CAPRI: A Critical Assessment of PRedicted Interactions

Cited by (705)

Items 601–700 of 705

1. Bioinformatics Resources, Tools, and Strategies in Designing Therapeutic Proteins
   M. Sudhan, Jency Roshni, V. Janakiraman, Mahema Sivakumar, Shiek Fareeth Ahmed · 2022 · Springer eBooks
2. Investigation of translation initiation factor through protein–protein interactions and molecular dynamics approaches
   P. Jayaprakash, Jayashree Biswal, Chitra Jeyaraj Pandian, Jemima D. Kingsley, J. Jeyakanthan · 2023 · Molecular Simulation
3. Challenges of Protein-Protein Docking of the Membrane Proteins
   Yusra Sajid Kiani, Ishrat Jabeen · 2024 · Methods in molecular biology
4. Software and Databases for Protein–Protein Docking
   Małgorzata Jarończyk, Ruben A Abagyan, Maxim M. Totrov · 2024 · Methods in molecular biology
5. Disrupting Protein–Protein Interfaces Using GRID Molecular Interaction Fields
   Simon Cross, Massimo Baroni, Francesco Ortuso, Stefano Alcaro, Gabriele Cruciani · 2013 · Springer eBooks
6. Efficient search for the possible mutual arrangements of two rigid bodies with the use of the generalized five-dimensional Fourier transform
   Andrey Maksimovich Kazennov, Andrey Evgen'evich Alekseenko, Dima Kozakov, Dzmitry Padhorny, Yaroslav Aleksandrovich Kholodov · 2015 · Mathematical Models and Computer Simulations
7. Structure of a Fab Complex with the C-terminal fragment of merozoite surface protein-1 of Plasmodium vivax determined by Computational Docking
   María Luisa Serrano, Adriana Gauna, Hilda A Pérez, Emilio Squitieri, J. D. Medina · 2009 · Journal of Computational Methods in Sciences and Engineering
8. Bioinformatic Tools for Gene and Protein Sequence Analysis
   Bernd H. A. Rehm, Frank Reinecke · 2005 · Humana Press eBooks
9. Approximating net interactions among rigid domains
   Pouya Tavousi · 2018 · PLoS ONE
10. Controlled‐advancement rigid‐body optimization of nanosystems
    Petr A. Popov, Sergei Grudinin, Andrii Kurdiuk, Pavel Buslaev, Stéphane Redon · 2019 · Journal of Computational Chemistry
11. Structure-based prediction of protein-protein interaction sites
    Rafael A. Jordan · 2012
12. F 3 Dock: A Fast, Flexible and Fourier Based Approach to Protein-Protein Docking
    Chandrajit Bajaj, Rezaul Chowdhury, Vinay Siddavanahalli, Ices Report · 2009
13. Hotspot coevolution at protein-protein interfaces is a key identifier of native protein complexes
    Sambit Kumar Mishra, Connor J. Cooper, Jerry M. Parks, Julie C. Mitchell · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
14. ZIPPI: proteome-scale sequence-based evaluation of protein-protein interaction models
    Haiqing Zhao, Donald S. Petrey, Diana Murray, Barry H. Honig · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
15. Network-Based Analysis for Biological Knowledge Discovery
    Lokesh P. Tripathi, Rodolfo S. Allendes Osorio, Yoichi Murakami, Y. Ann Chen, Kenji Mizuguchi · 2024 · Elsevier eBooks
16. Utilisation de la tessellation de Voronoï pour l'étude des complexes protéine-protéine
    Julie Bernauer · 2006 · HAL
17. SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons
    Julie‐Anne Chemelle, Emmmanuel Bettler, Christophe Combet, Raphaël Terreux, C. Geourjon, Gilbert Deléage · 2012 · Focus on structural biology
18. The stability of monomeric class Mu GST M1
    Tshepo Mashapa · 2013 · University of the Witwatersrand, Johannesburg Institutional Repository on DSpace (University of the Witwatersrand, Johannesburg)
19. Protein-protein interface: database, analysis and prediction
    Feihong Wu · 2009
20. DockingShop: A Tool for Interactive Molecular Docking
