Critical assessment of methods of protein structure prediction ( CASP )—Round XV

Cited by (148)

Items 101–148 of 148

1. Scrutinization on Docking against Individually Generated Target Pockets for each Ligand
   Rui Zhan, Wenyi Zhang, Jing Huang · 2026 · Journal of Pharmaceutical Analysis
2. Predicting Protein Folding on Intel’s Data Center GPU Max Series Architecture (PVC)
   Dhani Ruhela, M. Prasanna, Aaditya Saxena · 2024 · International Conference for High Performance Computing, Networking, Storage and Analysis (SC)
3. Energy-driven innovations in computational de novo protein engineering
   Kevser Kübra Kırboğa, Ecir Uğur Küçüksille · 2026 · Progress in Biophysics and Molecular Biology
4. REALM: A Real-to-Sim Validated Benchmark for Generalization in Robotic Manipulation
   Martin Sedlacek, Pavlo Yefanov, Georgy Ponimatkin, Jai Bardhan, Simon Pilc, Médéric Fourmy, Evangelos Kazakos, Cees G. M. Snoek, Josef Šivic, Vladimír Petrík · 2026 · IEEE Robotics and Automation Letters
5. 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
6. Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset
   Konstantinos Tornesakis, Jonathan W. Essex, Paul A. Cox, Gerhard König · 2026 · Journal of Computer-Aided Molecular Design
7. Roadmapping Report: Focused Research Organizations in Atomistic Simulation
   Sam Holton · 2024
8. Method for Recognizing the Characteristic Elements of Protein Secondary Structure From the Llm of Its Amino Acid Sequence
   Yaroslav Teplyi · 2024 · Vìsnik Nacìonalʹnogo unìversitetu Lʹvìvsʹka polìtehnìka Serìâ Ìnformacìjnì sistemi ta merežì
9. Protocol for Protein Structure Modeling
   Vaanathi Chidambara Thanu, Amara Jabeen, Shoba Ranganathan · 2024 · Elsevier eBooks
10. Protein Structure Modeling and Refinement
    Harvinder Singh, Parampal Singh, Gajendra Chaudhary, Harpreet Singh · 2024 · Elsevier eBooks
11. Sequence-based coevolutionary prediction of species-specific interactomes
    Miguel Fernandez-Martin, Camila Ferreira Thé Pontes, Victoria Ruiz‐Serra, Alfonso Valencia · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
12. Machine Learning-based Host–Pathogen Protein–Protein Interaction Prediction
    Erdem Türk, Onur Can Karabulut, Al-shaima Khaled Abdullah Al-alie, Barış Ethem Süzek · 2025 · Current Clinical Microbiology Reports
13. Missense mutation knowledge can decrease prediction inaccuracies on protein secondary structure
    Ivan Perez, Ulrike Stege, Hosna Jabbari · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
14. The integration of artificial intelligence and protein science: the protein structure prediction and protein design revolution behind the 2024 Nobel Prize in Chemistry
    Shenhui Liu, Zhi‐Jie Liu · 2025 · Chinese Science Bulletin (Chinese Version)
15. The proteomic code: Novel amino acid residue pairing models “encode” protein folding and protein-protein interactions
    Tareq Hameduh, Andrew David Miller, Zbyněk Heger, Yazan Haddad · 2025 · Computers in Biology and Medicine
16. PackPPI: An integrated framework for protein–protein complex side‐chain packing and ΔΔG prediction based on diffusion model
    Jingkai Zhang, Yuanyan Xiong · 2025 · Protein Science
17. Characterization of PROTACs by Ternary Complex Landscape Exploration using Monte Carlo simulations
    Anna M. Díaz-Rovira, Carles Perez‐Lopez, Jordi Martín-Pérez, Chiara Pallara, Lucía Díaz, Vı́ctor Guallar · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
18. Peptide-mimetics derived from leucyl-tRNA synthetase are potential agents for the therapy of mt-tRNA related diseases
    Annalinda Pisano, Sara Belloli, Maria Gemma Pignataro, Paolo Rainone, Silvia Valtorta, Angela Coliva, Valeria de Turris, Luciana Mosca, Patrizio Di Micco, Rosa Maria Moresco et al. · 2025 · Frontiers in Pharmacology
19. Open Benchmarking for Cell-Based Multiscale Models: Lessons from a Community Initiative
    Thaleia Ntiniakou, James M. Osborne, Jieling Zhao, Jules Dichamp, Nicolò Cogno, Randy W. Heiland, Kwabena Amponsah, Jiří Pešek, Tobias Duswald, Othmane Hayoun-Mya et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
20. Multiple minima problem in protein folding solved appying multi criterial optimisation
    Roterman Irena, Leszek Konieczny · 2025 · Computational and Structural Biotechnology Reports
21. GCP-VQVAE: A Geometry-Complete Language for Protein 3D Structure
    Mahdi Pourmirzaei, Alex Morehead, Farzaneh Esmaili, J. Ren, Mohammadreza Pourmirzaei, Dong Xu · 2026 · bioRxiv
22. Spontaneous Emergence of Symmetry in a Generative Model of Protein Structure
    Anton Oresten, Kenta Sato, Aron Stålmarck, Lukas Billera, Hedwig Nora Nordlinder, Jack Collier Ryder, Mateusz Kaduk, Ben Murrell · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
23. Machine Learning for Protein Structure Prediction and Design
    David R. Bell, Serena H. Chen · 2025 · Springer handbooks
24. DPI-score: A deep learning-based metric for assessing protein-protein interfaces in cryoEM derived assemblies
