Cited by 1,988Protein Structure and Dynamicsthermodynamics and calorimetric analysesEnzyme Structure and Function

The DOI matches its Crossref record; 69 of the 71 references it cites were found in a registry or an index.

Anatomy of hot spots in protein interfaces

Bogan, Andrew A, Thorn, Kurt S·1998·Journal of Molecular Biology

DOI 10.1006/jmbi.1998.1843

Open this paper in CoChat — free account

Abstract

Binding of one protein to another is involved in nearly all biological functions, yet the principles governing the interaction of proteins are not fully understood. To analyze the contributions of individual amino acid residues in protein-protein binding we have compiled a database of 2325 alanine mutants for which the change in free energy of binding upon mutation to alanine has been measured (available at http://motorhead. ucsf.edu/thorn/hotspot). Our analysis shows that at the level of side-chains there is little correlation between buried surface area and free energy of binding. We find that the free energy of binding is not evenly distributed across interfaces; instead, there are hot spots of binding energy made up of a small subset of residues in the dimer interface. These hot spots are enriched in tryptophan, tyrosine and arginine, and are surrounded by energetically less important residues that most likely serve to occlude bulk solvent from the hot spot. Occlusion of solvent is found to be a necessary condition for highly energetic interactions.

Integrity signals

Registry

Crossref · 10.1006/jmbi.1998.1843

Cites

69 of 69 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,011
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
Principles of protein-protein interactions
Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684
Raster3D Version 2.0. A program for photorealistic molecular graphics
Merritt, E. A., & Murphy, M. E. P. (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994006396 · Cited by 2,493
Stability of Proteins Small Globular Proteins
Privalov, P. L. (1979) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60460-x · Cited by 2,163
A Hot Spot of Binding Energy in a Hormone-Receptor Interface
Clackson, T., & Wells, J. A. (1995) · Science · doi:10.1126/science.7529940 · Cited by 1,987
High-Resolution Epitope Mapping of hGH-Receptor Interactions by Alanine-Scanning Mutagenesis
Cunningham, B. C., & Wells, J. A. (1989) · Science · doi:10.1126/science.2471267 · Cited by 1,361
Shape Complementarity at Protein/Protein Interfaces
Lawrence, M. C., & Colman, P. M. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1648 · Cited by 1,224
Shape complementarity at protein–protein interfaces
Norel, R., Lin, S. L., Wolfson, H. J., & Nussinov, R. (1994) · Biopolymers · doi:10.1002/bip.360340711 · Cited by 1,208
An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families
Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0167 · Cited by 1,196

Flagged first, then by citations

Show all 71 references

2 of the 71 references couldn’t be matched to a known paper.

Research works printed but not linked: 2

Judice, 1997, Small molecule inhibitors of human growth hormone/receptor binding, FASEB J., 11, A839
Schreiber, 1995, Energetics of protein-protein interactions, J. Mol. Biol., 248, 478, 10.1006/jmbi.1995.0235 · DOI

