Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12

Cited by (168)

Items 101–168 of 168

1. Computational approach for binding prediction of SARS-CoV-2 with neutralizing antibodies
   D. Beshnova, Yan Fang, Mingjian Du, Yehui Sun, Feng-He Du, Jianfeng Ye, Zhi-Jian J. Chen, Bo Li · 2022 · Computational and Structural Biotechnology Journal
2. Protein Structure Annotations
   Mirko Torrisi, Gianluca Pollastri · 2019 · Springer eBooks
3. Machine learning-assisted substrate binding pocket engineering based on structural information
   Xinglong Wang, Kangjie Xu, Xuan Zeng, Kai Linghu, Beichen Zhao, Shangyang Yu, Kun Wang, Shuyao Yu, Xinyi Zhao, Weizhu Zeng et al. · 2024 · Briefings in Bioinformatics
4. Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes
   Bénédicte Gnangnon, Aline Fréville, Katia Cailliau, C. Leroy, Caroline De Witte, David Tulasne, Alain Martoriati, Vincent A. Jung, Ida Chiara Guerrera, Sabrina Marion et al. · 2019 · Scientific Reports
5. OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding
   Gang Xu, Qinghua Wang, Jianpeng Ma · 2021 · Bioinformatics
6. A Survey of Deep Learning Methods and Tools for Protein Binding Site Prediction
   Alina Rohulia, Yanli Wang, Jianlin Jack Cheng · 2025 · Methods in molecular biology
7. PointSite: a point cloud segmentation tool for identification of protein ligand binding atoms
   Zhen Li, Yan Lei Xu, Qing Wei, Xin Gao, Sheng Wang, Shuguang Robert Cui · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
8. E1: Retrieval-Augmented Protein Encoder Models
   Sarthak Jain, Joel Beazer, Jeffrey A. Ruffolo, Aadyot Bhatnagar, Ali Madani · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
9. Evaluation of the structural models of the human reference proteome: AlphaFold2 versus ESMFold
   Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio · 2025 · Current Research in Structural Biology
10. Studying protein–protein interaction through side-chain modeling method OPUS-Mut
    Gang Xu, Yilin Wang, Qinghua Wang, Jianpeng Ma · 2022 · Briefings in Bioinformatics
11. Jenipapo, Genipa americana L., essential oil and Curvularia lunata control: Potential mode-of-action; plant immune responses and selectivity against beneficial non-target organisms
    Eduardo Oliveira Guilherme, Marcos Vinicius Giongo, Sabrina Helena da Cruz Araujo, Talita Pereira de Souza Ferreira, Cristiano B. Moraes, Wellington S. Moura, Luis Oswaldo Viteri Jumbo, Thiago Svacina, Ana C. S. S. Oliveira, Raimundo W.A. Aguiar et al. · 2023 · Industrial Crops and Products
12. Chemical genomics language model toward reliable and explainable compound-protein interaction exploration
    Koyama, Takuto, Tsumura, Hayato, Okita, Ryunosuke, Yamazaki, Kimihiro, Hasegawa, Aki, Imamura, Keiko, Kato, Takashi, Iwata, Hiroaki, Kojima, Ryosuke, Inoue, Haruhisa et al. · 2026 · Journal of Cheminformatics
13. Protein Analysis: From Sequence to Structure
    Jaykumar Jani, Anju Pappachan · 2021 · Springer eBooks
14. Protein Functions and Structure Prediction with I-TASSER, a Novel Technology
    2022 · Journal of Chemical Biological and Physical Sciences
15. MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
    Bo Chen, Zhilei Bei, Xingyi Cheng, Pan Li, Jie Tang, Le Song · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
