F. Kellici, Dimitar Hristozov, Iñaki Morao · 2024 · Wiley eBooks
21. Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures
    Christopher J. Williams, Vincent B. Chen, David C. Richardson, Jane S. Richardson · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
22. Viral replication modulated by hallmark conformational ensembles: how AlphaFold-predicted features of RdRp folding dynamics combined with intrinsic disorder-mediated function enable RNA virus discovery
    Rachid Tahzima, Justine Charon, Adrián Díaz, Kris De Jonghe, Sébastien Massart, Thierry Michon, Wim Vranken · 2025 · Frontiers in Virology
23. Structural disorder and distinctive motifs in the C-terminal region of the MADS-domain transcription factors are conserved across diverse taxa
    Erandi Ramírez-Aguirre, Teresa Nava-Ramírez, Alejandra Alicia Covarrubias, Adriana Garay‐Arroyo · 2025 · PLoS ONE
24. Metal‐Coordination Specificity and Structural Dynamics of C. elegans Metallothionein I: Insights From 3D Modeling and MD Simulations
    Nilvea Ramalho de Oliveira, Andrei Santos Siqueira, Paulo Sérgio Alves Bueno, Evonnildo Costa Gonçalves, Juliano Zanette · 2025 · Proteins Structure Function and Bioinformatics
25. A Survey of Predicted Protein–Protein Interactions Involving Disordered Regions in Humans
    Jimin Pei, J. Jillian Zhang, Qian Cong · 2026 · Journal of Molecular Biology
26. Comparative Analysis of AlphaFold2 Models and Intrinsic Disorder Illuminates Structural Divergence as a Symptom of Functional Divergence Across the Calmodulin Superfamily
    Kyoko Motomochi Nakamura, Jessica Siltberg-Liberles · 2026 · Journal of Molecular Evolution
27. ProtCross: Bridging the PDB-AlphaFold Gap for Binding Site Prediction with Protein Point Clouds
    Shuyu Zhong, Yuying Jiang · 2026 · Journal of Chemical Information and Modeling
28. The intrinsic disorder challenge for AlphaFold: A case study of G3BP1 and pathogenic peptide
    Yucong Li, Zhiying Yao, Zilin Song, Peiguo Yang, Jing Huang, Kai Lei, You Cheng Xu · 2026 · iScience
29. Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families
    Shivani Singh, Ruhani Singh, Sunita Sharma · 2026 · BioData Mining
30. Decoding full-length factor VIII through the structural and functional lens of its B domain
    Samhitha Urs Ramaraje Urs, Jean‐Luc Pellequer, Jean‐Marie Teulon, Boxue Ma, Deniz Ugurlar, Simone Gasper, Anna Pepanian, Jens Müller, Diana Imhof, Sneha Singh et al. · 2026 · Blood Vessels Thrombosis & Hemostasis
31. Computational prediction of analog compounds of the membrane protein MCHR1 antagonists ALB-127158 and KRX-104130
    Emrah Sarıyer, Ayşegül Saral · 2023 · Journal of Bioenergetics and Biomembranes
32. Enhancing ProteinBERT: Integrating Intrinsically Disordered Proteins for Comprehensive Proteomic Predictions
    J. Stone, H. B. Tabrizi, Rittika Shamsuddin · 2023 · IEEE International Conference on Bioinformatics and Biomedicine
33. Identification of Catechins Binding Pockets in Monomeric A β 42 Through Ensemble Docking and MD Simulations
    Rohoullah Firouzi, Shahin Sowlati‐Hashjin, Cecilia Chávez-García, Mitra Ashouri, Mohammad Hossein Karimi‐Jafari, Mikko Karttunen · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
34. Dissection of the role of a SH3 domain in the evolution of binding preference of paralogous proteins
    Pascale Lemieux, David T. Carreon Bradley, Alexandre K. Dubé, Ugo Dionne, Christian R. Landry · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
