Protein structure prediction using multiple deep neural networks in the 13th critical assessment of protein structure prediction (CASP13)

Cited by (350)

Items 201–300 of 350

1. A Reversible Spherical Geometric Conversion of Protein Backbone Structure Coordinate Matrix to Three Independent Vectors of ρ, θ and φ
   Wei Li · 2024 · Preprints.org
2. Advances in Protein Function Prediction from the Fifth CAFA Challenge
   M. Clara De Paolis Kaluza, Rashika Ramola, Parnal Joshi, Damiano Piovesan, Walter Reade, Sandra E. Orchard, Maria Jesus Martin, Alexandr Ignatchenko, Burkhard Rost, Christine Anne Orengo et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
3. AlphaFold2 assists in providing novel mechanistic insights into the interactions among the LUBAC subunits
   Chenchen Wang, Chunying Gu, Ying Lv, Hongyu Liu, Yanan Wang, Yongmei Zuo, Guangyu Jiang, Liu Lili, Jiafu Liu · 2024 · Acta Biochimica et Biophysica Sinica
4. Deep Genomics: Deep Learning-Based Analysis of Genome-Sequenced Data for Identification of Gene Alterations
   Sourabh Kumar, Prabudh Goel · 2025 · Methods in molecular biology
5. Black-box data: a new paradigm for biomedicine in the AI era
   Luca Naef, Michael M. Bronstein · 2026 · Chemical Science
6. Deep learning methods for Hamiltonian parameter estimation and magnetic domain image generation in twisted van der Waals magnets
   Woo Seok Lee, Taegeun Song, Kyoung-Min Kim · 2024 · Machine Learning Science and Technology
7. Computational Methods for Peptide Macrocycle Drug Design
   Vikram Khipple Mulligan · 2022 · AAPS advances in the pharmaceutical sciences series
8. Entropy and Variability: A Second Opinion by Deep Learning
   Daniel T. Rademaker, Li C. Xue, Peter A.C. ’t Hoen, Gert Vriend · 2022 · Biomolecules
9. A novel algorithm based on a modified PSO to predict 3D structure for proteins in HP model using Transfer Learning
   Mojtaba Rezaei, Mohammad Kheyrandish, Mohammad Mosleh · 2023 · Expert Systems with Applications
10. Mining the ZINC database of natural products for specific, testosterone-like, OXER1 antagonists
    Athanasios A. Panagiotopoulos, Evangelia K. Konstantinou, Stergios Pirintsos, Elias Castanas, Marilena Kampa · 2023 · Steroids
11. Artificial Intelligence in Bioinformatics
    V. Samuel Raj, Anjali Priyadarshini, Manoj Kumar Yadav, Ramendra Pati Pandey, Archana Anshuman Gupta, Arpana Vibhuti · 2021 · Wiley eBooks
12. Bridging functional annotation gaps in non-model plant genes with AlphaFold, DeepFRI and small molecule docking
    Georgie Stephan, Benjamin Dugdale, Pradeep Chand Deo, Robert M. Harding, James Langham Dale, Paul Visendi · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
13. xTrimoDock: Rigid Protein Docking via Cross-Modal Representation Learning and Spectral Algorithm
    Yujie Luo, Shaochuan Li, Yiwu Sun, Ruijia Wang, Tingting Tang, Beiqi Hongdu, Xingyi Cheng, Chuan Shi, Hui Li, Le Song · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
14. A novel approach to Caudoviricetes taxonomy utilising whole proteome structure-structure comparison
    Linda Ann Smith, Thomas Schmidt, Igor Tolstoy, Timofey Skvortsov, Colin Hill, Andrey Nikolaevich Shkoporov · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
15. Advancements in characterization of protein dynamics with machine learning
    Mohammad Madani, Anna Tarakanova · 2026 · npj Soft Matter
16. AlphaFold-based peptide structure prediction: Opportunities, limitations, and future directions
    Buke Zhang, Junjie Zhu, Hai-Feng Chen, Lu‐Ning Liu · 2026 · Biotechnology Advances
17. Membrane signalosome: Where biophysics meets systems biology
    Sreeja Kutti Kandy, Paul A. Janmey, Ravi Radhakrishnan · 2021 · Current Opinion in Systems Biology
18. New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction
    Jacob Barger, Badri Adhikari · 2021 · IEEE Transactions on Computational Biology and Bioinformatics
19. Smart Microfluidics: Synergy of Machine Learning and Microfluidics in the Development of Medical Diagnostics for Chronic and Emerging Infectious Diseases
    David Madukwe, Moore Ikechi Mike-Ogburia, Nonso Nduka, Japhet Nzeobi · 2023 · Critical Reviews in Biomedical Engineering
20. The saclayvirus Aci01-1 very long and complex fiber and its receptor at the Acinetobacter baumannii surface
    2023
