Performance and Its Limits in Rigid Body Protein-Protein Docking

ZDOCK: An initial‐stage protein‐docking algorithm

Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393

Protein 3D Structure Computed from Evolutionary Sequence Variation

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CAPRI: A Critical Assessment of PRedicted Interactions

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Sequence co-evolution gives 3D contacts and structures of protein complexes

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DockQ: A Quality Measure for Protein-Protein Docking Models

Basu, S., & Wallner, B. (2016) · PLOS ONE · doi:10.1371/journal.pone.0161879 · Cited by 460

Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2

Vreven, T., Moal, I. H., Vangone, A., Pierce, B. G., Kastritis, P. L., Torchala, M., Chaleil, R., Jiménez-García, B., Bates, P. A., Fernandez-Recio, J., et al. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.07.016 · Cited by 424

Docking, scoring, and affinity prediction in CAPRI

Lensink, M. F., & Wodak, S. J. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24428 · Cited by 249

Docking and scoring protein interactions: CAPRI 2009

Lensink, M. F., & Wodak, S. J. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22818 · Cited by 226

Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition

Lensink, M. F., Velankar, S., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25215 · Cited by 222

Blind prediction of homo- and hetero-protein complexes: the CASP13-CAPRI experiment

Lensink, M. F., Brysbaert, G., Nadzirin, N., Velankar, S., Chaleil, R. A. G., Gerguri, T., Bates, P. A., Laine, E., Carbone, A., Grudinin, S., et al. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25838 · Cited by 122

SARS-CoV-2 accessory proteins ORF7a and ORF3a use distinct mechanisms to down-regulate MHC-I surface expression

Arshad, N., Laurent-Rolle, M., Ahmed, W. S., Hsu, J. C.-C., Mitchell, S. M., Pawlak, J., Sengupta, D., Biswas, K. H., & Cresswell, P. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2208525120 · Cited by 119

Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro

Ghani, U., Desta, I., Jindal, A., Khan, O., Jones, G., Hashemi, N., Kotelnikov, S., Padhorny, D., Vajda, S., & Kozakov, D. (2021) · doi:10.1101/2021.09.07.459290 · Cited by 68

Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence

Duran-Frigola, M., Cigler, M., & Winter, G. E. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.2c11098 · Cited by 50

Flexible protein–protein docking with a multitrack iterative transformer

Chu, L., Ruffolo, J. A., Harmalkar, A., & Gray, J. J. (2024) · Protein Science · doi:10.1002/pro.4862 · Cited by 41

RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks

Szymborski, J., & Emad, A. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac429 · Cited by 34

Cracked actin filaments as mechanosensitive receptors

(2024) · doi:10.1016/j.bpj.2024.06.014 · Cited by 25

Arf GTPase activates the WAVE regulatory complex through a distinct binding site

Yang, S., Tang, Y., Liu, Y., Brown, A. J., Schaks, M., Ding, B., Kramer, D. A., Mietkowska, M., Ding, L., Alekhina, O., et al. (2022) · Science Advances · doi:10.1126/sciadv.add1412 · Cited by 24

Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions

Gomes, D. E. B., Yang, B., Vanella, R., Nash, M. A., & Bernardi, R. C. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c05869 · Cited by 18

PRMT4 interacts with NCOA4 to inhibit ferritinophagy in cisplatin‐induced acute kidney injury

Zhou, L., Deng, Z., Wang, Y., Zhang, H., Yan, S., Kanwar, Y. S., Wang, Y., Dai, Y., & Deng, F. (2024) · The FASEB Journal · doi:10.1096/fj.202302596r · Cited by 16

Calcium-Bound S100P Protein Is a Promiscuous Binding Partner of the Four-Helical Cytokines

Kazakov, A. S., Deryusheva, E. I., Permyakova, M. E., Sokolov, A. S., Rastrygina, V. A., Uversky, V. N., Permyakov, E. A., & Permyakov, S. E. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231912000 · Cited by 15

The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells

Fernández, I., Dynesen, L. T., Coquin, Y., Pederzoli, R., Brun, D., Haouz, A., Gessain, A., Rey, F. A., Buseyne, F., & Backovic, M. (2023) · Nature Communications · doi:10.1038/s41467-023-36923-0 · Cited by 11

Assessing the binding properties of CASP14 targets and models

Egbert, M., Ghani, U., Ashizawa, R., Kotelnikov, S., Nguyen, T., Desta, I., Hashemi, N., Padhorny, D., Kozakov, D., & Vajda, S. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26209 · Cited by 10

Sampling and Ranking of Protein Conformations Using Machine Learning Techniques Do Not Improve the Quality of Rigid Protein–Protein Docking

Stratiichuk, R., Kyrylenko, R., Koleiev, I., Savchenko, I., Voitsitskyi, T., Husak, V., Yesylevskyy, S., Starosyla, S., & Nafiiev, A. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01765 · Cited by 6

Computational Procedure for Predicting Excipient Effects on Protein–Protein Affinities

Dignon, G. L., & Dill, K. A. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01197 · Cited by 5

A PTP1B-Cdk3 Signaling Axis Promotes Cell Cycle Progression of Human Glioblastoma Cells through an Rb-E2F Dependent Pathway

(2023) · doi:10.1080/10985549.2023.2273193 · Cited by 5

Whole-exome sequencing screening for candidate genes and potential pathogenic variants associated with early-onset high myopia in 47 Chinese families

Rui, X., Li, H., Ma, R., Yang, S., lian, Y., Cheng, W., Ma, M., Rong, W., & Sheng, X. (2025) · Scientific Reports · doi:10.1038/s41598-025-95574-x · Cited by 4

Structure-Based Deep Learning Framework for Modeling Human–Gut Bacterial Protein Interactions

Kiouri, D. P., Batsis, G. C., & Chasapis, C. T. (2025) · Proteomes · doi:10.3390/proteomes13010010 · Cited by 3

Mutant KRAS Suppresses DNA Sensing by Remodeling Membrane Tension to Clear Extracellular Tumor DNA

Cao, D., Zhou, W., Li, Z., Lu, S., Hou, Z., Yu, L., Guan, Y., Wang, G., Liu, Y., Huang, Z., et al. (2026) · Cancer Research · doi:10.1158/0008-5472.can-25-4447