35. AI-driven discovery of host thioredoxin as a CRISPR enhancer of phage-encoded miniature Cas12 hacker nuclease
    Zhipeng Wang, Yujue Wang, Hui Gao, Jian Dai, Na Tang, Yannan Wang, Quanjiang Ji · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
36. Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins
    Cong Wang, Bin Zhang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
37. ESMDisPred: A Structure-Aware CNN-Transformer Architecture for Intrinsically Disordered Protein Prediction
    Md Wasi Ul Kabir, Ayon Dey, Farzeen Nafees, Md Tamjidul Hoque · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
38. Disentangling the Protein Order/Disorder Continuum Using a Sequence-Based Foldability Score
    Apolline Bruley, Tristan Bitard‐Feildel, Isabelle Callebaut, Élodie Duprat · 2022 · SSRN Electronic Journal
39. Integrative Data Mining Pipeline for Identification of a Protein- Based Prognostic Signature in Lung Squamous Cell Carcinoma
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40. Identification of short protein-destabilizing sequences in Arabidopsis cyclin-dependent kinase inhibitors, ICKs
    Shengjian Ye, Sheng Wang, Ron Chan, Ling Cao, Hong Wang · 2023 · Journal of Experimental Botany
41. Additional file 1 of Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set
    David F. Stein, Meltem Ece Kars, Yiming Wu, Çiğdem Sevim Bayrak, Peter D. Stenson, D.N. Cooper, Avner Schlessinger, Yuval Itan · 2023 · Figshare
42. B-Cell Epitope Prediction for Antipeptide Paratopes with the HAPTIC2/HEPTAD User Toolkit (HUT)
    Salvador Eugenio C. Caoili · 2012 · Methods in molecular biology
43. Complexes of HMO1 with DNA: Structure and Affinity
    Daria K. Malinina, Grigoriy A. Armeev, O. V. Geraskina, Anna N. Korovina, Vasily M. Studitsky, Alexey V. Feofanov · 2024 · Biomolecules
44. Identification of a cooperative effect between amino acids 169 and 174 in the rotavirus NSP4 double-layered particle-binding domain
    Jayme Herbert, Alberdina Aike van Dijk · 2024 · Journal of General Virology
45. Proton selective conductance and gating of lysosomal cation channel TMEM175
    Tobias Schulze, Timon Sprave, Carolin Groebe, Jan H. Krumbach, Magnus Behringer, Kay Hamacher, Gerhard Thiel, Christian M. Grimm, Oliver Rauh · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
46. Structural characterization of pyruvic oxime dioxygenase, a key enzyme in heterotrophic nitrification
    Tsujino, Shuhei, Yamada, Yusuke, Senda, Miki, Nakamura, Akihiko, Senda, Toshiya, Fujiwara, Taketomo · 2025 · Journal of Bacteriology
47. Environmental sensitivity of amyloidogenic motifs in fungal NOD-like receptor-mediated immunity: Molecular and structural insights into amyloid assembly
    Oliwia Polańska, Natalia Szulc, Witold Dyrka, Alicja W. Wojciechowska, Małgorzata Kotulska, Andrzej Marek Żak, Marlena Gąsior‐Głogowska, Monika Szefczyk · 2025 · International Journal of Biological Macromolecules
48. N-Myc downstream regulated gene 1b is a regulator of cell adhesion during early muscle development
    Prableen K Chowdhary, Rachel M. Brewster · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
49. Variant characterization in the intrinsically disordered human proteome
    Dalmira Hubrich, Jesús Alvarado-Valverde, Chop Yan Lee, Milena Djokic, Mareen Welzel, Kristina Hintz, Joelle Morgan Strom, Katja Luck · 2026 · Nature Structural & Molecular Biology