21. Role of quantum technology and artificial intelligence for nano-enabled microfluidics
    Surendra Kumar Yadav, Kolleboyina Jayaramulu · 2024 · Elsevier eBooks
22. Advancing Pharmaceuticals with Machine Learning: A Short Review of Research and Development Applications
    Wajeeha Khalid, Muhammad Yahya Khalid, Madiha Hena, Atif Sarwar, Shahzaib Iqbal · 2023 · Pharmaceutical Communications
23. PolyFold: An interactive visual simulator for distance-based protein folding
    Andrew J. McGehee, Sutanu Bhattacharya, Rahmatullah Roche, Debswapna Bhattacharya · 2020 · PLoS ONE
24. A Stabilized Dense Network Approach for High-Dimensional Prediction
    Wenjing Yang, Yuhong Yang · 2021 · International Joint Conference on Neural Networks (IJCNN)
25. Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps
    Bahareh Behkamal, Mahmoud Naghibzadeh, Mohammad Reza Saberi, Zeinab Amiri‐Tehranizadeh, Andrea Pagnani, Kamal Al Nasr · 2021 · Biomolecules
26. Asymptotic Proximal Point Methods for Global Optimization
    Xiaopeng Luo, Xin Xu, Herschel Rabitz · 2025 · Journal of Scientific Computing
27. Identifying Native and Non-native Membrane Protein Loops by Using Stabilizing Energetic Terms of Three Popular Force Fields
    Konda Mani Saravanan, Haiping Zhang, Yanjie Wei · 2020 · Current Chinese Science
28. Identification, Characterization, and In Silico Analysis of New Imine Reductases From Native Streptomyces Genomes
    César Iglesias, Ariel Tijman, Gonzalo López, María Inés Lapaz, María Julia Pianzzola, Paola Panizza, Sonia Rodríguez Giordano · 2021 · Frontiers in Catalysis
29. Development of Integrated Machine Learning and Data Science Approaches for the Prediction of Cancer Mutation and Autonomous Drug Discovery of Anti-Cancer Therapeutic Agents
    Steve Agajanian · 2021 · Chapman University Digital Commons (Chapman University)
30. A machine learning protocol for predicting structural distributions of amyloid-forming proteins from 2D IR spectra
    Sheng Ye, Binbin Wang, Жипенг Ли, Lvshuai Zhu, Chang Yin Sun, Shaul Mukamel, Jun Jiang · 2025 · Proceedings of the National Academy of Sciences
31. Designing synthetic transcription factors: A structural perspective
    Aparna Boral, Madhurima Khamaru, Devrani Mitra · 2022 · Advances in protein chemistry and structural biology
32. Scoring protein sequence alignments using deep learning
    Bikash Shrestha, Badri Adhikari · 2022 · Bioinformatics
33. Phytochemical screening, in vitro and in silico antibacterial investigation of Elaeocarpus ganitrus extract
    Cicilia Novi Primiani, Weka Sidha Bhagawan, Pujiati Pujiati, Dewi Ratih Tirto Sari · 1970 · Jurnal Biota
34. Chemogenomic approach to identifying nematode chemoreceptor drug targets in the entomopathogenic nematode Heterorhabditis bacteriophora
    Reeham Motaher, Emilia Grill, Elise L. McKean, Eric Kenney, Ioannis Eleftherianos, John M. Hawdon, Damien M. O’Halloran · 2021 · Computational Biology and Chemistry
35. Artificial intelligence in early stages of structure-based drug discovery
    Rahul Ravichandran, Sumin Park, Stasa Skorupan, Kaitlyn Bessette, Francesco Gentile · 2024 · Elsevier eBooks
36. A Peptides Prediction Methodology with Fragments and CNN for Tertiary Structure Based on GRSA2
    Juan Paulo Sánchez-Hernández, Juan Frausto–Solís, Diego A. Soto-Monterrubio, Juan Javier González Barbosa, Edgar Román-Rangel · 2022 · Axioms
37. Rejoinder on: Recent advances in directional statistics
    Arthur Pewsey, Eduardo García‐Portugués · 2021 · Test
38. Computational studies of the mitochondrial carrier family SLC25. Present status and future perspectives
    Andrea Pasquadibisceglie, Fabio Polticelli · 2021 · Bio-Algorithms and Med-Systems
39. Near-complete protein structural modelling of the minimal genome
    Joe G. Greener, Nikita Desai, Shaun M. Kandathil, David T. Jones · 2020 · arXiv (Cornell University)
40. Efficient Generative Modelling of Protein Structure Fragments using a Deep Markov Model
    Christian Bahne Thygesen, Ahmad Salim Al-Sibahi, Christian S. Steenmanns, Lys Sanz Moreta, Anders B. Sørensen, Thomas Hamelryck · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
41. Graph Convolutional Network for predicting secondary structure of RNA
    Dmitry Korkin, Aukkawut Ammartayakun, Palawat Busaranuvong, Roya Khosravi‐Far · 2024 · Research Square
