Anatomy of hot spots in protein interfaces

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

Protein and Antibody Engineering by Phage Display

Frei, J. C., & Lai, J. R. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.05.005 · Cited by 59

Structural Basis for Molecular Recognition in an Affibody:Affibody Complex

Lendel, C., Dogan, J., & Härd, T. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.043 · Cited by 59

Solid-Phase Synthesis of an A−B Loop Mimetic of the Cε3 Domain of Human IgE: Macrocyclization by Sonogashira Coupling

Spivey, A. C., McKendrick, J. E., Srikaran, R., & Helm, B. A. (2003) · The Journal of Organic Chemistry · doi:10.1021/jo026693e · Cited by 58

Protein epitope mimetic macrocycles as biopharmaceuticals

Luther, A., Moehle, K., Chevalier, É., Dale, G. E., & Obrecht, D. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.02.004 · Cited by 60

Characterization of Three Druggable Hot-Spots in the Aurora-A/TPX2 Interaction Using Biochemical, Biophysical, and Fragment-Based Approaches

McIntyre, P. J., Collins, P. M., Vrzal, L., Birchall, K., Arnold, L. H., Mpamhanga, C., Coombs, P. J., Burgess, S. G., Richards, M. W., Winter, A., et al. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00537 · Cited by 58

SAR by (Protein-Observed) 19F NMR

Divakaran, A., Kirberger, S. E., & Pomerantz, W. C. K. (2019) · Accounts of Chemical Research · doi:10.1021/acs.accounts.9b00377 · Cited by 58

Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network

Keil, M., Exner, T. E., & Brickmann, J. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.10361 · Cited by 58

Mutational and Energetic Studies of Notch1 Transcription Complexes

Bianco, C. D., Aster, J. C., & Blacklow, S. C. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.11.061 · Cited by 57

Design and synthesis of type-III mimetics of ω-conotoxin GVIA

Baell, J. B., Forsyth, S. A., Gable, R. W., Norton, R. S., & Mulder, R. J. (2001) · Journal of Computer-Aided Molecular Design · doi:10.1023/a:1015930031890 · Cited by 57

Thermodynamics of antibody–antigen interaction revealed by mutation analysis of antibody variable regions

Akiba, H., & Tsumoto, K. (2015) · The Journal of Biochemistry · doi:10.1093/jb/mvv049 · Cited by 57

Identification of hot regions in protein-protein interactions by sequential pattern mining

Hsu, C., Chen, C., Liu, B., Huang, C.-C., Laio, M.-H., Lin, C.-C., & Wu, T.-L. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s5-s8 · Cited by 57

Small Molecule Inhibition of the TNF Family Cytokine CD40 Ligand through a Subunit Fracture Mechanism

Silvian, L. F., Friedman, J. E., Strauch, K., Cachero, T. G., Day, E. S., Qian, F., Cunningham, B. C., Fung, A. D., Sun, L., Su, L., et al. (2011) · ACS Chemical Biology · doi:10.1021/cb2000346 · Cited by 57

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences

Chen, P., Li, J., Wong, L., Kuwahara, H., Huang, J. Z., & Gao, X. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24278 · Cited by 57

Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application

Metz, A., Ciglia, E., & Gohlke, H. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212802651553 · Cited by 59

Efficient Classification of Hot Spots and Hub Protein Interfaces by Recursive Feature Elimination and Gradient Boosting

Lin, X., Zhang, X., & Xu, X. (2019) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2019.2931717 · Cited by 58

The high-affinity interaction of human IL-4 and the receptor α chain is constituted by two independent binding clusters

Zhang, J.-L., Simeonowa, I., Wang, Y., & Sebald, W. (2002) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5243 · Cited by 57

The Carboxyl-Terminal Lobe of Hsc70 ATPase Domain Is Sufficient for Binding to BAG1

Brive, L., Takayama, S.-I. J., Briknarová, K., Homma, S. T., Ishida, S. K., Reed, J. C., & Ely, K. R. (2001) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2001.6087 · Cited by 57

Peptide Aptamers That Bind to a Geminivirus Replication Protein Interfere with Viral Replication in Plant Cells

López-Ochoa, L., Ramírez-Prado, J. H., & Hanley-Bowdoin, L. K. (2006) · Journal of Virology · doi:10.1128/jvi.02698-05 · Cited by 57