16. Siparuna gesnerioides and Siparuna guianensis Essential Oils in Aedes aegypti Control: Phytoanalysis, Molecular Insights for Larvicidal Activity and Selectivity to Non-Target Organisms
    Milton L. Montaño-Campaz, Eugenio Eduardo de Oliveira, Beatriz Toro-Restrepo, Tito Bacca, Carolina Feuillet-Hurtado, Javier G. Mantilla‐Afanador, Renata Pereira Lopes Moreira, Luiza Alves Mendes, Raimundo Wagner de Souza Aguiar, Lucimar Gomes Dias · 2025 · Plants
17. Phytochemistry, Mode of Action Predictions, and Synergistic Potential of Hypenia irregularis Essential Oil Mixtures for Controlling Aedes aegypti
    Luis Oswaldo Viteri Jumbo, Wellington S. Moura, Richard Dias Possel, Osmany Manuel Herrera Armijos, Rodrigo Ribeiro Fidélis, Bruno Silva Andrade, Guy J. Smagghe, Gil Rodrigues dos Santos, Eugenio Eduardo de Oliveira, Raimundo Wagner de Souza Aguiar · 2025 · Toxins
18. Secondary metabolites produced by solid-state fermentation of a neotropical Aspergillus flavus strain confer anti-mosquito activity with long shelf-life
    Mellanie K. C. Félix, Eduardo R. T. Leite, Liliane R. Dutra, Murilo A. Ribeiro, Wellington S. Moura, Talita Pereira de Souza Ferreira, Gil Rodrigues dos Santos, Vanessa Mara Chapla, Willie Anderson dos Santos Vieira, Marcos Paz Saraiva Câmara et al. · 2022 · Industrial Crops and Products
19. The Preventive and Curative Potential of Morinda citrifolia Essential Oil for Controlling Anthracnose in Cassava Plants: Fungitoxicity, Phytotoxicity and Target Site
    Jossimara Ferreira Damascena, Luis Oswaldo Viteri Jumbo, Matheus H. P. Souza, Raimundo W.A. Aguiar, Marcos Paz Saraiva Câmara, Wellington S. Moura, Eugenio Eduardo de Oliveira, Gil Rodrigues dos Santos · 2024 · Stresses
20. IMPROVING ALPHAFOLD2 PERFORMANCE WITH A GLOBAL METAGENOMIC & BIOLOGICAL DATA SUPPLY CHAIN
    Geraldene Munsamy, Tanggis Bohnuud, Philipp Lorenz · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
21. Beyond Single Chains: Benchmarking Macromolecular Complex Prediction Methods With the Continuous Automated Model EvaluatiOn (CAMEO)
    X. Robin, Peter Škrinjar, A. Waterhouse, G. Studer, G. Tauriello, J. Durairaj, T. Schwede · 2025 · Proteins: Structure, Function, and Bioinformatics
22. Protein quality assessment with a loss function designed for high-quality decoys
    Soumyadip Roy, Asa Ben‐Hur · 2023 · Frontiers in Bioinformatics
23. Using an Aluminum Hydroxide–Chitosan Matrix Increased the Vaccine Potential and Immune Response of Mice against Multi-Drug-Resistant Acinetobacter baumannii
    Túllio Teixeira Deusdará, Mellanie K. C. Félix, Helio de S. Brito, Edson W. S. Cangussu, Wellington S. Moura, Benedito Albuquerque, Marcos G. Silva, Gil Rodrigues dos Santos, Paula B. Morais, Elizangela Farias da Silva et al. · 2023 · Vaccines
24. Alzheimer’s Disease: The Role of Mutations in Protein Folding
    Eleftheria Polychronidou, Antigoni Avramouli, Panagiotis Vlamos · 2020 · Advances in experimental medicine and biology
25. Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry
    Alexander Leitner, Alexandre M. J. J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot‐Rooke, Colin Combe, Jürgen Cox, Meng‐Qiu Dong, Lutz Fischer, Michael Götze et al. · 2020 · arXiv (Cornell University)