Sorted by citations

Items 301–400 of 1,003

Aromatic clusters in protein–protein and protein–drug complexes
Lanzarotti, E., Defelipe, L. A., Marti, M. A., & Turjanski, A. G. (2020) · Journal of Cheminformatics · doi:10.1186/s13321-020-00437-4 · Cited by 102
Evolutionary diversification of the multimeric states of proteins
Lynch, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310980110 · Cited by 93
Protein-protein interface hot spots prediction based on a hybrid feature selection strategy
Qiao, Y., Xiong, Y., Gao, H., Zhu, X., & Chen, P. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2009-5 · Cited by 92
Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures
Clark, J. J., Benson, M. L., Smith, R. D., & Carlson, H. A. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006705 · Cited by 92
Crystallographic and Functional Characterization of the Fluorodifen-inducible Glutathione Transferase from Glycine max Reveals an Active Site Topography Suited for Diphenylether Herbicides and a Novel L-site
Axarli, I., Dhavala, P., Papageorgiou, A. C., & Labrou, N. E. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.10.084 · Cited by 92
Binding Hot Spots in the TEM1–BLIP Interface in Light of its Modular Architecture
Reichmann, D., Cohen, M., Abramovich, R., Dym, O., Lim, D., Strynadka, N. C. J., & Schreiber, G. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.09.076 · Cited by 92
Crystal structure of the receptor-binding domain of human B7-2: Insights into organization and signaling
Zhang, X., Schwartz, J.-C. D., Almo, S. C., & Nathenson, S. G. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252771499 · Cited by 93
A Bipartite Mechanism for ERK2 Recognition by Its Cognate Regulators and Substrates
Zhang, J., Zhou, B., Zheng, C.-F., & Zhang, Z. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303909200 · Cited by 92
Three-Dimensional Structures of the Free and Antigen-Bound Fab from Monoclonal Antilysozyme Antibody HyHEL-63,
Li, Y., Li, H., Smith‐Gill, S. J., & Mariuzza, R. A. (2000) · Biochemistry · doi:10.1021/bi000054l · Cited by 92
Immunogenicity of Immunotoxins Containing Pseudomonas Exotoxin A: Causes, Consequences, and Mitigation
Mazor, R., & Pastan, I. H. (2020) · Frontiers in Immunology · doi:10.3389/fimmu.2020.01261 · Cited by 91
A Detailed Thermodynamic Analysis of Ras/Effector Complex Interfaces
Kiel, C., Serrano, L. G., & Herrmann, C. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.05.050 · Cited by 95
Stability of macromolecular complexes
Brooijmans, N., Sharp, K., & Kuntz, I. D. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10139 · Cited by 82
Inhibition of protein crystallization by evolutionary negative design
Doye, J. P. K., Louis, A. A., & Vendruscolo, M. (2004) · Physical Biology · doi:10.1088/1478-3967/1/1/p02 · Cited by 87
The urokinase plasminogen activator receptor (uPAR) as a target for the diagnosis and therapy of cancer
Mazar, A. P. (2001) · Anti-Cancer Drugs · doi:10.1097/00001813-200106000-00001 · Cited by 91
Protein–RNA interactions: structural characteristics and hotspot amino acids
Krüger, D. M., Neubacher, S., & Grossmann, T. N. (2018) · RNA · doi:10.1261/rna.066464.118 · Cited by 88
Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors
Sable, R. V., & Jois, S. D. S. (2015) · Molecules · doi:10.3390/molecules200611569 · Cited by 93
SOS-NMR: A Saturation Transfer NMR-Based Method for Determining the Structures of Protein−Ligand Complexes
Hajduk, P. J., Mack, J. C., Olejniczak, E. T., Park, C., Dandliker, P. J., & Beutel, B. A. (2004) · Journal of the American Chemical Society · doi:10.1021/ja039480v · Cited by 90
Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid
Reguera, J., Carreira, A., Riolobos, L., Almendral, J. M., & Mateu, M. G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307748101 · Cited by 90