    Niraj Bhujel, Nicholas Whyatt, Agnel Praveen Joseph, Jyothish Thomas, Luc G. Elliott, Tamilarasan Sabapathy, Jeyan Thiyagalingam, Sony Malhotra · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
25. MAKA-Map: Real-Valued Distance Prediction for Protein Folding Mechanisms via a Hybrid Neural Framework Integrating the Mamba and Kolmogorov–Arnold Networks
    Benzhi Dong, Yumeng Hua, Chang Hou, Dali Xu, Guohua Wang · 2026 · Biomolecules
26. Hierarchical latent representations reveal protein organization for functional discovery and design
    Zhengyang Guo, Zi Wang, Shimin Wang, Yongping Chai, Kaiming Xu, Ming Li, Wei Li, Guangshuo Ou · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
27. From implicit learning to explicit structural constraints for efficient protein language modeling
    Lingdong Shen, Linlin Chao, Tang Liu, Qi Liu, Guowei Zhou, Hao Wang, Xinyue Dong, Tianhong Li, Xiaoming Zhang, jinren Ni · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
28. Ion channels: Medicinal chemistry and modeling interface
    Paul Galatsis · 2026 · Elsevier eBooks
29. Beyond AlphaFold: Charting the Future of AI in Protein Structure Prediction
    Ankush Kumar, Rajwinder Kaur, Rohit Bhatia · 2026 · Current Drug Targets
30. The landscape of machine learning approaches for modeling protein conformational ensembles
    Samuel Sledzieski, Sonya M. Hanson · 2026 · Current Opinion in Structural Biology
31. Two-dimensional geometric template diffusion for boosting single-sequence protein structure prediction
    Xudong Wang, Tong Zhang, Zhen Cui, Xu Guo, Fuyun Wang, Yuanzhi Wang, Xing Cai, Wenming Zheng · 2026 · Nature Machine Intelligence
32. Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study
    Deyin Wang, Yangwei Jiang, Linli He, Lin-Xi Zhang, Ru-Hong Zhou, Dong Zhang · 2025 · bioRxiv
33. PROPTIMUS LIVE: local constrained α-carbon optimization of proteins
    Tomáš Svoboda, Michal Mikuš, Lukáš Bohuš, Tomáš Raček, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová Vařeková, Ondřej Schindler · 2026 · Nucleic Acids Research
34. CB-Search: a method for searching for similar protein motifs with biased compositions
    Patryk Jarnot · 2026 · BMC Bioinformatics
35. Standardizing Benchmarks for Plant Genomic Prediction
    Min Yan, Wenying Wang, Ying Zhang, Han Guo, Zhen Xue, X Wang, Jun Yan · 2026 · Agronomy
36. AI-guided prediction of ncRNA biochemical features for therapeutic targeting.
    Jun-Wei Chan, C. Daly, A. M. Vargas-Velazquez, P. Chow, Jin-Miao Chen, V. Tergaonkar · 2026 · TIPS - Trends in Pharmacological Sciences
37. OpenChallenges: A FAIR-aligned, centralized platform for crowdsourced challenges in biomedical research
    Verena Chung, Rongrong Chai, Hallie A. Swan, Maria Diaz, Shysta Bynum, Adam Hindman, Jacob W. Albrecht, Serghei Mangul, Susheel Varma, Jay Hodgson et al. · 2026 · Patterns
38. Machine Learning in Protein Structure Prediction
    Khac‐Minh Thai, Dac-Nhan Nguyen, Thanh-Phuong Vo, Minh-Tri Le · 2026 · Royal Society of Chemistry eBooks
39. Spectral analysis and AI/ML-based data-driven approaches for enhanced protein conformation selection and prediction in drug discovery
    Shivangi Gupta, Vineetha Menon, Jerome Y. Baudry · 2026 · Frontiers in Drug Discovery
40. Tokenization in Protein Language Models: Methods, Taxonomy, and Applications
    Abir Linoubli, Khairi Abidi, Mohamed Farah · 2026 · Communications in computer and information science
41. Transformers in protein informatics: A survey of structure prediction, function annotation, interactions, and drug discovery
    Yumin Zhang, Xiaowen Ling, Zhiqiang Li, Liangliang Song, Yifan Jia, Yanbin Wang, Zhuhong You · 2026 · Engineering Applications of Artificial Intelligence
42. A Pre-registered, Cryptographically Timestamped Proving Protocol for Directional Market Forecasting, with Announced Echo State Network and Quantum Reservoir Computing Examinations
    Timur Karatyhin · 2026 · SSRN Electronic Journal
43. Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly
    Chandran Nithin, Smita P. Pilla, Sebastian Kmiecik · 2026 · Bioinformatics
44. Peering beyond the fourth wall: should protein quaternary structure be a state space?
    Daniela Diana, Yimon Aye, Marcus J.C. Long · 2026 · Frontiers in Biophysics
45. Recent advances in AI-driven biotherapeutic discovery using protein generative models
    Haelyn Kim, Hakyung Lee, Jinung Song, Juyong Lee · 2026 · Digital Discovery
46. HDOCK-Multimer: improved structure prediction of large protein complexes by integrating docking and combinatorial assembly
    Xuan Yao, Yifan Ya, Hao Li, Sheng‐You Huang · 2026 · Nature Computational Science
47. Beyond structure prediction: Translating D‐I‐TASSER models into functional and mechanistic hypotheses
    Yujie Mo, Tianrui Jia, Yang Zhang · 2026 · Clinical and Translational Medicine
48. AlphaFold-driven structure-based drug discovery: Capabilities, benchmarks and limitations for medicinal chemistry
    Manish Pathak · 2026 · European Journal of Medicinal Chemistry