Prediction of protein binding sites and hot spots

Fernández‐Recio, J. (2011) · Wiley Interdisciplinary Reviews Computational Molecular Science · doi:10.1002/wcms.45 · Cited by 58

Identification of Sequences in the Polysialyltransferases ST8Sia II and ST8Sia IV That Are Required for the Protein-specific Polysialylation of the Neural Cell Adhesion Molecule, NCAM

Foley, D., Swartzentruber, K. G., & Colley, K. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m809696200 · Cited by 56

The Interaction of Capping Protein with the Barbed End of the Actin Filament

Kim, T., Cooper, J. A., & Sept, D. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.017 · Cited by 56

An Epidemiologically Significant Epitope of a 1998 Human Influenza Virus Neuraminidase Forms a Highly Hydrated Interface in the NA–Antibody Complex

Venkatramani, L., Bochkareva, E. S., Lee, J. T., Gulati, U., Laver, W. G., Bochkarev, A. V., & Air, G. M. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.11.061 · Cited by 56

Determinants of Binding Affinity and Specificity for the Interaction of TEM-1 and SME-1 β-Lactamase with β-Lactamase Inhibitory Protein

Zhang, Z., & Palzkill, T. G. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m308572200 · Cited by 55

Identification of a Surface for Binding to the GDNF-GFRα1 Complex in the First Cadherin-like Domain of RET

Kjær, S., & Ibáñez, C. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m309772200 · Cited by 57

Selective Incorporation of 19 F‐Labeled Trp Side Chains for NMR‐Spectroscopy‐Based Ligand–Protein Interaction Studies

Leone, M., Rodríguez‐Mias, R. A., & Pellecchia, M. (2003) · ChemBioChem · doi:10.1002/cbic.200300597 · Cited by 56

Covalent modification as a strategy to block protein–protein interactions with small-molecule drugs

Way, J. (2000) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(99)00049-6 · Cited by 55

Prediction of Protein–Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets

Xie, Z., Deng, X., & Shu, K. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21020467 · Cited by 55

MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4 + T cells

Logunova, N. N., Kriukova, V., Shelyakin, P. V., Egorov, E. S., Pereverzeva, A. R., Bozhanova, N. G., Shugay, M., Shcherbinin, D. S., Pogorelyy, M. V., Merzlyak, E. M., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2003170117 · Cited by 55

Human Proteome-scale Structural Modeling of E2–E3 Interactions Exploiting Interface Motifs

Kar, G., Keskin, Ö., Nussinov, R., & Gürsoy, A. (2011) · Journal of Proteome Research · doi:10.1021/pr2009143 · Cited by 55

Fragment Screening and Druggability Assessment for the CBP/p300 KIX Domain through Protein‐Observed 19F NMR Spectroscopy

Gee, C. T., Koleski, E. J., & Pomerantz, W. C. K. (2015) · Angewandte Chemie International Edition · doi:10.1002/anie.201411658 · Cited by 56

Conformational ensembles, signal transduction and residue hot spots: application to drug discovery.

Acuner, S. E., Gürsoy, A., Keskin, Ö., & Nussinov, R. (2010) · PubMed · Cited by 55

Thermodynamic characterization of specific interactions between the human Lon protease and G-quartet DNA

Chen, S., Suzuki, C. K., & Wu, S. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1140 · Cited by 53

Reverse MAPPIT: screening for protein-protein interaction modifiers in mammalian cells

Eyckerman, S., Lemmens, I. H., Catteeuw, D., Verhee, A., Vandekerckhove, J. S., Lievens, S., & Tavernier, J. H. (2005) · Nature Methods · doi:10.1038/nmeth760 · Cited by 55

Characterization of the Active Sites in Decay-Accelerating Factor

Kuttner-Kondo, L. A., Mitchell, L. M., Hourcade, D. E., & Medof, M. E. (2001) · The Journal of Immunology · doi:10.4049/jimmunol.167.4.2164 · Cited by 55

Carboxylates Stacked over Aromatic Rings Promote Salt Bridge Formation in Water

Thompson, S., & Smithrud, D. B. (2001) · Journal of the American Chemical Society · doi:10.1021/ja011973h · Cited by 55

The interdigitating loop of the enolase superfamily as a specificity binding determinant or ‘flying buttress’

Bearne, S. L. (2017) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2017.02.006 · Cited by 54

Evolution of oligomeric state through geometric coupling of protein interfaces

Perica, T., Chothia, C., & Teichmann, S. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120028109 · Cited by 54

Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations

Liang, S., Li, L., Hsu, W.-L., Pilcher, M. M., Uversky, V. N., Zhou, Y., Dunker, A. K., & Meroueh, S. O. (2008) · Biochemistry · doi:10.1021/bi8017043 · Cited by 55

Emerging themes in the computational design of novel enzymes and protein–protein interfaces

Khare, S. D., & Fleishman, S. J. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.12.009 · Cited by 54

Solvent Accessible Surface Area-Based Hot-Spot Detection Methods for Protein–Protein and Protein–Nucleic Acid Interfaces

Munteanu, C. R., Pimenta, A. C., Fernandez-Lozano, C., Melo, A., Cordeiro, M. N. D. S., & Moreira, I. S. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500760m · Cited by 54

Structure-Based Design of Small-Molecule Protein–Protein Interaction Modulators: The Story so Far

Falchi, F., Caporuscio, F., & Recanatini, M. (2014) · Future Medicinal Chemistry · doi:10.4155/fmc.13.204 · Cited by 56

Protein function annotation from sequence: prediction of residues interacting with RNA

Spriggs, R. V., Murakami, Y., Nakamura, H., & Jones, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp257 · Cited by 54

Breaking and entering

Clackson, T. (2005) · Nature Chemical Biology · doi:10.1038/nchembio0106-14 · Cited by 55

Chicken avidin-related proteins show altered biotin-binding and physico-chemical properties as compared with avidin

Laitinen, O. H., Hytönen, V. P., Ahlroth, M. K., Pentikäinen, O. T., Gallagher, C. M., Nordlund, H. R., Ovod, V., Marttila, A. T., Porkka, E. J., Heino, S., et al. (2002) · Biochemical Journal · doi:10.1042/0264-6021:3630609 · Cited by 54

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

PIII‐Directed Late‐Stage Ligation and Macrocyclization of Peptides with Olefins by Rhodium Catalysis

Liu, L., Fan, X., Wang, B., Deng, H. X., Wang, T., Zheng, J., Chen, J., Shi, Z., & Wang, H. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202206177 · Cited by 53

A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations

Martin, J., & Frezza, E. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.970109 · Cited by 54

Leveraging machine learning models for peptide–protein interaction prediction

Song, Y., Mi, X., & Shukla, D. (2024) · RSC Chemical Biology · doi:10.1039/d3cb00208j · Cited by 58

GPIHBP1 Missense Mutations Often Cause Multimerization of GPIHBP1 and Thereby Prevent Lipoprotein Lipase Binding

Beigneux, A. P., Fong, L. G., Bensadoun, A., Davies, B. S. J., Oberer, M., Gårdsvoll, H., Ploug, M., & Young, S. G. (2014) · Circulation Research · doi:10.1161/circresaha.116.305085 · Cited by 53

Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design

Álvarez-García, D., & Barril, X. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500182z · Cited by 54

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces

Simões, I. C. M., Costa, I. P. D., Coimbra, J. T. S., Ramos, M. J., & Fernandes, P. A. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00378 · Cited by 52

X-ray structure determination of human profilin II: a comparative structural analysis of human profilins

Nodelman, I. M., Bowman, G. D., Lindberg, U., & Schutt, C. E. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3318 · Cited by 53

Structural Determinants of the Calpain Inhibitory Activity of Calpastatin Peptide B27-WT

Betts, R. L., Weinsheimer, S., Blouse, G. E., & Anagli, J. Y. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m208350200 · Cited by 53

Evolutionary, Physicochemical, and Functional Mechanisms of Protein Homooligomerization

Nishi, H., Hashimoto, K., Madej, T., & Panchenko, A. R. (2013) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-386931-9.00001-5 · Cited by 52

Structural basis for the recognition–evasion arms race between Tomato mosaic virus and the resistance gene Tm-1