Exploring the Capacity of Minimalist Protein Interfaces: Interface Energetics and Affinity Maturation to Picomolar KD of a Single-domain Antibody with a Flat Paratope
Koide, A., Tereshko, V. A., Uysal, S., Margalef, K., Kossiakoff, A. A., & Koide, S. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.08.027 · Cited by 92
Genetically Encoded 2-Aryl-5-carboxytetrazoles for Site-Selective Protein Photo-Cross-Linking
Tian, Y., Jacinto, M. P., Zeng, Y., Yu, Z., Qu, J., Liu, W. R., & Lin, Q. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b02615 · Cited by 90
Automated Detection of Conformational Epitopes Using Phage Display Peptide Sequences
Negi, S. S., & Braun, W. A. (2009) · Bioinformatics and Biology Insights · doi:10.4137/bbi.s2745 · Cited by 88
Hot Spots in Tcf4 for the Interaction with β-Catenin
Fasolini, M., Wu, X., Flocco, M. M., Trosset, J., Oppermann, U. C. T., & Knapp, S. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m301781200 · Cited by 89
Mapping structural determinants of biological activities in snake venom phospholipases A2 by sequence analysis and site directed mutagenesis
Chioato, L., & Ward, R. J. (2003) · Toxicon · doi:10.1016/j.toxicon.2003.11.027 · Cited by 89
Identification and Functional Characterization of Human Soluble Epoxide Hydrolase Genetic Polymorphisms
Sandberg, M., Hassett, C., Adman, E. T., Meijer, J., & Omiecinski, C. J. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m001153200 · Cited by 89
News from the Protein Mutability Landscape
Hecht, M., Bromberg, Y., & Rost, B. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.07.028 · Cited by 88
Computational Design of a Protein-Based Enzyme Inhibitor
Procko, E., Hedman, R., Hamilton, K., Seetharaman, J., Fleishman, S. J., Su, M., Aramini, J. M., Kornhaber, G. J., Hunt, J. F., Tong, L., et al. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.06.035 · Cited by 87
The architecture of the binding site in redox protein complexes: Implications for fast dissociation
Crowley, P. B., & Carrondo, M. A. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20043 · Cited by 88
The Evolution of Multimeric Protein Assemblages
Lynch, M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr300 · Cited by 86
GPIHBP1 and Plasma Triglyceride Metabolism
Fong, L. G., Young, S. G., Beigneux, A. P., Bensadoun, A., Oberer, M., Jiang, H., & Ploug, M. (2016) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2016.04.013 · Cited by 87
The Structure of the Lingo-1 Ectodomain, a Module Implicated in Central Nervous System Repair Inhibition
Mosyak, L., Wood, A., Dwyer, B. P., Buddha, M. R., Johnson, M., AULABAUGH, A. E., Zhong, X., Presman, E., Benard, S., Kelleher, K. S., et al. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m607314200 · Cited by 87
Unusual Arginine Formations in Protein Function and Assembly: Rings, Strings, and Stacks
Neves, M. A. C., Yeager, M. J., & Abagyan, R. A. (2012) · The Journal of Physical Chemistry B · doi:10.1021/jp3009699 · Cited by 87
The functional capacity of the natural amino acids for molecular recognition
Birtalan, S., Fisher, R. D., & Sidhu, S. S. (2010) · Molecular BioSystems · doi:10.1039/b927393j · Cited by 88
Exploiting sequence and structure homologs to identify protein–protein binding sites
Chung, J., Wang, W., & Bourne, P. E. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20741 · Cited by 87
A Dominant Conformational Role for Amino Acid Diversity in Minimalist Protein–Protein Interfaces
Gilbreth, R. N., Esaki, K., Koide, A., Sidhu, S. S., & Koide, S. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.06.014 · Cited by 87
Mapping the interactions between flavodoxin and its physiological partners flavodoxin reductase and cobalamin-dependent methionine synthase
Hall, D. A., Kooi, C. W. V., Stasik, C. N., Stevens, S. Y., Zuiderweg, E. R. P., & Matthews, R. G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.171168898 · Cited by 87
Small-molecule inhibitors of MDM2 as new anticancer therapeutics