26. OpenProteinSet: Training data for structural biology at scale.
    Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, I. Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi · 2023 · PubMed
27. OPUS-BFactor: Predicting protein B-factor with sequence and structure information
    Gang Xu, Yulu Yang, Ying Lv, Zhenwei Luo, Qinghua Wang, Jianpeng Ma · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
28. Structure and dynamics of the somatostatin receptor 3‐ligand binding in the presence of lipids examined using computational structural biology methods
    Santhosh Kumar Nagarajan, Sathya Babu, Panneer Devaraju, Honglae Sohn, Thirumurthy Madhavan · 2021 · Proteins Structure Function and Bioinformatics
29. Protein Homology Modeling for Effective Drug Design
    Natalia Gniado, Agata Krawczyk-Balska, Pakhuri Mehta, Przemysław Miszta, Sławomir Filipek · 2023 · Methods in molecular biology
30. Morinda citrifolia Essential Oil in the Control of Banana Anthracnose: Impacts on Phytotoxicity, Preventive and Curative Effects and Fruit Quality
    Maria Teresa Botti Rodrigues Santos, Luis Oswaldo Viteri Jumbo, Paulo Ricardo de Sena Fernandes, Rosilene Da Costa Porto de Carvalho, Manuel A. Gonzalez, Osmany Manuel Herrera Armijos, Pedro Raymundo Argüelles Osório, Dalmárcia de Souza Carlos Mourão, Sabrina Helena da Cruz Araujo, Cristiano Bueno de Moraes et al. · 2025 · Microbiology Research
31. Protein Structure Prediction for Disease-Related Insertions/Deletions in Presenilin 1 Gene
    Antigoni Avramouli, Marios G. Krokidis, Themis P. Exarchos, Panagiotis Vlamos · 2023 · Advances in experimental medicine and biology
32. CAMEO - Perspectives on the future of fully automated evaluation of structure prediction methods
    Xavier Robin, Juergen Haas, Rafal Gumienny, Gerardo Tauriello, Torsten F. Schwede · 2021
33. From Genome Mining to Protein Engineering: A Structural Bioinformatics Route
    Derek John Smith · 2022 · Methods in molecular biology
34. A High-Throughput Computational Pipeline for Selection of Effective Antibody Therapeutics Against Viruses
    Rahul Kaushik, Naveen Kumar, Thomas Launey · 2024 · Livestock diseases and management
35. Chemosensory Receptors in Vertebrates: Structure and Computational Modeling Insights
    Aurore Lamy, Durairaj Rajesh, Patrick Pageat · 2025 · International Journal of Molecular Sciences
36. Potential of mucochloric acid derivatives for controlling Euschistus heros: Synthesis, in silico predictions of molecular targets and selectivity toward pollinator bees
    Sabriny F Gomes, Elson S. Alvarenga, Lara T. M. Costa, Javier G. Mantilla‐Afanador, Lorenzo B. Ferrazza, Thiago Svacina, Eugenio Eduardo de Oliveira · 2025 · Pesticide Biochemistry and Physiology
37. Homology Modeling in Protein Structure Predictions
    Khac‐Minh Thai, Trong-Khoa Nguyen, Dac-Nhan Nguyen, Minh-Tri Le · 2025 · Springer handbooks
38. Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy
    Recep Adiyaman, Liam James McGuffin · 2023 · Methods in molecular biology
39. Quality Estimates for 3D Protein Models
    Ali H. A. Maghrabi, Fahd M. F. Aldowsari, Liam James McGuffin · 2023 · Methods in molecular biology
40. OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow
    Xu, Gang, Luo, Zhenwei, Zhou, Ruhong, Wang, Qinghua, Ma, Jianpeng · 2023 · Briefings in Bioinformatics
41. Exploring Post-Training Quantization of Protein Language Models
    Shuang Peng, Fei Yang, Ning Sun, Sheng Chen, Yanfeng Jiang, Aimin Pan · 2023 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
42. MEFold: Memory-Efficient Optimization for Protein Language Models via Chunk and Quantization
    Yanfeng Jiang, Ning Sun, Zhengxian Lu, Shuang Peng, Yi Zhang, Fei Yang, Tao Li · 2024 · International Joint Conference on Neural Networks (IJCNN)
43. ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques
    Joshua M. Toth, Paul J DePietro, Juergen Haas, William A. McLaughlin · 2020 · Bioinformatics
44. Homologous Protein Detection
    Xuefeng Cui, Yaosen Min · 2018 · Elsevier eBooks
45. Automated benchmarking of combined protein structure and ligand conformation prediction
    Xavier Robin, Michèle Leemann, Ander Sagasta, Jérôme Eberhardt, Torsten F. Schwede, Janani Durairaj · 2023
46. Protein Secondary Structure Prediction Approaches
    Fawaz H. H. Mahyoub, Rosni Abdullah · 2019 · Advances in systems analysis, software engineering, and high performance computing book series
47. Directed Evolution of Enzymes Driving Innovation in API Manufacturing at GSK
    Jonathan Latham, Anne A. Ollis, Chris MacDermaid, Katherine Honicker, Douglas E. Fuerst, Gheorghe‐Doru Roiban · 2020
48. Assessment of Structure Quality (RNA and Protein)
    Nicolás Palópoli · 2018 · Elsevier eBooks
49. Faculty Opinions recommendation of Improved protein structure prediction using predicted interresidue orientations.
    Patrice Koehl · 2020 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
50. Faculty Opinions recommendation of Improved protein structure refinement guided by deep learning based accuracy estimation.