    Ting-Cheng Lu, Nelson Max, Jinhui Ding, E. Wes Bethel, Silvia N. Crivelli · 2005 · University of North Texas Digital Library (University of North Texas)
21. Informatics (Computational Biology)
    Thomas Lengauer · 2004 · Encyclopedia of Molecular Cell Biology and Molecular Medicine
22. Improving the resolution of interaction maps : a middleground between high-resolution complexes and genome-wide interactomes
    Joan Segura · 2013 · UPT. Syiah Kuala University Library (Syiah Kuala University)
23. Auto-organização da população em sistemas imunológicos artificiais aplicada ao docking de proteínas
    Helder Ken Shimo · 2012
24. Development of computational methods for predicting structural characteristics of helical membrane proteins
    Yungki Park · 2007 · Publications of the UdS (Saarland University)
25. 3D shape analysis approaches for protein docking and similarity search
    Απόστολος Αξενόπουλος · 2014
26. Graph-based approaches to protein structure- and function prediction
    Henning Stehr · 2011 · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver
27. Unbound Protein-Protein Docking Selections by the DFIRE-based Statistical Pair Potential
    Song Liu, Chi Zhang, Yaoqi Zhou · 2004 · arXiv (Cornell University)
28. Structural Fluctuations and Conformational Changes in Proteins and Protein Complexes
    Anatoly M. Ruvinsky, Tatsiana Kirus, Alexander V. Tuzikov, Ilya A. Vakser · 2011 · Biophysical Journal
29. Prediction of the Binding Mode between the Small Peptide Inhibitor EBR28 with Integrase through Molecular Modeling Methods
    Jianping Hu, Xinqi Gong, Shan Chang, W.Z. Chen, C.X. Wang · 2007 · ICME International Conference on Complex Medical Engineering (CME)
30. Identification of interface residues involved in protein-protein and protein-DNA interactions from sequence using machine learning approaches
    Changhui Yan · 2005
31. Screening interactions between proteins and disordered peptides by a novel computational method
    Weiyi Zhang · 2013 · D-Scholarship@Pitt (University of Pittsburgh)
32. Protein dimer interfaces : ligands, sidechains, hot spots and binding
    Lei Li · 2006
33. Modelos caracterizando a interação entre as toxinas da família Cry1A de Bacillus thuringiensis e o receptor BT-R1 de Manduca sexta
    Diogo Martins de Sá · 2015
34. Implementação de uma abordagem híbrida utilizando modelagem comparativa e ab initio para predição de estruturas tridimensionais de proteínas contendo múltiplos domínios com conectores flexíveis
    Rodrigo V. Honorato · 2016
35. Improving Protein Docking with Constraint Programming and Coevolution Data
    Ludwig Krippahl, Fábio Madeira · 2014 · bioRxiv (Cold Spring Harbor Laboratory)
36. IDENTIFICACION DE POTENCIALES RESIDUOS DETERMINANTES DE MAYOR AFINIDAD A CELULOSA EN UNA ENDOGLUCANASA MEDIANTE ESTUDIOS DE DOCKING MOLECULAR
    Facultad De Ciencias Físicas, Y Matemáticas · 2012
37. Prediction of protein structures and protein-protein interactions
    Huiling Chen, Huan‐Xiang Zhou, Frank A. Ferrone · 2005
38. DOCTEUR DE L'UNIVERSITÉ DE GRENOBLE
    Petr A. Popov · 2015
39. Scoring Functions for Predicting Structure and Binding of Proteins
    Bhaskar Dasgupta, Jie Liang · 2016
40. Gene/Protein Sequence Analysis
    Bernd H. A. Rehm, Frank Reinecke · 2008 · Springer protocols handbooks/Springer protocols
41. Understanding structure, function, and evolution of protein-protein interactions by computational modeling and analysis
    Nan Zhao · 2013
42. Development of protein-protein docking methodology and benchmarking environment
    Ivan V. Anishchenko · 2016 · KU ScholarWorks (University of Kansas)
