Docking, scoring, and affinity prediction in CAPRI

Cited by (242)

Items 101–200 of 242

1. Structural templates for comparative protein docking
   Ivan V. Anishchenko, Petras J. Kundrotas, Alexander V. Tuzikov, Ilya A. Vakser · 2014 · Proteins Structure Function and Bioinformatics
2. Modeling complexes of modeled proteins
   Ivan V. Anishchenko, Petras J. Kundrotas, Ilya A. Vakser · 2016 · Proteins Structure Function and Bioinformatics
3. DAMpred: Recognizing Disease-Associated nsSNPs through Bayes-Guided Neural-Network Model Built on Low-Resolution Structure Prediction of Proteins and Protein–Protein Interactions
   Lijun Quan, Hongjie Wu, Qiang Lyu, Yang Zhang · 2019 · Journal of Molecular Biology
4. Limits and potential of combined folding and docking
   Pozzati, Gabriele, Zhu, Wensi, Bassot, Claudio, Lamb, John, Kundrotas, Petras, Elofsson, Arne · 2022 · Bioinformatics
5. Protein–Peptide Docking with ESMFold Language Model
   Mateusz Zalewski, Björn Wallner, Sebastian Kmiecik · 2025 · Journal of Chemical Theory and Computation
6. Template-based protein–protein docking exploiting pairwise interfacial residue restraints
   Li C. Xue, João Rodrigues, Drena L Dobbs, Vasant Honavar, Alexandre M. J. J. Bonvin · 2016 · Briefings in Bioinformatics
7. Novel Structural Parameters of Ig–Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity
   Simon Marillet, Marie‐Paule Lefranc, Pierre Boudinot, Frédéric Cazals · 2017 · Frontiers in Immunology
8. Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study
   Hugo Schweke, Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten F. Schwede, Frédéric Cazals, Alix Lhéritier, Juan Fernández‐Recio, Luis Angel Rodríguez‐Lumbreras, Ora Schueler‐Furman et al. · 2023 · PROTEOMICS
9. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase
   Nuo Wang, James Andrew McCammon · 2015 · Protein Science
10. CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys
    Qingzhen Hou, Marc Ferdinand Lensink, Jaap Heringa, K. Anton Feenstra · 2016 · PLoS ONE
11. Integrating Cross-Linking Experiments with Ab Initio Protein–Protein Docking
    Thom Vreven, Devin K. Schweppe, Juan D. Chavez, Chad R. Weisbrod, Sayaka Shibata, Chunxiang Zheng, James E. Bruce, Zhiping Weng · 2018 · Journal of Molecular Biology
12. Protein models docking benchmark 2
    Ivan V. Anishchenko, Petras J. Kundrotas, Alexander V. Tuzikov, Ilya A. Vakser · 2015 · Proteins Structure Function and Bioinformatics
13. Binding free energy analysis of protein-protein docking model structures by evERdock
    Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao · 2018 · The Journal of Chemical Physics
14. Toward a better understanding of the interaction between somatostatin receptor 2 and its ligands: a structural characterization study using molecular dynamics and conceptual density functional theory
    Santhosh Kumar Nagarajan, Sathya Babu, Honglae Sohn, Panneer Devaraju, Thirumurthy Madhavan · 2018 · Journal of Biomolecular Structure and Dynamics
15. Text Mining for Protein Docking
    Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser · 2015 · PLoS Computational Biology
16. Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock
    Hasup Lee, Chaok Seok · 2017 · Methods in molecular biology
17. High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function
    Kelsey Aadland, Charles S. G. Pugh, Bryan D. Kolaczkowski · 2018 · Methods in molecular biology
18. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI
    Schindler, Christina E. M., Chauvot de Beauchêne, Isaure, de Vries, Sjoerd J., Zacharias, Martin · 2017 · Proteins Structure Function and Bioinformatics
19. A Review of Current Computational Tools for Peptide–Protein Docking
    Fábio G. Martins, Hélder A. Santos, Sérgio Filipe Sousa · 2026 · Journal of Computational Chemistry
20. Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a
    Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan Edward Mark · 2015 · Journal of Chemical Information and Modeling
21. Monte Carlo replica-exchange based ensemble docking of protein conformations
    Zhe Zhang, Uwe Ehmann, Martin Zacharias · 2017 · Proteins Structure Function and Bioinformatics
22. Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling
    Toshiyuki Tsuji, Takao Yoda, Tsuyoshi Shirai · 2015 · Scientific Reports
23. Information-Driven Structural Modelling of Protein–Protein Interactions
    João Rodrigues, Ezgi Karaca, Alexandre M. J. J. Bonvin · 2014 · Methods in molecular biology
24. Template‐based modeling by ClusPro in CASP13 and the potential for using co‐evolutionary information in docking
    Kathryn A. Porter, Dzmitry Padhorny, Israel Desta, Mikhail Ignatov, Dmitri Beglov, Sergei Kotelnikov, Zhuyezi Sun, Andrey Evgen'evich Alekseenko, Ivan V. Anishchenko, Qian Cong et al. · 2019 · Proteins Structure Function and Bioinformatics
25. Assessing scoring metrics for <scp>AlphaFold2</scp> and <scp>AlphaFold3</scp> protein complex predictions
    Genz, Luca R., Nair, Sanjana, Nagar, Natan, Topf, Maya · 2025 · Protein Science
26. A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison
    Erik Pfeiffenberger, Raphaël A. G. Chaleil, Iain H. Moal, Paul A. Bates · 2016 · Proteins Structure Function and Bioinformatics
27. Refining evERdock: Improved selection of good protein-protein complex models achieved by MD optimization and use of multiple conformations
    Ai Shinobu, Kazuhiro Takemura, Nobuyuki Matubayasi, Akio Kitao · 2018 · The Journal of Chemical Physics
28. Performance of MDockPP in CAPRI rounds 28‐29 and 31‐35 including the prediction of water‐mediated interactions
    Xianjin Xu, Liming Qiu, Chengfei Yan, Zhiwei Ma, Sam Z. Grinter, Xiaoqin Zou · 2016 · Proteins Structure Function and Bioinformatics
29. ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking
    Mikhail Ignatov, Andrey Maksimovich Kazennov, Dima Kozakov · 2018 · Journal of Molecular Biology
30. Update of the ATTRACT force field for the prediction of protein-protein binding affinity
    Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci · 2017 · Journal of Computational Chemistry
31. An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45
    Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li C. Xue, Rodrigo V. Honorato, Irina Sousa Moreira et al. · 2019 · Proteins Structure Function and Bioinformatics
32. Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools
    Yudan Shi, Jerry M. Parks, Jeremy C. Smith · 2025 · Journal of Chemical Information and Modeling
33. Intracellular co-localization of the Escherichia coli enterobactin biosynthetic enzymes EntA, EntB, and EntE
    Paknoosh Pakarian, Peter D. Pawelek · 2016 · Biochemical and Biophysical Research Communications
34. Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46
    Yumeng Yan, Jiahua He, Yuyu Feng, Peicong Lin, Huanyu Tao, Sheng‐You Huang · 2020 · Proteins Structure Function and Bioinformatics
35. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)
    Christine Anne Orengo, Sameer S Velankar, Shoshana J. Wodak, Vincent Zoete, Alexandre M. J. J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock et al. · 2020 · F1000Research
36. Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization
    Shruthi Viswanath, Laura Domı́nguez, Leigh S. Foster, John E. Straub, Ron Elber · 2015 · Proteins Structure Function and Bioinformatics
37. Refinement of protein-protein complexes in contact map space with metadynamics simulations
    Pfeiffenberger, Erik, Bates, Paul A. · 2019 · Proteins Structure Function and Bioinformatics
38. Recent advances and challenges in protein complex model accuracy estimation
    Fang Liang, Meng Sun, Lei Xie, Xuanfeng Zhao, Dong Liu, Kailong Zhao, Guijun Zhang · 2024 · Computational and Structural Biotechnology Journal
39. 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
40. A new scoring function for protein–protein docking that identifies native structures with unprecedented accuracy
    Irina Sousa Moreira, João Miguel da Silva Martins, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes · 2014 · Physical Chemistry Chemical Physics
41. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling
    Sjoerd J. de Vries, Isaure Chauvot de Beauchêne, Christina Schindler, Martin Zacharias · 2016 · Biophysical Journal
42. Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein–Protein Encounters
    Chiara Pallara, Manuel Rueda, Ruben A Abagyan, Juan Fernández‐Recio · 2016 · Journal of Chemical Theory and Computation
43. New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
    Enrico Spiga, Matteo T. Degiacomi, Matteo Dal Peraro · 2014 · Advances in protein chemistry and structural biology
44. Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45
    Alisa Khramushin, Orly Marcu, Nawsad Alam, Orly Shimony, Dzmitry Padhorny, Emiliano Brini, Ken A. Dill, Sándor Vajda, Dima Kozakov, Ora Schueler‐Furman · 2019 · Proteins Structure Function and Bioinformatics
45. Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape
    Pernille Sønderby, Åsmund Rinnan, Jesper J. Madsen, Pernille Harris, Jens T. Bukrinski, Günther Herbert Johannes Peters · 2017 · Journal of Chemical Information and Modeling
46. In silico optimization of RNA–protein interactions for CRISPR-Cas13-based antimicrobials
    Ho-min Park, Yunseol Park, Urta Berani, Eunkyu Bang, Joris Vankerschaver, Arnout Van Messem, Wesley De Neve, Hyunjin Shim · 2022 · Biology Direct
47. Protein–ligand docking using FFT based sampling: D3R case study
    Dzmitry Padhorny, David R. Hall, Hanieh Mirzaei, Artem B. Mamonov, Mohammad Moghadasi, Andrey Evgen'evich Alekseenko, Dmitri Beglov, Dima Kozakov · 2017 · Journal of Computer-Aided Molecular Design
48. How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking
    Chakravarty, Devlina, McElfresh, GW, Kundrotas, Petras J., Vakser, Ilya A. · 2020 · Proteins Structure Function and Bioinformatics
49. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations
    Yong Gyu Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant Honavar · 2023 · Biomolecules
50. Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility
    Haoran Chen, Yuanfei Sun, Yang Shen · 2016 · Proteins Structure Function and Bioinformatics
51. GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
    Jan Walther Perthold, Chris Oostenbrink · 2019 · Journal of Chemical Information and Modeling
52. Protein–protein docking with interface residue restraints*
    Hao Li, Sheng‐You Huang · 2020 · Chinese Physics B
53. Simulated unbound structures for benchmarking of protein docking in the Dockground resource
    Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, Ilya A. Vakser · 2015 · BMC Bioinformatics
54. Inferring the microscopic surface energy of protein–protein interfaces from mutation data
    Iain H. Moal, Justas Dapkūnas, Juan Fernández‐Recio · 2015 · Proteins Structure Function and Bioinformatics
55. Comparing side chain packing in soluble proteins, protein‐protein interfaces, and transmembrane proteins
    Jennifer C. Gaines, S. Acebes, Alejandro Virrueta, Mitchell P. Butler, Lynne Regan, Corey S. O’Hern · 2018 · Proteins Structure Function and Bioinformatics
56. Performance of human and server prediction in CAPRI rounds 38‐45
    Rui Duan, Liming Qiu, Xianjin Xu, Zhiwei Ma, Benjamin Ryan Merideth, Chi‐Ren Shyu, Xiaoqin Zou · 2020 · Proteins Structure Function and Bioinformatics
57. Prediction of Biomolecular Complexes
    Anna Vangone, Romina Oliva, Luigi Cavallo, Alexandre M. J. J. Bonvin · 2017 · Springer eBooks
58. Meta-server for automatic analysis, scoring and ranking of docking models
    Anastasia A. Anashkina, Yuri V. Kravatsky, Eugene Kuznetsov, Alexander А. Makarov, Alexei A. Adzhubei · 2017 · Bioinformatics
59. Molecular-Level Understanding of the Somatostatin Receptor 1 (SSTR1)–Ligand Binding: A Structural Biology Study Based on Computational Methods
    Santhosh Kumar Nagarajan, Sathya Babu, Honglae Sohn, Thirumurthy Madhavan · 2020 · ACS Omega
60. 3D STRUCTURAL MODELING OF NEUTRALIZING SCFV AGAINST GLYCOPROTEIN-D OF HSV-1 AND EVALUATION OF ANTIGEN-ANTIBODY INTERACTIONS BY BIOINFORMATIC METHODS
    Mozafar Mohammadi, Foroogh Nejatollahi · 2014 · International Journal of Pharma and Bio Sciences
61. Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design
    Balasubramanian Harihar, Konda Mani Saravanan, M. Michael Gromiha, Samuel Selvaraj · 2024 · Molecular Biotechnology
62. Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine
    Emil G Alexov · 2014 · Advances in Biology
63. Modeling of protein complexes in CAPRI Round 37 using template‐based approach combined with model selection
    Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas · 2017 · Proteins Structure Function and Bioinformatics
64. Template‐based modeling and ab‐initio docking using CoDock in CAPRI
    Ren Kong, Ran‐Ran Liu, Ximing Xu, Dawei Zhang, Xiaoshuang Xu, Hang Shi, Shan Chang · 2020 · Proteins Structure Function and Bioinformatics
65. Investigating the structural impact of S311C mutation in DRD2 receptor by molecular dynamics & docking studies
    Avijit Podder, Deeksha Pandey, N. Latha · 2016 · Biochimie
66. evERdock BAI: Machine-learning-guided selection of protein-protein complex structure
    Kei Terayama, Ai Shinobu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao · 2019 · The Journal of Chemical Physics
67. From workstations to workbenches: Towards predicting physicochemically viable protein–protein interactions across a host and a pathogen
    Gayatri Ramakrishnan, Nagasuma R Chandra, Narayanaswamy Srinivasan · 2014 · IUBMB Life
68. Development of a New Benchmark for Assessing the Scoring Functions Applicable to Protein–Protein Interactions
    Li Han, Qifan Yang, Zhihai Liu, Yan Li, Renxiao Wang · 2018 · Future Medicinal Chemistry
69. Interaction of the Inhibitory Peptides ShK and HmK with the Voltage-Gated Potassium Channel KV1.3: Role of Conformational Dynamics
    Karoline Sanches, Viktor Prypoten, K. George Chandy, David K. Chalmers, Raymond S. Norton · 2023 · Journal of Chemical Information and Modeling
70. Biomolecular Interaction Prediction in the Pre‐ and Post‐ AlphaFold Era: The 8th CAPRI Evaluation
    Marc Ferdinand Lensink, Nessim RAOURAOUA, Guillaume Brysbaert, Sameer S Velankar, Shoshana J. Wodak, Alexandre M. J. J. Bonvin · 2025 · Proteins Structure Function and Bioinformatics
71. Focused grid‐based resampling for protein docking and mapping
    Artem B. Mamonov, Mohammad Moghadasi, Hanieh Mirzaei, Shahrooz Zarbafian, Laurie E. Grove, Tanggis Bohnuud, Pirooz Vakili, Ioannis Ch. Paschalidis, Sándor Vajda, Dima Kozakov · 2016 · Journal of Computational Chemistry
72. Structural prediction of antibody‐APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data
    Andrew M. Wollacott, Luke N. Robinson, Boopathy Ramakrishnan, Hamid Tissire, Karthik Viswanathan, Zachary H. Shriver, Gregory J. Babcock · 2019 · Journal of Molecular Recognition
73. Protein docking with predicted constraints
    Ludwig Krippahl, Pedro Barahona · 2015 · Algorithms for Molecular Biology
74. Evolution of a Novel Antiviral Immune-Signaling Interaction by Partial-Gene Duplication
    Bryan Korithoski, Oralia M. Kolaczkowski, Krishanu Mukherjee, Reema Kola, Chandra Earl, Bryan D. Kolaczkowski · 2015 · PLoS ONE
75. Subunit orientation in the Escherichia coli enterobactin biosynthetic EntA-EntE complex revealed by a two-hybrid approach
    Paknoosh Pakarian, Peter D. Pawelek · 2016 · Biochimie
76. Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers
    Lim Heo, Hasup Lee, Minkyung Baek, Chaok Seok · 2016 · Methods in molecular biology
77. PIQLE: protein–protein interface quality estimation by deep graph learning of multimeric interaction geometries
    Md Hossain Shuvo, Mohimenul Karim, Rahmatullah Roche, Debswapna Bhattacharya · 2023 · Bioinformatics Advances
78. Small Paramagnetic Co-solute Molecules
    Tobias Madl, Frans A. A. Mulder · 2018 · Royal Society of Chemistry eBooks
79. Current Computational Methods for Protein-peptide Complex Structure Prediction
    Chao Yang, Xianjin Xu, Changcheng Xiang · 2023 · Current Medicinal Chemistry
80. Properties that rank protein:protein docking poses with high accuracy
    Inês C. M. Simões, João T. S. Coimbra, Rui P. P. Neves, Inês P. D. Costa, Maria João Ramos, Pedro Alexandrino Fernandes · 2018 · Physical Chemistry Chemical Physics
81. Assessing Structural Predictions of Protein–Protein Recognition: The CAPRI Experiment
    Joël Janin, Shoshana J. Wodak, Marc Ferdinand Lensink, Sameer S Velankar · 2015 · Reviews in computational chemistry