Dickens, M. P., Fitzgerald, R. P., & Fischer, P. M. (2009) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2009.10.003 · Cited by 90
Integrating Fragment Assembly and Biophysical Methods in the Chemical Advancement of Small-Molecule Antagonists of IL-2: An Approach for Inhibiting Protein−Protein Interactions
Raimundo, B. C., Oslob, J. D., Braisted, A. C., Hyde, J., McDowell, R. S., Randal, M., Waal, N. D., Wilkinson, J., Yu, C. H., & Arkin, M. R. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm049967u · Cited by 86
Fluorinated Aromatic Amino Acids Are Sensitive 19F NMR Probes for Bromodomain-Ligand Interactions
Mishra, N. K., Urick, A. K., Ember, S. W., Schönbrunn, E., & Pomerantz, W. C. K. (2014) · ACS Chemical Biology · doi:10.1021/cb5007344 · Cited by 87
Potential Nectin-1 Binding Site on Herpes Simplex Virus Glycoprotein D
Connolly, S. A., Landsburg, D. J., Carfı́, A., Whitbeck, J. C., Zuo, Y., Wiley, D. C., Cohen, G. H., & Eisenberg, R. J. (2004) · Journal of Virology · doi:10.1128/jvi.79.2.1282-1295.2005 · Cited by 86
Antibody‐reactive epitope determination with HLAMatchmaker and its clinical applications
Duquesnoy, R. J. (2011) · Tissue Antigens · doi:10.1111/j.1399-0039.2011.01646.x · Cited by 86
Tryptophan 32 Potentiates Aggregation and Cytotoxicity of a Copper/Zinc Superoxide Dismutase Mutant Associated with Familial Amyotrophic Lateral Sclerosis
Taylor, D. M., Gibbs, B. F., Kabashi, E., Minotti, S., Durham, H. D., & Agar, J. N. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m610119200 · Cited by 85
Biological responses towards cationic peptides and drug carriers
Verdurmen, W. P. R., & Brock, R. E. (2010) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2010.11.005 · Cited by 85
Strategien zur Modulation von Protein‐Protein‐Wechselwirkungen mit synthetischen Substanzen
Yin, H. H., & Hamilton, A. D. (2005) · Angewandte Chemie · doi:10.1002/ange.200461786 · Cited by 87
Computational Identification of Inhibitors of Protein-Protein Interactions
Zhong, S., Macias, A. T., & MacKerell, A. D. (2006) · Current Topics in Medicinal Chemistry · doi:10.2174/156802607779318334 · Cited by 85
How Oligomerization Contributes to the Thermostability of an Archaeon Protein
Tanaka, Y., Tsumoto, K., Yasutake, Y., Umetsu, M., Yao, M., Fukada, H., Tanaka, I., & Kumagai, I. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m404405200 · Cited by 84
Structural and Molecular Characterization of a Preferred Protein Interaction Surface on G Protein βγ Subunits
Davis, T. L., Bonacci, T. M., Sprang, S. R., & Smrcka, A. V. (2005) · Biochemistry · doi:10.1021/bi050655i · Cited by 87
D ockground resource for studying protein–protein interfaces
Douguet, D., Chen, H.-C., Tovchigrechko, A., & Vakser, I. A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl447 · Cited by 84
Molecular Determinants for Antibody Binding on Group 1 House Dust Mite Allergens
Chruszcz, M., Pomés, A., Glesner, J., Vailes, L. D., Osinski, T., Porebski, P. J., Majorek, K. A., Heymann, P. W., Platts‐Mills, T. A. E., Minor, W., et al. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.311159 · Cited by 84
Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy
Bernardi, R. C., Durner, E., Schoeler, C., Malinowska, K. H., de Carvalho, B. G., Bayer, E. A., Luthey-Schulten, Z. A., Gaub, H. E., & Nash, M. A. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b06776 · Cited by 83
High-Affinity Insulin Binding: Insulin Interacts with Two Receptor Ligand Binding Sites
Whittaker, L. J., Hao, C., Fu, W., & Whittaker, J. (2008) · Biochemistry · doi:10.1021/bi801693h · Cited by 85
How Optimal Are the Binding Energetics of Barnase and Barstar?
Wang, T., Tomić, S., Gabdoulline, R. R., & Wade, R. C. (2004) · Biophysical Journal · doi:10.1529/biophysj.104.040964 · Cited by 83
Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases
Castillo, V., & Ventura, S. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000476 · Cited by 84
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design
Conchúir, S. Ó., Barlow, K. A., Pache, R. A., Ollikainen, N., Kundert, K., O’Meara, M. J., Smith, C. A., & Kortemme, T. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130433 · Cited by 81
In silico structure-based approaches to discover protein-protein interaction-targeting drugs
Shin, W., Christoffer, C. W., & Kihara, D. (2017) · Methods · doi:10.1016/j.ymeth.2017.08.006 · Cited by 89
The many faces of Ras: recognition of small GTP-binding proteins
Corbett, K. D., & Alber, T. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01974-0 · Cited by 83
Dual Interaction of a Geminivirus Replication Accessory Factor with a Viral Replication Protein and a Plant Cell Cycle Regulator
Settlage, S. B., Miller, A. B., Gruissem, W., & Hanley-Bowdoin, L. K. (2001) · Virology · doi:10.1006/viro.2000.0719 · Cited by 83
iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations
Geng, C., Vangone, A., Folkers, G. E., Xue, L. C., & Bonvin, A. M. J. J. (2019) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25630 · Cited by 82
Toward Small-Molecule Inhibition of Protein–Protein Interactions: General Aspects and Recent Progress in Targeting Costimulatory and Coinhibitory (Immune Checkpoint) Interactions
Bojadzic, D., & Buchwald, P. (2018) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026618666180531092503 · Cited by 85
TEAD–YAP Interaction Inhibitors and MDM2 Binders from DNA‐Encoded Indole‐Focused Ugi Peptidomimetics
Kunig, V. B. K., Potowski, M., Akbarzadeh, M., Škopić, M. K., Smith, D. D. S., Arendt, L., Dormuth, I., Adihou, H., Andlovic, B., Karataş, H., et al. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.202006280 · Cited by 81
Antigen–Antibody Complexes
Kapingidza, A. B., Kowal, K., & Chruszcz, M. (2020) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-030-41769-7_19 · Cited by 88
Tackling the Antibiotic Resistance Caused by Class A β-Lactamases through the Use of β-Lactamase Inhibitory Protein
Eiamphungporn, W., Schaduangrat, N., Malik, A. A., & Nantasenamat, C. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19082222 · Cited by 81
CD19 CAR antigen engagement mechanisms and affinity tuning
He, C., Mansilla‐Soto, J., Khanra, N., Hamieh, M., Bustos, V., Paquette, A. J., Angus, A. G., Shore, D. M., Rice, W. J., Khelashvili, G., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.adf1426 · Cited by 83
Alanine-Scanning Mutagenesis Defines a Conserved Energetic Hotspot in the CaVα1 AID-CaVβ Interaction Site that Is Critical for Channel Modulation
Petegem, F. V., Duderstadt, K. E., Clark, K. A., Wang, M. Y., & Minor, D. L. (2008) · Structure · doi:10.1016/j.str.2007.11.010 · Cited by 81
Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers
Jones, A. X., Cao, Y., Tang, Y., Wang, J., Ding, Y., Tan, H., Chen, Z., Fang, R.-Q., Yin, J., Chen, R., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11917-z · Cited by 84
Luxury accommodations: the expanding role of structural plasticity in protein–protein interactions
Sundberg, E. J., & Mariuzza, R. A. (2000) · Structure · doi:10.1016/s0969-2126(00)00167-2 · Cited by 81
Context-Based Identification of Protein-Protein Interfaces and “Hot-Spot” Residues
Geppert, T., Hoy, B., Wessler, S., & Schneider, G. (2011) · Chemistry & Biology · doi:10.1016/j.chembiol.2011.01.005 · Cited by 80
Late‐Stage Diversification of Tryptophan‐Derived Biomolecules
Gruß, H., & Sewald, N. (2019) · Chemistry - A European Journal · doi:10.1002/chem.201903756 · Cited by 80
Mutational Analysis of the IFNAR1 Binding Site on IFNα2 Reveals the Architecture of a Weak Ligand–Receptor Binding-site
Roisman, L. C., Jaitin, D. A., Baker, D. P., & Schreiber, G. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.08.042 · Cited by 80
PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces
Assi, S. A., Tanaka, T. U., Rabbitts, T. H., & Fernández‐Fuentes, N. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1158 · Cited by 83
Prism: Protein-Protein Interaction Prediction by Structural Matching
Keskin, O., Nussinov, R., & Gursoy, A. (2008) · Methods in Molecular Biology · doi:10.1007/978-1-59745-398-1_30 · Cited by 80
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
Preferred Conformers of Proteinogenic Glutamic Acid
Peña, I., Sanz, M. E., López, J. C., & Alonso, J. L. (2011) · Journal of the American Chemical Society · doi:10.1021/ja2101449 · Cited by 79
Evaluation of AlphaFold 3’s Protein–Protein Complexes for Predicting Binding Free Energy Changes upon Mutation
Wee, J., & Wei, G. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00976 · Cited by 103
AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking
Ben‐Shimon, A., & Niv, M. Y. (2015) · Structure · doi:10.1016/j.str.2015.03.010 · Cited by 80
Robust protein–protein interactions in crowded cellular environments
Deeds, E. J., Ashenberg, O., Gerardin, J., & Shakhnovich, E. I. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702766104 · Cited by 78
Inhibiting transient protein–protein interactions: lessons from the Cdc25 protein tyrosine phosphatases
Rudolph, J. (2007) · Nature reviews. Cancer · doi:10.1038/nrc2087 · Cited by 79
Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation
Berliner, N., Teyra, J., Çolak, R., Lopez, S. G., & Kim, P. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0107353 · Cited by 77
Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
Zhao, N., Han, J. G., Shyu, C., & Korkin, D. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003592 · Cited by 81
Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer
Mabonga, L., & Kappo, A. P. (2019) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-019-09831-5 · Cited by 81
Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions
Cukuroglu, E., Gürsoy, A., Nussinov, R., & Keskin, Ö. (2014) · PLoS ONE · doi:10.1371/journal.pone.0086738 · Cited by 76
From Laptop to Benchtop to Bedside: Structure-based Drug Design on Protein Targets
Chen, L., Morrow, J. K., Tran, H. T., Phatak, S. S., Du‐Cuny, L., & Zhang, S. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212799436386 · Cited by 81
The self-organizing fractal theory as a universal discovery method: the phenomenon of life
Kurakin, A. V. (2011) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-8-4 · Cited by 84
Protein nitrotryptophan: Formation, significance and identification
Nuriel, T., Hansler, A., & Gross, S. S. (2011) · Journal of Proteomics · doi:10.1016/j.jprot.2011.05.032 · Cited by 78
Exploration of Backbone Space in Foldamers Containing α‐ and β‐Amino Acid Residues: Developing Protease‐Resistant Oligomers that Bind Tightly to the BH3‐Recognition Cleft of Bcl‐xL
Sadowsky, J., Murray, J. K., Tomita, Y. A., & Gellman, S. H. (2007) · ChemBioChem · doi:10.1002/cbic.200600546 · Cited by 77
Protein-Associated Cation Clusters in Aqueous Arginine Solutions and Their Effects on Protein Stability and Size
Vagenende, V., Han, A. X., Mueller, M., & Trout, B. L. (2012) · ACS Chemical Biology · doi:10.1021/cb300440x · Cited by 77
Bcl-XL-Templated Assembly of Its Own Protein−Protein Interaction Modulator from Fragments Decorated with Thio Acids and Sulfonyl Azides
Hu, X., Sun, J., Wang, H., & Manetsch, R. (2008) · Journal of the American Chemical Society · doi:10.1021/ja802683u · Cited by 76
The IL-10R2 Binding Hot Spot on IL-22 is Located on the N-terminal Helix and is Dependent on N-linked Glycosylation
Logsdon, N. J., Jones, B. C., Allman, J. C., Izotova, L. S., Schwartz, B., Pestka, S., & Walter, M. R. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.069 · Cited by 76
Design of compound libraries for fragment screening
Blomberg, N., Cosgrove, D. A., Kenny, P. W., & Kolmodin, K. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9264-5 · Cited by 77