Ishibashi, K., Kezuka, Y., Kobayashi, C., Katô, M., Tsuyoshi Inoue, A., Nonaka, T., Ishikawa, M., Matsumura, H., & Katoh, E. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1407888111 · Cited by 52

Structure-based inhibition of protein–protein interactions

Watkins, A. M., & Arora, P. S. (2014) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2014.09.047 · Cited by 56

Calcium-induced tetramerization and zinc chelation shield human calprotectin from degradation by host and bacterial extracellular proteases

Stephan, J. R., & Nolan, E. M. (2015) · Chemical Science · doi:10.1039/c5sc03287c · Cited by 57

Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library

Traxlmayr, M. W., Kiefer, J. D., Srinivas, R. R., Laurent, E., Tisdale, A. W., Mehta, N. K., Yang, N. J., Tidor, B., & Wittrup, K. D. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.741314 · Cited by 52

Functional variation in phyllogen, a phyllody‐inducing phytoplasma effector family, attributable to a single amino acid polymorphism

Iwabuchi, N., Kitazawa, Y., Maejima, K., Koinuma, H., Miyazaki, A., Matsumoto, O., Suzuki, T., Nijo, T., Oshima, K., NAMBA, S., et al. (2020) · Molecular Plant Pathology · doi:10.1111/mpp.12981 · Cited by 52

Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces

Negi, S. S., & Braun, W. A. (2007) · Journal of Molecular Modeling · doi:10.1007/s00894-007-0237-0 · Cited by 52

Dissecting the Protein-Protein Interface between β-Lactamase Inhibitory Protein and Class A β-Lactamases

Zhang, Z., & Palzkill, T. G. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m406157200 · Cited by 51

The impact of protein flexibility on protein–protein docking

Ehrlich, L. P., Nilges, M., & Wade, R. C. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20272 · Cited by 52

Binding Efficiency of Protein–Protein Complexes

Day, E. S., Cote, S. M., & Whitty, A. (2012) · Biochemistry · doi:10.1021/bi301039t · Cited by 51

SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network

Huang, Y., Wuchty, S., Zhou, Y., & Zhang, Z. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad020 · Cited by 51

Structural Biology of Proline Catabolic Enzymes

Tanner, J. J. (2017) · Antioxidants and Redox Signaling · doi:10.1089/ars.2017.7374 · Cited by 51

An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge

Perricone, U., Gulotta, M. R., Lombino, J., Parrino, B., Cascioferro, S., Diana, P., Cirrincione, G., & Padova, A. (2018) · MedChemComm · doi:10.1039/c8md00166a · Cited by 54

Interaction between Collagen and the α2 I-domain of Integrin α2β1

Kamata, T., Liddington, R., & Takada, Y. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.45.32108 · Cited by 51

Clathrin light and heavy chain interface: α‐helix binding superhelix loops via critical tryptophans

Chen, C.-Y., Reese, M. L., Hwang, P. K., Ota, N., Agard, D. A., & Brodsky, F. M. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf594 · Cited by 51

A 13C Labeling Strategy Reveals a Range of Aromatic Side Chain Motion in Calmodulin

Kasinath, V., Valentine, K. G., & Wand, A. J. (2013) · Journal of the American Chemical Society · doi:10.1021/ja4001129 · Cited by 50

Hotspot-Centric De Novo Design of Protein Binders

Fleishman, S. J., Corn, J. E., Strauch, E., Whitehead, T. A., Karanicolas, J., & Baker, D. A. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.09.001 · Cited by 50

Characterization of Protein-Protein Interaction Interfaces from a Single Species

Talavera, D., Robertson, D. L., & Lovell, S. C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021053 · Cited by 51

Receptor–Receptor Interactions in Multiple 5-HT1A Heteroreceptor Complexes in Raphe-Hippocampal 5-HT Transmission and Their Relevance for Depression and Its Treatment

Borroto‐Escuela, D. O., Narváez, M., Ambrogini, P., Ferraro, L., Brito, I., Romero‐Fernandez, W., Andrade‐Talavera, Y., Flores‐Burgess, A., Millón, C., Gago, B., et al. (2018) · Molecules · doi:10.3390/molecules23061341 · Cited by 51

Hydrophobic Surface Enhances Electrostatic Interaction in Water

Sato, T., SASAKI, T., Ohnuki, J., Umezawa, K., & Takano, M. (2018) · Physical Review Letters · doi:10.1103/physrevlett.121.206002 · Cited by 49

Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA

Pooley, J. R., Rivers, C. A., Kilcooley, M., Paul, S. N., Cavga, A. D., Kershaw, Y. M., Muratcioğlu, S., Gürsoy, A., Keskin, Ö., & Lightman, S. L. (2020) · PLoS ONE · doi:10.1371/journal.pone.0227520 · Cited by 53

Protein stabilization by specific binding of guanidinium to a functional arginine‐binding surface on an SH3 domain

Zarrine‐Afsar, A., Mittermaier, A., Kay, L. E., & Davidson, A. R. (2005) · Protein Science · doi:10.1110/ps.051829106 · Cited by 50

The analysis of the human high affinity IgE receptor FcεRIα from multiple crystal forms11Edited by I. A. Wilson

Garman, S. C., Sechi, S., Kinet, J., & Jardetzky, T. S. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4929 · Cited by 50

Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development

Ranaivoson, F. M., Liu, Q., Martini, F., Bergami, F., von Daake, S., Li, S., Lee, D. E., Demeler, B., Hendrickson, W. A., & Comoletti, D. (2015) · Structure · doi:10.1016/j.str.2015.06.022 · Cited by 49

Screening of Protein–Protein Interaction Modulators via Sulfo-Click Kinetic Target-Guided Synthesis

Kulkarni, S. S., Hu, X., Doi, K., Wang, H., & Manetsch, R. (2011) · ACS Chemical Biology · doi:10.1021/cb200085q · Cited by 52

Atomic-Level Mapping of Antibody Epitopes on a GPCR

Paes, C., Ingalls, J., Kampani, K., Sulli, C., Kakkar, E., Murray, M., Kotelnikov, V. M., Greene, T. A., Rucker, J. B., & Doranz, B. J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja900186n · Cited by 49

Solution Structure of the Iron−Sulfur Cluster Cochaperone HscB and Its Binding Surface for the Iron−Sulfur Assembly Scaffold Protein IscU

Füzéry, A. K., Tonelli, M., Ta, D. T., Cornilescu, G., Vickery, L. E., & Markley, J. L. (2008) · Biochemistry · doi:10.1021/bi800502r · Cited by 51

Structural Consequences of Mutations in Interfacial Tyr Residues of a Protein Antigen-Antibody Complex

Shiroishi, M., Tsumoto, K., Tanaka, Y., Yokota, A., Nakanishi, T., Kondo, H., & Kumagai, I. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m605197200 · Cited by 49

Energetics of oligomeric protein folding and association

Doyle, C., Rumfeldt, J., Broom, H. R., Broom, A., Stathopulos, P. B., Vassall, K. A., Almey, J., & Meiering, E. M. (2012) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2012.12.005 · Cited by 50

High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains

Woldring, D., Holec, P. V., Zhou, H., & Hackel, B. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138956 · Cited by 52

In Vivo Delivery of Synthetic Human DNA-Encoded Monoclonal Antibodies Protect against Ebolavirus Infection in a Mouse Model

Patel, A. R., Park, D. H., Davis, C. W., Smith, T. R. F., Leung, A., Tierney, K. J., Bryan, A. L., Davidson, E., Yu, X., Racine, T., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.10.062 · Cited by 49

Antibody specificity and promiscuity

Jain, D., & Salunke, D. M. (2019) · Biochemical Journal · doi:10.1042/bcj20180670 · Cited by 47

THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY‐MASS SPECTROMETRY

McCabe, J. W., Hebert, M. J., Shirzadeh, M., Mallis, C. S., Denton, J. K., Walker, T. E., & Russell, D. H. (2020) · Mass Spectrometry Reviews · doi:10.1002/mas.21642 · Cited by 54

Mapping the Binding Site on Small Ankyrin 1 for Obscurin

Borzok, M. A., Catino, D. H., Nicholson, J. D., Kontrogianni‐Konstantopoulos, A., & Bloch, R. J. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m704089200 · Cited by 49

Generation and analysis of a protein–protein interface data set with similar chemical and spatial patterns of interactions