50. Predicting blood group antigens: accessible or not?
    Piers J. Walser · 2025 · Blood
51. Exploring the Bottleneck in Cryo-EM Dynamic Disorder Feature and Advanced Hybrid Prediction Model
    Sen Zheng · 2025 · Biophysica
52. Comparative assessment of binding residue predictions in intrinsically disordered regions
    Sushmita Basu, Lukasz Kurgan · 2025 · Protein Science
53. Harnessing protein-folding algorithms to drug intrinsically disordered epitopes
    Jakub Lála, Stefano Angioletti‐Uberti · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
54. Liquid-liquid phase separation (LLPS) as a sensing and adaptation mechanism: An evidence-based hypothesis on AP2 transcription factors in the malaria parasite
    Valentín Iglesias, Yunuen Avalos‐Padilla, Oriol Bárcenas, Xavier Fernàndez‐Busquets · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
55. Additional file 2 of Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set
    David F. Stein, Meltem Ece Kars, Wu, Yiming, Bayrak, Çiğdem Sevim, Peter D. Stenson, D.N. Cooper, Avner Schlessinger, Yuval Itan · 2024 · Figshare
56. ZNRD2 Mediated Nucleoprotein Aggregation Impairs Respiratory Syncytial Virus Replication
    Haiwu Zhou, Mingbin He, Jinhong Du, Cong Liu, Weiwei Wang, Yuewen Han, Zhifei Li, Yali Qin, Mingzhou Chen · 2026 · Advanced Science
57. Computational Preprocessing Framework for Small-Molecule and $\alpha$-Synuclein Data Towards Parkinson's Drug Repurposing
    G. Angel, P.L. Sujatha · 2026 · International Conference on Mobile Computing and Sustainable Informatics (ICMCSI)
58. Comparison of clinical, pathological and genomic characteristics between Lynch and non-Lynch patients with MMRd endometrial carcinoma
    Haixin Mo, Weijian Zhang, Jihong Wei, Jiaqing Chen, Jiadi He, Xueqing Zeng, Baoyi Liu, Jing Huang, Liangliang Ren, Ronggang Li et al. · 2026 · BMC Cancer
59. Why is it so difficult to discover drugs for amyotrophic lateral sclerosis? A protein intrinsic disorder perspective
    Vladimir Nikolaevich Uversky · 2026 · Expert Opinion on Drug Discovery
60. Structural prediction of protein assemblies with deep learning
    Hélène Bret · 2023 · theses.fr (ABES)
61. Étude structurale de la calcyanine, nouvelle protéine impliquée dans la biominéralisation intracellulaire chez les cyanobactéries
    Geoffroy Gaschignard · 2023
62. Contribution of Cryo-Holography in electron microscopy for the study of biological materials
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63. Structural and interaction study of MEG family proteins and their role in liver fibrosis onset
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64. Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms
    Yanlin Mi, Arpit Shukla, Mark Tangney, Sabin Tabirca, Venkata V. B. Yallapragada · 2026 · Computational and Structural Biotechnology Journal
65. Location dependence of protein intrinsic disorder in Drosophila melanogaster
    Hassan-Sibroe A. Daanaa, Shigehiro Kuraku, Hiroshi D. Akashi, Kuniaki Saito · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
66. Comparative Sequence–Structural Analysis of TdNV-Korea Entry Factors Identifies Candidate Regions Associated with Host-Range Variation
    Yoon Ho Park, Rana Kim, Kun-Ho Song, Hyun Suk Jung · 2026 · International Journal of Molecular Sciences
67. AlphaFold-derived local structural confidence in BRCA1 missense variant interpretation: a ClinVar-based computational analysis
    Yaroslav Yasinskyi, Marianna Chopei, Andrei Sivolob · 2026 · Research Square
68. Short linear motifs—underexplored players driving Toxoplasma gondii infection
    Jesús Alvarado-Valverde, Karine Lapouge, Arne Boergel, Kim Remans, Katja Luck, Toby J. Gibson · 2026 · Microbiology Spectrum
69. Acid–Base Properties of Model Copolypeptides from Molecular Simulations and Experiments
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70. Structural T‐Cell Receptor Analysis in the Age of Machine Learning
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71. Pathogen effectors and their implications for crop genetic improvement
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72. Structural thermodynamics by cryo-EM resolves minute energy differences in heterogeneous protein complexes
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73. The Disordome Paradigm: How Intrinsic Disorder Encodes Emergent Biological Function
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74. Endogenous targets of Zuo1-mediated mRNA surveillance encode proteins with higher predicted disorder
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