42. Should We Expect a Second Wave of AlphaFold Misuse After the Nobel Prize?
    Alexandre G. de Brevern · 2024 · BioMedInformatics
43. Editorial: Revolutionizing life sciences: the nobel leap in artificial intelligence-driven biomodeling
    Valentina Tozzini, Cecilia Giulivi · 2025 · Frontiers in Molecular Biosciences
44. Protein Structure Description with ρ, θ and ϕ : A Case Study with Caenopore-5
    Wei Li · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
45. Highly Accurate Protein Structure Classification and Prediction
    Anirban Saha, Indranil Sarkar · 2023 · International Conference on Computational Systems and Communication (ICCSC)
46. AlphaFold 2: revolucionando a modelagem de estruturas 3D de macromoléculas
    Vivian Morais Paixão, Angie Lissette Atoche Puelles, Eduardo U. M. Moreira, Luana Luiza Bastos, Raquel C. de Melo-Minardi · 2023 · BIOINFO
47. Quantum chemical “Aufbau” principles: how to estimate the shape of highly flexible (bio-)polymers? A recursively extendable “chemion picture” of Euler-Hückel-type
    Wolfhard H. G. Koch · 2024 · Journal of Molecular Modeling
48. Three-Dimensional Interaction Homology: Deconstructing Residue–Residue and Residue–Lipid Interactions in Membrane Proteins
    Glen E. Kellogg · 2024 · Molecules
49. Redefining Protein Structure Prediction: Insights from AlphaFold’s Methodology and Applications
    Reema Abdallah, Sarah Alshumayri, Lujain Bukassim · 2025 · Learning and Technology Conference (L&T)
50. Cryogenic electron microscopy and tomography of ex vivo and in situ virus particles
    Lily Xu, Wah Chiu · 2025 · Elsevier eBooks
51. Homology Modeling in Protein Structure Predictions
    Khac‐Minh Thai, Trong-Khoa Nguyen, Dac-Nhan Nguyen, Minh-Tri Le · 2025 · Springer handbooks
52. Competitive interplay of cotton SELF PRUNING, FLOWERING LOCUS T, and FLOWERING LOCUS D proteins governing indeterminate flowering
    Muhammad Zubair Ghouri, Sultan Habibullah Khan, Zunaira Afzal Naveed, Iqrar Ahmad Rana, Aftab Ahmad · 2026 · Journal of Cotton Research
53. Quantum time-dependent statistical mechanics
    Mark E. Tuckerman · 2023 · Oxford University Press eBooks
54. Fisher’s legacy of directional statistics, and beyond to statistics on manifolds
    Kanti V. Mardia · 2025 · Journal of Multivariate Analysis
55. Big Data Analytics in Bioinformatics and Healthcare
    Zaharaddeen Karami Lawal, Rufai Yusuf Zakari, Navod Neranjan Thilakarathne, Haji Gul, Najib Abdulrazak, Hayati Yassin · 2025 · Studies in big data
56. Enhanced Methodology for Peptide Tertiary Structure Prediction Using GRSA and Bio-Inspired Algorithm
    Diego A. Soto-Monterrubio, Hernán Peraza-Vázquez, Adrián Fermín Peña-Delgado, José Genaro González-Hernández · 2025 · International Journal of Molecular Sciences
57. Precision Editing of NLRS Improves Effector Recognition for Enhanced Disease Resistance
    Vinit Kumar, Vishwa I. P. W. A. Kumara, P. C. G. Bandaranayake, Dong Yawen, Yangyang Gao, Junfeng Liu, Ge‐Fei Hao, Xiu‐Fang Xin · 2026 · Advanced Science
58. Fold recognition by scoring protein maps using the congruence coefficient
    Pietro Di Lena, Pierre Baldi · 2020 · Bioinformatics
59. Aviation Surveillance Information Fusion Based on Multi Neural Network
    Zhanchun Gao, Meng Zhiyuan · 2020 · IEEE International Conference on Computer and Communications (ICCC)
60. AIM in Pharmacology and Drug Discovery
    Hiroaki Iwata, Ryosuke Kojima, Yasushi Okuno · 2021 · Springer eBooks
61. Quantitative analysis of visual codewords of a protein distance matrix
    Jure Pražnikar, Nuwan T. Attygalle · 2022 · PLoS ONE
62. LPTD: a novel linear programming-based topology determination method for cryo-EM maps
    Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al Nasr · 2022 · Bioinformatics
63. ST-ChIP: Accurate prediction of spatiotemporal ChIP-seq data with recurrent neural networks
    Tong Liu, Zheng Wang · 2022 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
64. Biochemist Investigates Protein Folding
    Richard F. Dods · 2023 · Biomedical Materials & Devices
65. Myelin Basic Protein Attenuates Furin-Mediated Bri2 Cleavage and Postpones Its Membrane Trafficking
    Evgeniya V. Smirnova, Vladimir I. Timofeev, Tatiana V. Rakitina, Dmitry E. Petrenko, Olga S. Elmeeva, George A. Saratov, Anna A. Kudriaeva, Eduard Valeryevich Bocharov, Alexey A. Belogurov · 2024 · International Journal of Molecular Sciences
66. Protein Structure Prediction to Function Prediction Using AlphaFold
    Kentaro Tomii · 2024 · Seibutsu Butsuri
67. Nuclear translocation of the membrane oxoeicosanoid/androgen receptor, OXER1: Possible mechanisms involved
    Panagiotis Malamos, Konstantina Kalyvianaki, Athanasios A. Panagiotopoulos, Amalia P. Vogiatzoglou, Athanasia Artemis Tsikalaki, Anastasia Katifori, Hara Polioudaki, Maria N. Darivianaki, Panayiotis A. Theodoropoulos, Christos Α. Panagiotidis et al. · 2024 · Molecular and Cellular Endocrinology
68. Recapturing Cooperativity of α-Helix Formation and Packing in Coarse-Grained Protein Structure Modeling with Multitorsional Potentials
    Elizaveta F. Petrusevich, Adam Liwo · 2025 · The Journal of Physical Chemistry B
69. Structure-based drug design
    Syed Mudasir Ahmad, Nazir Ahmad Ganai, Basharat Ahmad Bhat · 2025 · Elsevier eBooks
70. Open Innovation Platform using Cloud-based Applications and Collaborative Space: A Case Study of Solubility Prediction Model Development
    Tsuyoshi Esaki, Keiko Kumazawa, Kazutoshi Takahashi, Reiko Watanabe, Tomohide Masuda, Hirofumi Watanabe, Yugo Shimizu, Akitoshi Okada, Seisuke Takimoto, Tomohiro Shimada et al. · 2020 · Chem-Bio Informatics Journal
71. Protein Decoy Generation via Adaptive Stochastic Optimization for Protein Structure Determination
    Ahmed Bin Zaman, Toki Tahmid Inan, Amarda Shehu · 2020 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
72. Computational Design of Potential Binder Protein for SARS-CoV-2 Spike RBD through A Novel Deep Neural Network Based-Protein Outpainting Algorithm
    Bingya Duan, Yingfei Sun · 2021 · International Conference on Biological Information and Biomedical Engineering (BIBE)
73. Model-based Data-Complexity Estimator for Deep Learning Systems
    Yuta Ojima, Shingo Horiuchi, Fuyuki Ishikawa · 2021 · IEEE International Conference on Artificial Intelligence Testing (AITest)
74. Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
    Adam Liwo, Adam K. Sieradzan, Agnieszka S. Karczyńska, Emilia A. Lubecka, Sergey A. Samsonov, Cezary R. Czaplewski, Paweł Krupa, Magdalena A. Mozolewska · 2021 · Springer eBooks
75. A Review of Protein Structure Prediction using Deep Learning
    Meredita Susanty, Tati Latifah Erawati Rajab, Rukman Hertadi · 2021 · BIO Web of Conferences
76. RNA Secondary Structures in Neurodegeneration
    Niraj Kumar Jha, Anna Maria Louka, Christos Tsagkaris, Panagiotis Christoforou, Filia Alexiou, Panagiota Simou, Ioannis Iraklis Haranas, Ioannis Gkigkitzis, George D. Zouganelis, Md. Sahab Uddin et al. · 2021 · Springer eBooks
77. AIM in Pharmacology and Drug Discovery
    Hiroaki Iwata, Ryosuke Kojima, Yasushi Okuno · 2022 · Springer eBooks
78. Guiding Protein Conformation Sampling with Conformation Space Maps
    Ahmed Bin Zaman, Kenneth Alan De Jong, Amarda Shehu · 2022 · EPiC series in computing
79. Improved Protein Real-Valued Distance Prediction Using Deep Residual Dense Network (DRDN)
    S. Geethu, E. R. Vimina · 2022 · The Protein Journal