    Patrice Koehl · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
51. Homology modelling and molecular docking study of TMPRSS2 with small-molecule protease inhibitors to control SARS-CoV-2
    Salha M. Tawati, Aisha A. Alsfouk, Asma S.mohamed Elmabruk · 2022 · International Journal of Research in Pharmaceutical Sciences
52. Faculty Opinions recommendation of Highly accurate protein structure prediction for the human proteome.
    Wenjun Zhang, Rui Zhai · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
53. State-of-the-art experimental and computational approaches to investigate structure, substrate recognition, and catalytic mechanism of enzymes
    Camila Ramos dos Santos, Clelton A. Santos, Evandro Ares de Araújo, M.A.B. Morais, Maxuel O. Andrade, Tatiani B. Lima, Wesley Cardoso Generoso, Mario Tyago Murakami · 2023 · Elsevier eBooks
54. Recent Advances in Estimation of Protein Structure Model Accuracy
    Dong Liu, Xin-Yue Cui, Hao-Dong Wang, Gui-Jun Zhang · 2023 · Acta Physica Sinica
55. Protein Secondary Structure Prediction Approaches
    Fawaz H. H. Mahyoub, Rosni Abdullah · 2023 · IGI Global eBooks
56. CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
    Yuxin Yang, Abby Jerger, Song Feng, Zixu Wang, Christina Brasfield, Margaret S. Cheung, Jeremy Zucker, Qiang Guan · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
57. OPUS-Design: Designing Protein Sequence from Backbone Structure with 3DCNN and Protein Language Model
    Gang Xu, Yulu Yang, Yiqiu Zhang, Qinghua Wang, Jianpeng Ma · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
58. Homologous Protein Detection
    Xuefeng Cui, Yaosen Min · 2019 · Elsevier eBooks
59. Assessment of Structure Quality (RNA and Protein)
    Nicolás Palópoli · 2019 · Elsevier eBooks
60. OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information
    Yulu Yang, Ying Lv, Zhenwei Luo, Qinghua Wang, Gang Xu, Jianpeng Ma · 2025 · Molecules
61. ELEN – Predicting Loop Quality in Protein Structure Models
    Florian Wieser, Sigrid Kaltenbrunner, Andreas Zechner, Martin Zach, Thomas Pock, Gustav Oberdorfer · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
62. Odyssey: reconstructing evolution through emergent consensus in the global proteome
    Ankit Singhal, Shyam Venkatasubramanian, Sean Moushegian, Steven C. Strutt, Michael Y. Lin, Connor Lee · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
63. exploration de l’utilisation d’une technologie de mutagenèse à haut débit et de l’évolution pour la prédiction structurale des complexes protéiques
    Aravindan Arun Nadaradjane · 2020 · theses.fr (ABES)
64. Exploration and structural modelling of protein interactions using evolutionary information
    Chloé Quignot · 2020 · theses.fr (ABES)
65. Structural prediction of protein assemblies with deep learning
    Hélène Bret · 2023 · theses.fr (ABES)
66. Developmental Consequences of Early-Life Exposure and Adulticidal Effects of Siparuna Species Essential Oils in Aedes aegypti
    Milton L. Montaño-Campaz, Javier G. Mantilla‐Afanador, Tarciza Fernandes Nascimento, Joshua Fernandes Santos, Mathews Otavio Nascimento de Novaes, Juan Guillermo Orrego-Meza, Beatriz Toro-Restrepo, Lucimar G. Dias, Patrícia Fontes Pinheiro, Raimundo Wagner de Souza Aguiar et al. · 2026 · Molecules
67. Tokenization in Protein Language Models: Methods, Taxonomy, and Applications
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68. SparseFold: Index-Based Block Sparse Attention for Training-Free Alphafold 3 Acceleration
    Yunzhong Ren, Xin You, Hailong Yang · 2026 · IEEE International Conference on Cluster Computing (CLUSTER)