82. Molecular modeling of neurological membrane proteins − from binding sites to synapses
    Lucy Kate Ladefoged, Talia Zeppelin, Birgit Schiøtt · 2018 · Neuroscience Letters
83. More efficient screening of protein-protein complex model structures for reducing the number of candidates
    Kazuhiro Takemura, Akio Kitao · 2019 · Biophysics and Physicobiology
84. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition
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85. GPU optimizations for a production molecular docking code
    Raphael Landaverde, Martin Herbordt · 2014 · IEEE High Performance Extreme Computing Conference
86. Analysis of the interface variability in NMR structure ensembles of protein–protein complexes
    Luisa Calvanese, Gabriella D’Auria, Anna Vangone, Lucia Falcigno, Romina Oliva · 2016 · Journal of Structural Biology
87. Assessment of data‐assisted prediction by inclusion of crosslinking/mass‐spectrometry and small angle X‐ray scattering data in the 12th Critical Assessment of protein Structure Prediction experiment
    Giorgio E. Tamò, Luciano A. Abriata, Giulia Fonti, Matteo Dal Peraro · 2017 · Proteins Structure Function and Bioinformatics
88. Template‐based modeling of diverse protein interactions in CAPRI rounds 38‐45
    Justas Dapkūnas, Visvaldas Kairys, Kliment Olechnovič, Česlovas Venclovas · 2019 · Proteins Structure Function and Bioinformatics
89. Theoretical analysis of somatostatin receptor 5 with antagonists and agonists for the treatment of neuroendocrine tumors
    Santhosh Kumar Nagarajan, Sathya Babu, Thirumurthy Madhavan · 2017 · Molecular Diversity
90. Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin‐α7 mediated nuclear import pathway
    Patricia Resa‐Infante, Jaume Bonet, Swantje Thiele, Malik Alawi, Stephanie Stanelle‐Bertram, Berfin Tuku, Sebastian Beck, Baldomero Oliva, Gülşah Gabriel · 2019 · FEBS Journal
91. Regulation of microRNA expression by the adaptor protein GRB2
    Amy K. Stainthorp, Chi‐Chuan Lin, Dapeng Wang, Ragini Medhi, Zamal Ahmed, Kin Man Suen, Eric Alexander Miska, Adrian Whitehouse, John Edward Ladbury · 2023 · Scientific Reports
92. Updates to the CASP Infrastructure in 2024
    Andriy Kryshtafovych, Maciej Miłostan, Marc Ferdinand Lensink, Sameer S Velankar, Alexandre M. J. J. Bonvin, John Moult, Krzysztof A. Fidelis · 2025 · Proteins Structure Function and Bioinformatics
93. Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces
    Matthias Dietzen, Olga V. Kalinina, Katerina Taškova, Benny Kneissl, Anna‐Katharina Hildebrandt, Elmar Jaenicke, Heinz Decker, Thomas Lengauer, Andreas Hildebrandt · 2015 · Proteins Structure Function and Bioinformatics
94. Inhibition of protein interactions: co-crystalized protein–protein interfaces are nearly as good as holo proteins in rigid-body ligand docking
    Saveliy Belkin, Petras J. Kundrotas, Ilya A. Vakser · 2018 · Journal of Computer-Aided Molecular Design
95. Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes
    Jérôme de Ruyck, Guillaume Brysbaert, Vincent Villeret, Marc Aumercier, Marc Ferdinand Lensink · 2018 · Proteins Structure Function and Bioinformatics
96. Complex Stability is Encoded in Binding Patch Softness: a Monomer-Based Approach to Predict Inter-Subunit Affinity of Protein Dimers
    Hamid Hadi‐Alijanvand · 2019 · Journal of Proteome Research
97. EquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks
    Md Hossain Shuvo, Debswapna Bhattacharya · 2024 · Computational and Structural Biotechnology Journal
98. Benchmarking TCR–pMHC structure prediction: a unified evaluation and CDR3-based functional insights
    J D Lu, Xinyuan Zhu, Xinting Hu, Cheng Zhang, Fuli Feng · 2026 · Briefings in Bioinformatics
99. Performance of Hybrid Strategies Combining MDockPP and AlphaFold2 in CAPRI Rounds 47–55
    Rui Duan, Xianjin Xu, Liming Qiu, Shuang Zhang, Xiaoqin Zou · 2025 · Proteins Structure Function and Bioinformatics
100. In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase
     Jordi Zamarreño Beas, Marco A.M. Videira, Val Karavaeva, Frederico M. Lourenço, Mafalda R. Almeida, Filipa L. Sousa, Lı́gia M. Saraiva · 2023 · Frontiers in Genetics