80. Classical mechanics
    Mark E. Tuckerman · 2023 · Oxford University Press eBooks
81. Introduction to machine learning in statistical mechanics
    Mark E. Tuckerman · 2023 · Oxford University Press eBooks
82. Statistical methods for biological sequence analysis for DNA binding motifs and protein contacts
    Roth, Christian · 2021
83. Theoretical and computational modeling of rna-ligand interactions
    Yuanzhe Zhou · 2021
84. Protein Redesign and Engineering Using Machine Learning
    Zhuha Basit, Hira Akram, Muhammad Mudassir Iqbal, Gulzar Muhammad, Muhammad Aslam, Iram Gul, Muhammad Jamil, Mudassir Hussain Tahir · 2022 · Wiley eBooks
85. From sequence to structure to mechanism to phenotype: The new frontiers of structural biology
    Annalisa Pastore, Eugene Shakhnovich · 2023 · Current Opinion in Structural Biology
86. Copyright Page
    2023 · Oxford University Press eBooks
87. Correlation Modeling of Intelligent Manufacturing Industry Upgrading and International Trade based on Deep Neural Network
    Pengwen Xiao, Guoping Li · 2021 · International Conference on Inventive Computation Technologies (ICICT)
88. Contribución a la identificación de potenciales antagonistas asociados al quorum sensing en Pseudomonas aeruginosa a través de métodos quimioinformáticos
    Victoria Muñoz, Daniel Felipe · 2021
89. Adjusting Local Conformational Sampling For Fragment Assembly Protein Structure Prediction Based On Secondary Structure Complexity
    Jad Abbass, Jean‐Christophe Nebel · 2021 · IEEE International Multidisciplinary Conference on Engineering Technology (IMCET)
90. Conclusions
    Saneh Lata Yadav, Ritika Dhaiya, Surbhi Bhatia · 2021 · Elsevier eBooks
91. A deep reinforcement learning approach to reconstructing quaternary structures of protein dimers through self-learning
    Elham Soltanikazemi, Raj S. Roy, Farhan Quadir, Jianlin Jack Cheng · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
92. ArgosMol: A Web Tool for Protein Structure Prediction and Visualization
    E. Sejje Condori, J. Soncco Lupa, S. Barrios Cornejo, Vicente Enrique Machaca Arceda · 2022 · Lecture notes in networks and systems
93. Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.
    Arockia Jeyaprakash Arulanandam · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
94. Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.
    Sutirtha Chakraborty · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
95. Decline in direction in CASP experiments
    Sergey Feranchuk · 2020
96. ZeroFold-Understanding Mutations of SARS-CoV-2 Spike Protein base on Secondary Structure Event Extracting for guiding Vaccine development
    Weibin Chen, Zhiyuan Xu · 2020
97. AI and Big Data for Cancer Segmentation, Detection and Prevention
    Zodwa Dlamini, Rodney Hull, Rahaba Makgotso Marima, Amanda Skepu, Stylianos Makrogkikas, Elias P. Koumoulos, George Bakas, Ioannis N. Vamvakaris, Konstantinos Nikolaos Syrigos, George Evangelou et al. · 2022 · Integrated science
98. Protein Structure Prediction with AlphaFold2, How it Works, Limitations and Solution for Less number of Homotypic and Large number of Heterotypic Contacts
    Hassan Kaleem, Muhammad Noman Khalid · 2022 · Innovative Computing Review
99. Avoiding Machine Learning Becoming Pseudoscience in Biomedical Research
    Meredita Susanty, Ira Puspasari, Nilam Fitriah, Dimitri Mahayana, Tati Latifah Erawati Rajab, Hasballah Zakaria, Agung Wahyu Setiawan, Rukman Hertadi · 2023 · Jurnal Informatika
100. Automated Protein Affinity Optimization using a 1D-CNN Deep Learning Model
     J. Liam McWhirter, Abhishek Mukhopadhyay, Patrick J. Farber, Greg Lakatos, Surjit B. Dixit · 2023 · bioRxiv (Cold Spring Harbor Laboratory)