43. Basic Principles of Protein–Protein Interaction
    Ruth Nussinov, Gideon Schreiber · 2009 · CRC Press eBooks
44. Docking HPr to HPr Kinase with Partial Backbone Flexibility By
    Lian Guo · 2004
45. EFFICIENT DISCOVERY OF BINDING MOTIF PAIRS FROM PROTEIN-PROTEIN INTERACTIONS
    Haiquan Li · 2006
46. Template Based Modeling and Structural Refinement of Protein-Protein Interactions.
    Brandon Govindarajoo · 2016 · Deep Blue (University of Michigan)
47. Application of Molecular Modelling to Speed-up the Lead Discovery Process
    Iuni Margaret Laura Trist, Maurizio Botta, Anna Lucia Fallacara · 2017 · Royal Society of Chemistry eBooks
48. Computational Methods Applicable to the Discovery of Small-Molecule Inhibitors of Protein-Protein Interactions
    Li Han, Renxiao Wang · 2018 · Springer eBooks
49. Computational Structural Biology of Macromolecular Interactions
    J. Garcia Lopes Maia Rodrigues · 2014 · Utrecht University Repository (Utrecht University)
50. Epitope Characterization and Isotype Selection
    Gopalan Raghunathan, Edward J. Hsieh, Grigori Ermakov · 2018 · Springer eBooks
51. Structure-Based Drug Design with a Special Emphasis on Herbal Extracts
    Devadasan Velmurugan, N.H.V. Kutumbarao, Vijayan Viswanathan, Atanu Bhattacharjee · 2019 · Challenges and advances in computational chemistry and physics
52. Modélisation bio-informatique du mécanisme d'action d'inhibiteurs de la voie de biosynthèse du peptidoglycane
    Élénie Godzaridis · 2012
53. Side-chain conformational changes upon protein-protein association
    Anatoly M. Ruvinsky, Tatsiana Kirys, Alexander V. Tuzikov, Ilya A. Vakser · 2010 · arXiv (Cornell University)
54. Application of Deep Architecture in Bioinformatics
    Sagnik Sen, Rangan Das, Swaraj Dasgupta, Ujjwal Maulik · 2019 · Studies in big data
55. Structural Modeling in Systems Biology
    Javier Klett · 2019 · Elsevier eBooks
56. Plataforma computacional de acoplamiento de proteínas basado en plantillas
    Ricardo Román-Brenes, Francisco Siles-Canales, Daniel Zamora-Mata · 2020 · Revista Tecnología en Marcha
57. Complete configuration space analysis for structure determination of symmetric homo-oligomers by NMR.
    Shobha Potluri · 2007
58. Modelar Molecular das interações do complexo NS1/anti-NS1 para aplicação no diagnóstico diferencial de Flaviroses
    Renan Faria Guerra · 2021
59. Comment on mr-2021-59
    Adam D. Schuyler · 2021 · Magnetic Resonance
60. Restoration of hemopoiesis in patients following chronic radiation sickness
    I.A. Gribova, V.A. Soldatva · 1975 · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)
61. Comment on mr-2021-59
    2021 · Magnetic Resonance
62. Comment on mr-2021-59
    2021 · Magnetic Resonance
63. Protein Modeling
    Marian R. Zlomislic, Valentina Corradi, D. Peter Tieleman · 2011 · Encyclopedia of Molecular Cell Biology and Molecular Medicine
64. References
    2012 · Wiley eBooks
65. Faculty Opinions recommendation of Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling.
    Gloria Ann Brar · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
66. Background
    M. V. K. Karthik, Pratyoosh Shukla · 2012 · SpringerBriefs in systems biology
67. Protein Modeling
    Marian R. Zlomislic, D. Peter Tieleman · 2006 · Encyclopedia of Molecular Cell Biology and Molecular Medicine
68. Basic Principles of Protein–Protein Interaction
    2009 · CRC Press eBooks
69. 蛋白质复合物结构预测的集成分子对接方法
    2009 · Science in China Series C-Life Sciences (in Chinese)
70. Faculty Opinions recommendation of Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.
    Richard Lavery, Alberto Pérez · 2011 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
71. Defesa bioquímica de plantas às pragas agrícolas: desenho racional de inibidores de proteases peptídicos a serem utilizados nas formulações biopesticidas
    Rafael de Almeida Barros · 2022
72. A scoring function for the prediction of protein complex interfaces based on the neighborhood preferences of amino acids
    Mulpuri Nagaraju, Haiguang Liu · 2022 · Acta Crystallographica Section D Structural Biology
73. New methods for protein structure prediction using machine learning and deep learning
    Junlin Wang · 2022
74. The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15
    Ezgi Karaca, Burcu Ozden, Andriy Kryshtafovych · 2023
75. Recent Advances in Estimation of Protein Structure Model Accuracy
    Dong Liu, Xin-Yue Cui, Hao-Dong Wang, Gui-Jun Zhang · 2023 · Acta Physica Sinica
76. Prediction of Protein-Protein Interactions
    Aditi Pathak, Vikas Ramyagya Tiwari, Revathy Menon, Ramanathan Sowdhamini · 2024 · Elsevier eBooks
77. Protein Complex Structure Prediction With AlphaFold ‐Enhanced HDOCK in CAPRI Rounds 47–55
    Hao Li, Peicong Lin, Yurui Li, Sheng‐You Huang · 2025 · Proteins Structure Function and Bioinformatics
78. Quantifying Protein-Protein Interaction with a Spatial Attention Kinetic Graph Neural Network
    Yuzhi Xu, Wei Xia, Chao Zhang, Xinxin Liu, Cheng‐Wei Ju, Xuhang Dai, Pujun Xie, Yuanqing Wang, Guangyong Chen, John Z. H. Zhang · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
79. Increasing the fraction of correct solutions in ensembles of protein–protein docking models by an iterative consensus algorithm
    Tiziana Ricciardelli, Didier Barradas‐Bautista, Zhen Zhu Cao, Mohit Chawla, Luigi Cavallo, Romina Oliva · 2025 · Protein Science
80. Additional file 1 of The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
    Didier Barradas‐Bautista, Cao, Zhen, Cavallo, Luigi, Romina Oliva · 2020 · Figshare
81. A Scalable Heuristic for Molecular Docking on Neutral-Atom Quantum Processors
    Mathieu Garrigues, Victor Onofre, Wesley Coelho, Shaheen Acheche · 2026 · IEEE International Conference on Quantum Control, Computing and Learning (qCCL)
82. Navigating the Pre‐ and Post‐ AlphaFold Divide: CAPRI 8th Evaluation Meeting, February 12–14, Grenoble, FR
    Alexandre M. J. J. Bonvin, Marc Ferdinand Lensink · 2025 · Proteins Structure Function and Bioinformatics
83. A Compilation of Software Tools for Studying Protein–Protein Interactions
    Arpan Chowdhury, Seetharama D. S. Jois · 2026 · Challenges and advances in computational chemistry and physics
84. Going Deep: The Power of Deep Learning to Uncover Disease-Driven Protein–Protein Interactions and Accelerate Drug Design
    Cristina Correia, Choong Yong Ung, Caleb M. Grenko, Shizhen Zhu, Daniel D. Billadeau, Hu Li · 2026 · Challenges and advances in computational chemistry and physics
85. Transformers as a substrate for structural biology
    Ashar J. Malik, Stephanie Portelli, David Benjamin Ascher · 2026 · Current Opinion in Structural Biology
86. Differentiation of RNA–protein docking structures through molecular dynamics simulation and machine learning methods
    Bui Tien Thanh, Yoichi Kurumida, Kaito Kobayashi, Michiaki Hamada, Tomoshi Kameda · 2026 · Briefings in Bioinformatics
87. Evaluating AlphaFold Tools and Related Scoring Functions for Protein–peptide Complex Prediction
    Negin Manshour, Jarett Zida Ren, Farzaneh Esmaili, Erik Bergstrom, Dong Xu · 2026 · Genomics Proteomics & Bioinformatics
88. Modélisation de l'assemblage de protéines multi-domaines avec des contraintes expérimentales de microscopie à force atomique.
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89. Heligeom : a multiscale approach to studying biomolecular helical assemblies with an application to RecA fillaments
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90. A docking-based method for in silico epitope determination
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91. 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)
92. Développement de méthodologies innovantes pour la caractérisation d’interfaces protéine-protéine et la conception d’inhibiteurs spécifiques : exploration de l’interface protéique de RhoA /ArhGEF1
    Ennys Gheyouche · 2020 · theses.fr (ABES)
93. Exploration and structural modelling of protein interactions using evolutionary information
    Chloé Quignot · 2020 · theses.fr (ABES)
94. Structural prediction of protein assemblies with deep learning
    Hélène Bret · 2023 · theses.fr (ABES)
95. Variant-aware computational assessment of neutralizing antibody binding robustness to botulinum toxin A
    Eqram Rahman, Parinitha Rao, Golam Saklayen, Alain Michon, Munim Ahmed, John H. Joseph, William Richard Webb · 2026 · Toxicon
96. Screening and identification of Kringle 5-inhibitory microRNAs from Astragali radix decoction pieces using immobilized magnetic beads
    Meijiao Duan, Qiyue Sun, Jiaqi Duan, Zhuo Chen, Chunyan Yang, Cui Zhai, Meng Cao, Huan Liu, Mengqian Wei, Yunong Chen et al. · 2026 · International Journal of Biological Macromolecules
97. Folding scFv–Antigen Complexes at Scale
    Ravi Shah, Jeffrey Ouyang-Zhang, Zachary Cohen, Maria Rosaria Briglia, C H I Zhang, Adam R. Klivans, Daniel J. Diaz · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
98. ProtLID2.0: A Residue-Specific Pharmacophore Framework for Protein–Protein Docking
    Steven Grudman, Christopher B. McClain, András Fiser · 2026 · Journal of Chemical Information and Modeling
99. Combining AI Structure Prediction and Integrative Modeling for Nanobody-Antigen Complexes
    Miguel Sánchez-Marín, Marco Giulini, Alexandre M. J. J. Bonvin · 2026 · Journal of Chemical Information and Modeling
100. Conformational plasticity and sequence specificity interplay in noncanonical tandem RRM-RNA binding
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