Heterocyclic α-helix mimetics for targeting protein–protein interactions
Biros, S. M., Moisan, L., Mann, E., Carella, A., Zhai, D., Reed, J. C., & REBEK, J. J. (2007) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2007.05.075 · Cited by 74
Protein docking prediction using predicted protein-protein interface
Li, B., & Kihara, D. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-7 · Cited by 75
Antibody Recognition of Disordered Antigens
MacRaild, C. A., Richards, J. S., Anders, R. F., & Norton, R. S. (2015) · Structure · doi:10.1016/j.str.2015.10.028 · Cited by 75
Fragment-based drug discovery and its application to challenging drug targets
Price, A. J., Howard, S., & Cons, B. D. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170029 · Cited by 79
The Multifunctional Character of a Geminivirus Replication Protein Is Reflected by Its Complex Oligomerization Properties
Orozco, B. M., Kong, L.-J., Batts, L. A., Elledge, S., & Hanley-Bowdoin, L. K. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.9.6114 · Cited by 75
Small Molecule Agents Targeting PD-1 Checkpoint Pathway for Cancer Immunotherapy: Mechanisms of Action and Other Considerations for Their Advanced Development
Sasikumar, P. G., & Ramachandra, M. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.752065 · Cited by 77
Polymer Nanoparticle–Protein Interface. Evaluation of the Contribution of Positively Charged Functional Groups to Protein Affinity
Yonamine, Y., Yoshimatsu, K., Lee, S.-H., Hoshino, Y., Okahata, Y., & Shea, K. J. (2012) · ACS Applied Materials & Interfaces · doi:10.1021/am302404q · Cited by 75
Restricted Mobility of Conserved Residues in Protein-Protein Interfaces in Molecular Simulations
Yogurtcu, O. N., Erdemli, S., Nussinov, R., Türkay, M., & Keskin, Ö. (2008) · Biophysical Journal · doi:10.1529/biophysj.107.114835 · Cited by 74
Mapping Part of the Functional Epitope for Ligand Binding on the Receptor for Urokinase-type Plasminogen Activator by Site-directed Mutagenesis
Gårdsvoll, H., Danø, K., & Ploug, M. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.53.37995 · Cited by 74
Molecular Basis of Ligand Recognition by Integrin α5β1
Humphries, J. D., Askari, J. A., Zhang, X.-P., Takada, Y., Humphries, M. J., & Mould, A. P. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m000568200 · Cited by 74
Oxidative cyclization reagents reveal tryptophan cation–π interactions
Xie, X., Moon, P. J., Crossley, S. W. M., Bischoff, A. J., He, D., Li, G., Dao, N., Gonzalez-Valero, A., Reeves, A. G., McKenna, J. M., et al. (2024) · Nature · doi:10.1038/s41586-024-07140-6 · Cited by 72
Computational Mapping of Anchoring Spots on Protein Surfaces
Ben‐Shimon, A., & Eisenstein, M. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.07.021 · Cited by 73

Authors: Bogan, A. A., & Thorn, K. S.
Affiliations: University of California, San Francisco (US)
Corresponding author: Bogan, Andrew A
ORCID: Thorn, Kurt S
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1998-07
Volume: 280
Issue: 1
Pages: 1-9
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1998.1843
OpenAlex: W2051710717
Cited by: 1,988
References: 71
Citations by year: 2026: 62 · 2025: 52 · 2024: 68 · 2023: 40 · 2022: 51 · 2021: 75 · 2020: 69 · 2019: 65 · 2018: 77 · 2017: 75 · 2016: 94 · 2015: 105 · 2014: 88 · 2013: 110 · 2012: 112
FWCI: 11.85
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords: protein-protein binding, binding hot spots, alanine scanning, binding free energy, protein interfaces, buried surface area, tryptophan, tyrosine, L-arginine, dimer interface, binding energy distribution
MeSH terms: Alanine, Amino Acids, Binding Sites, Humans, Protein Binding, Proteins, Structure-Activity Relationship

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Anatomy of hot spots in protein interfaces

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks