Principles of protein-protein interactions

Anatomy of hot spots in protein interfaces

Bogan, A. A., & Thorn, K. S. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1843 · Cited by 1,988 · see citing works

Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

Scott, D. E., Bayly, A. R., Abell, C., & Skidmore, J. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.29 · Cited by 1,137 · see citing works

Structural Symmetry and Protein Function

Goodsell, D. S., & Olson, A. J. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.105 · Cited by 950 · see citing works

PIPER: An FFT‐based protein docking program with pairwise potentials

Kozakov, D., Brenke, R., Comeau, S. R., & Vajda, S. (2006) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21117 · Cited by 865 · see citing works

Inhibiting the p53–MDM2 interaction: an important target for cancer therapy

Chène, P. (2003) · Nature Reviews Cancer · doi:10.1038/nrc991 · Cited by 765 · see citing works

Unraveling hot spots in binding interfaces: progress and challenges

DeLano, W. L. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00283-x · Cited by 767 · see citing works

Hot spots—A review of the protein–protein interface determinant amino‐acid residues

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21396 · Cited by 760 · see citing works

High-affinity binders selected from designed ankyrin repeat protein libraries

Binz, H. K., Amstutz, P., Kohl, A., Stumpp, M. T., Briand, C., Forrer, P., Grütter, M. G., & Plückthun, A. (2004) · Nature Biotechnology · doi:10.1038/nbt962 · Cited by 656 · see citing works

Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces

Ma, B., Elkayam, T., Wolfson, H., & Nussinov, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1030237100 · Cited by 595 · see citing works

The structural basis of antibody–antigen recognition

Sela-Culang, I., Kunik, V., & Ofran, Y. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00302 · Cited by 530 · see citing works

Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues

Keskin, O., Ma, B., & Nussinov, R. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.10.077 · Cited by 519 · see citing works

Visualization of transient encounter complexes in protein–protein association

Tang, C., Iwahara, J., & Clore, G. M. (2006) · Nature · doi:10.1038/nature05201 · Cited by 406 · see citing works

Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369 · see citing works

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

Dehouck, Y., Kwasigroch, J. M., Rooman, M., & Gilis, D. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt450 · Cited by 338 · see citing works

A simple definition of structural regions in proteins and its use in analyzing interface evolution

Levy, E. D. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.09.028 · Cited by 254 · see citing works

Proteins evolve on the edge of supramolecular self-assembly

Garcia-Seisdedos, H., Empereur-Mot, C., Elad, N., & Levy, E. D. (2017) · Nature · doi:10.1038/nature23320 · Cited by 253 · see citing works

Comparison of the Interactions of Transferrin Receptor and Transferrin Receptor 2 with Transferrin and the Hereditary Hemochromatosis Protein HFE

West, A. P., Bennett, M. J., Sellers, V. M., Andrews, N. C., Enns, C. A., & Bjorkman, P. J. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.c000664200 · Cited by 257 · see citing works

The Intrinsic Contributions of Tyrosine, Serine, Glycine and Arginine to the Affinity and Specificity of Antibodies

Birtalan, S., Zhang, Y., Fellouse, F. A., Shao, L., Schaefer, G., & Sidhu, S. S. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.01.093 · Cited by 244 · see citing works

Human Cancer Protein-Protein Interaction Network: A Structural Perspective

Kar, G., Gursoy, A., & Keskin, O. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000601 · Cited by 235 · see citing works

De novo protein design enables the precise induction of RSV-neutralizing antibodies

Sesterhenn, F., Yang, C., Bonet, J., Cramer, J. T., Wen, X., Wang, Y., Chiang, C.-I., Abriata, L. A., Kucharska, I., Castoro, G., et al. (2020) · Science · doi:10.1126/science.aay5051 · Cited by 191 · see citing works

Prediction of aggregation prone regions of therapeutic proteins

Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., & Trout, B. L. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp911706q · Cited by 200 · see citing works

<scp>AB</scp> ‐Bind: Antibody binding mutational database for computational affinity predictions

Sirin, S., Apgar, J. R., Bennett, E. M., & Keating, A. E. (2016) · Protein Science · doi:10.1002/pro.2829 · Cited by 179 · see citing works

State-of-the-art strategies for targeting protein–protein interactions by small-molecule inhibitors

Sheng, C., Dong, G., Miao, Z., Zhang, W., & Wang, W. (2015) · Chemical Society Reviews · doi:10.1039/c5cs00252d · Cited by 165 · see citing works

Can self‐inhibitory peptides be derived from the interfaces of globular protein–protein interactions?

London, N., Raveh, B., Movshovitz‐Attias, D., & Schueler‐Furman, O. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22785 · Cited by 164 · see citing works

Structural space of protein–protein interfaces is degenerate, close to complete, and highly connected

Gao, M., & Skolnick, J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012820107 · Cited by 139 · see citing works

Myostatin and its Regulation: A Comprehensive Review of Myostatin Inhibiting Strategies

Baig, M. H., Ahmad, K., Moon, J. S., Park, S.-Y., Ho Lim, J., Chun, H. J., Qadri, A. F., Hwang, Y. C., Jan, A. T., Ahmad, S. S., et al. (2022) · Frontiers in Physiology · doi:10.3389/fphys.2022.876078 · Cited by 135 · see citing works

Structural Basis for Interactions between Tenascins and Lectican C-Type Lectin Domains

Lundell, A., Olin, A. I., Mörgelin, M., al-Karadaghi, S., Aspberg, A., & Logan, D. T. (2004) · Structure · doi:10.1016/j.str.2004.05.021 · Cited by 127 · see citing works

Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database

Bourgeas, R., Basse, M.-J., Morelli, X., & Roche, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009598 · Cited by 126 · see citing works

Mechanism for Multiple Ligand Recognition by the Human Transferrin Receptor

Giannetti, A. M., Snow, P. M., Zak, O., & Björkman, P. J. (2003) · PLoS Biology · doi:10.1371/journal.pbio.0000051 · Cited by 122 · see citing works

Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery

Valkov, E., Sharpe, T., Marsh, M., Greive, S., & Hyvönen, M. (2011) · Topics in Current Chemistry · doi:10.1007/128_2011_265 · Cited by 107 · see citing works

iAlign: a method for the structural comparison of protein–protein interfaces

Gao, M., & Skolnick, J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq404 · Cited by 98 · see citing works

The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops

Kunik, V., & Ofran, Y. (2013) · Protein Engineering Design and Selection · doi:10.1093/protein/gzt027 · Cited by 96 · see citing works

Bottom-up de novo design of functional proteins with complex structural features

Yang, C., Sesterhenn, F., Bonet, J., van Aalen, E. A., Scheller, L., Abriata, L. A., Cramer, J. T., Wen, X., Rosset, S., Georgeon, S., et al. (2021) · Nature Chemical Biology · doi:10.1038/s41589-020-00699-x · Cited by 84 · see citing works

A credit-card library approach for disrupting protein–protein interactions

Xu, Y., Shi, J., Yamamoto, N., Moss, J. A., Vogt, P. K., & Janda, K. D. (2006) · Bioorganic &amp; Medicinal Chemistry · doi:10.1016/j.bmc.2005.11.052 · Cited by 93 · see citing works

A Review of Alpha-1 Antitrypsin Binding Partners for Immune Regulation and Potential Therapeutic Application

O’Brien, M. E., Murray, G., Gogoi, D., Yusuf, A., McCarthy, C., Wormald, M. R., Casey, M., Gabillard-Lefort, C., McElvaney, N. G., & Reeves, E. P. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23052441 · Cited by 91 · see citing works

Potential aggregation-prone regions in complementarity-determining regions of antibodies and their contribution towards antigen recognition: a computational analysis

Wang, X., Singh, S. K., & Kumar, S. (2010) · Pharmaceutical Research · doi:10.1007/s11095-010-0143-5 · Cited by 79 · see citing works

Structure and reactivity of LpxD, the <i>N</i> -acyltransferase of lipid A biosynthesis

Buetow, L., Smith, T. K., Dawson, A., Fyffe, S., & Hunter, W. N. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606356104 · Cited by 78 · see citing works

Targeting protein–protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies?

Cierpicki, T., & Grembecka, J. (2015) · Immunological Reviews · doi:10.1111/imr.12244 · Cited by 53 · see citing works

Aromatic components of two ferric enterobactin binding sites in <i>Escherichia coli</i> FepA

Cao, Z., Qi, Z., Sprencel, C., Newton, S. M. C., & Klebba, P. E. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.02093.x · Cited by 45 · see citing works

Structural determinants of co-translational protein complex assembly

Mallik, S., Venezian, J., Lobov, A., Heidenreich, M., Garcia-Seisdedos, H., Yeates, T. O., Shiber, A., & Levy, E. D. (2025) · Cell · doi:10.1016/j.cell.2024.11.013 · Cited by 42 · see citing works

Using statistical methods to model the fine-tuning of molecular machines and systems

Thorvaldsen, S., & Hössjer, O. (2020) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2020.110352 · Cited by 15 · see citing works

Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis

Zhou, T.-M., Wang, S., & Xu, J. (2017) · doi:10.1101/240754 · Cited by 25 · see citing works

Refinement of protein-protein complexes in contact map space with metadynamics simulations

Pfeiffenberger, E., & Bates, P. A. (2019) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25612 · Cited by 15 · see citing works

Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength

Zheng, F., Jiang, X., Wen, Y., Yang, Y., & Li, M. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.018 · Cited by 14 · see citing works

Reliable prediction of protein–protein binding affinity changes upon mutations with Pythia-PPI

Tao, F., Sun, J., Gao, P., Gao, G. F., & Wu, B. (2025) · National Science Review · doi:10.1093/nsr/nwaf231 · Cited by 10 · see citing works

Protein-Protein Interactions as Drug Targets

Wendt, M. D. (2012) · Topics in Medicinal Chemistry · doi:10.1007/978-3-642-28965-1_1 · Cited by 9 · see citing works