Mintz, S., Shulman‐Peleg, A., Wolfson, H. J., & Nussinov, R. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20580 · Cited by 49

Structure−Function Relationship of Amino Acid−[2]Rotaxanes

Smukste, I., & Smithrud, D. B. (2003) · The Journal of Organic Chemistry · doi:10.1021/jo026530q · Cited by 49

Adenosine heteroreceptor complexes in the basal ganglia are implicated in Parkinson’s disease and its treatment

Borroto‐Escuela, D. O., & Fuxé, K. (2019) · Journal of Neural Transmission · doi:10.1007/s00702-019-01969-2 · Cited by 50

Structure-based prediction of protein–protein binding affinity with consideration of allosteric effect

Tian, F., Lv, Y., & Li, Y. (2011) · Amino Acids · doi:10.1007/s00726-011-1101-1 · Cited by 50

Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface

Yu, C.-M., Peng, H., Chen, I.-C., Lee, Y., Chen, J.-B., Tsai, K., Chen, C.-T., Chang, J.-Y., Yang, E.-W., Hsu, P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033340 · Cited by 48

Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity

Wichmann, C. W., Becker, Y., Chen-Wichmann, L., Vogel, V., Vojtkova, A., Herglotz, J., Moore, S., Koch, J., Lausen, J., Mäntele, W., et al. (2010) · Blood · doi:10.1182/blood-2009-10-248047 · Cited by 49

Solvent‐accessible surface area: How well can be applied to hot‐spot detection?

Martins, J. M. D. S., Ramos, R. M., Pimenta, A. C., & Moreira, I. S. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24413 · Cited by 48

Protein Hydration Waters Are Susceptible to Unfavorable Perturbations

Rego, N. B., Xi, E., & Patel, A. J. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b11448 · Cited by 50

Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2−CycA Protein Substrate

Sohn, J., Parks, J. M., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A., Edelsbrunner, H., Yang, W., & Rudolph, J. (2005) · Biochemistry · doi:10.1021/bi0516879 · Cited by 48

Dissection of the protein G B1 domain binding site for human IgG Fc fragment

Sloan, D. J., & Hellinga, H. W. (1999) · Protein Science · doi:10.1110/ps.8.8.1643 · Cited by 48

Comprehensive Experimental and Computational Analysis of Binding Energy Hot Spots at the NF-κB Essential Modulator/IKKβ Protein–Protein Interface

Golden, M. S., Cote, S. M., Sayeg, M., Zerbe, B. S., Villar, E. A., Beglov, D., Sazinsky, S. L., Georgiadis, R. M., Vajda, S., Kozakov, D., et al. (2013) · Journal of the American Chemical Society · doi:10.1021/ja400914z · Cited by 47

Alanine-shaving Mutagenesis to Determine Key Interfacial Residues Governing the Assembly of a Nano-cage Maxi-ferritin

Zhang, Y., Raudah, S. H., Teo, H., Teo, G. W. S., Fan, R., Sun, X., & Orner, B. P. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.092445 · Cited by 47

Prescont: Predicting protein‐protein interfaces utilizing four residue properties

Zellner, H., Staudigel, M., Trenner, T., Bittkowski, M., Wolowski, V., Icking, C., & Merkl, R. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23172 · Cited by 47

Empirical estimation of the energetic contribution of individual interface residues in structures of protein–protein complexes

Guharoy, M., & Chakrabarti, P. (2009) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-009-9282-3 · Cited by 21

Hot Spots at the Protein-Protein Interface

Kangueane, P., & Nilofer, C. (2018) · Springer eBooks · doi:10.1007/978-981-10-7347-2_7

Identification of hot spot residues at protein-protein interface

Li, L., Zhao, B. T., Zhanhua, C., Gan, J. G.-K., Sakharkar, M. K., & Kangueane, P. (2006) · Bioinformation · doi:10.6026/97320630001121 · Cited by 40

Hot Spot Occlusion from Bulk Water: a Comprehensive Study of the Complex between the Lysozyme HEL and the Antibody FVD1.3

Moreira, I. S., Fernandes, P. A., & Ramos, M. J. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp067096p · Cited by 34

Analysis and redesign of protein-protein interactions: A hotspot-centric view

Layton, C. J. (2010) · DukeSpace (Duke University)