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

Principles of protein–protein recognition

Chothia, C., & Janin, J. (1975) · Nature · doi:10.1038/256705a0 · Cited by 1,049

Surface, subunit interfaces and interior of oligomeric proteins

Janin, J., Miller, S. M., & Chothia, C. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90606-7 · Cited by 653

A fast algorithm for rendering space-filling molecule pictures

Bacon, D., & Anderson, W. (1988) · Journal of Molecular Graphics · doi:10.1016/s0263-7855(98)80030-1 · Cited by 617

Functional Mimicry of a Protein Hormone by a Peptide Agonist: The EPO Receptor Complex at 2.8 Å

Livnah, O., Stura, E. A., Johnson, D. L., Middleton, S. A., Mulcahy, L. S., Wrighton, N. C., Dower, W. J., Jolliffe, L. K., & Wilson, I. A. (1996) · Science · doi:10.1126/science.273.5274.464 · Cited by 588

Energetics of protein-protein interactions: Analysis ofthe Barnase-Barstar interface by single mutations and double mutant cycles

Schreiber, G., & Fersht, A. R. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(95)80064-6 · Cited by 569

Comparison of a Structural and a Functional Epitope

Cunningham, B. C., & Wells, J. A. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1611 · Cited by 510

Vascular endothelial growth factor: Crystal structure and functional mapping of the kinase domain receptor binding site

Muller, Y. A., Li, B., Christinger, H. W., Wells, J. A., Cunningham, B. C., & de Vos, A. M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.14.7192 · Cited by 467

Studies of protein‐protein interfaces: A statistical analysis of the hydrophobic effect

Tsai, C., Lin, S. L., Wolfson, H. J., & Nussinov, R. (1997) · Protein Science · doi:10.1002/pro.5560060106 · Cited by 428

Peptide Agonist of the Thrombopoietin Receptor as Potent as the Natural Cytokine

Cwirla, S. E., Palaniappan, B., Duffin, D. J., Wagstrom, C. R., Gates, C. M., Singer, S. C., Davis, A. M., Tansik, R. L., Mattheakis, L. C., Boytos, C. M., et al. (1997) · Science · doi:10.1126/science.276.5319.1696 · Cited by 404

The X-ray structure of a growth hormone–prolactin receptor complex

Somers, W. S., Ultsch, M. H., de Vos, A. M., & Kossiakoff, A. A. (1994) · Nature · doi:10.1038/372478a0 · Cited by 393

Scanning mutagenesis of interleukin-8 identifies a cluster of residues required for receptor binding.

Hébert, C. A., Vitangcol, R. V., & Baker, J. B. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)55160-7 · Cited by 369

On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5

Novotný, J., Bruccoleri, R. E., & Saul, F. A. (1989) · Biochemistry · doi:10.1021/bi00437a034 · Cited by 367

[18] Systematic mutational analyses of protein-protein interfaces

Wells, J. A. (1991) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(91)02020-a · Cited by 345

Calculation of the free energy of association for protein complexes

Horton, N. C., & Lewis, M. (1992) · Protein Science · doi:10.1002/pro.5560010117 · Cited by 329

Design, synthesis, and application of a Protein A mimetic

Li, R., Dowd, V., Stewart, D. J., Burton, S. J., & Lowe, C. R. (1998) · Nature Biotechnology · doi:10.1038/nbt0298-190 · Cited by 297

A systematic mutational analysis of hormone-binding determinants in the human growth hormone receptor.

Bass, S., Mulkerrin, M. G., & Wells, J. A. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.10.4498 · Cited by 285

Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering

Schreiber, G., & Fersht, A. R. (1993) · Biochemistry · doi:10.1021/bi00070a025 · Cited by 284

Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity

Clackson, T., Ultsch, M. H., Wells, J. A., & de Vos, A. M. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1669 · Cited by 277

Electrostatic complementarity at protein/protein interfaces 1 1Edited by B. Honig

McCoy, A. J., Epa, V. C., & Colman, P. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0987 · Cited by 256

Theoretical studies of protein folding and unfolding

Karplus, M., & Šali, A. (1995) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(95)80010-x · Cited by 255

On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands

PADLAN, E. A. (1990) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340070203 · Cited by 233

Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation

Lee, K. H., Xie, D., Freire, E., & Amzel, L. M. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340200108 · Cited by 219

Antiviral and resistance studies of AG1343, an orally bioavailable inhibitor of human immunodeficiency virus protease

Patick, A. K., Mo, H., Markowitz, M. H., Appelt, K., Wu, B.-W., Musick, L., Kalish, V. J., Kaldor, S. W., Reich, S., Ho, D. D., et al. (1996) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.40.2.292 · Cited by 210

Rational design of receptor-specific variants of human growth hormone.

Cunningham, B. C., & Wells, J. A. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.8.3407 · Cited by 208

High resolution functional analysis of antibody-antigen interactions

Jin, L., FENDLY, B. M., & Wells, J. A. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90636-x · Cited by 207

Molecular recognition of human angiogenin by placental ribonuclease inhibitor—an X‐ray crystallographic study at 2.0 Å resolution

Papageorgiou, A. C., Shapiro, R., & Acharya, K. R. (1997) · The EMBO Journal · doi:10.1093/emboj/16.17.5162 · Cited by 193

Site-directed mutagenesis of histidine-13 and histidine-114 of human angiogenin. Alanine derivatives inhibit angiogenin-induced angiogenesis

Shapiro, R., & Vallée, B. L. (1989) · Biochemistry · doi:10.1021/bi00444a038 · Cited by 193

Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors

Hilpert, K., Ackermann, J., Banner, D. W., Gast, A., Gubernator, K., Hadváry, P., Labler, L., Müller, K., Schmid, G., Tschopp, T. B., et al. (1994) · Journal of Medicinal Chemistry · doi:10.1021/jm00049a008 · Cited by 189

Structural Plasticity in a Remodeled Protein-Protein Interface

Atwell, S., Ultsch, M. H., de Vos, A. M., & Wells, J. A. (1997) · Science · doi:10.1126/science.278.5340.1125 · Cited by 180

Mapping the CD4 binding site for human immunodeficiency virus by alanine-scanning mutagenesis.

Ashkenazi, A., Presta, L. G., Marsters, S. A., Camerato, T. R., Rosenthal, K., FENDLY, B. M., & Capon, D. J. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.18.7150 · Cited by 173

Identification of surface residues mediating tissue factor binding and catalytic function of the serine protease factor VIIa

Dickinson, C. D., Kelly, C. R., & Ruf, W. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.25.14379 · Cited by 169

Thermodynamic analysis of an antibody functional epitope

Kelley, R. F., & O'Connell, M. P. (1993) · Biochemistry · doi:10.1021/bi00078a005 · Cited by 168

Practical Application of Computer-Aided Drug Design

Charifson, P. S. (1997) · Marcel Dekker eBooks · Cited by 163

Mutational analysis of the interaction between staphylococcal protein A and human IgG1

Cedergren, L., Andersson, R., Jansson, B., Uhlén, M., & Nilsson, B. (1993) · Protein Engineering Design and Selection · doi:10.1093/protein/6.4.441 · Cited by 159

Elusive affinities

Janin, J. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340210105 · Cited by 146

Identification and concerted function of two receptor binding surfaces on basic fibroblast growth factor required for mitogenesis.

Springer, B. A., Pantoliano, M. W., Barbera, F. A., Gunyuzlu, P. L., Thompson, L. D., Herblin, W. F., Rosenfeld, S. A., & Book, G. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)47101-3 · Cited by 141

A Mutational Analysis of the Binding of Two Different Proteins to the Same Antibody

Dall’Acqua, W. F., Goldman, E. R., Eisenstein, E., & Mariuzza, R. A. (1996) · Biochemistry · doi:10.1021/bi960819i · Cited by 130

Identification of a Small Molecule Inhibitor of the IL-2/IL-2Rα Receptor Interaction Which Binds to IL-2

Tilley, J., Chen, L., Fry, D. C., Emerson, S. D., Powers, G. D., Biondi, D. A., Varnell, T. A., Trilles, R. V., Guthrie, R. W., Mennona, F. A., et al. (1997) · Journal of the American Chemical Society · doi:10.1021/ja970702x · Cited by 129

The Contribution of Contact and Non-contact Residues of Antibody in the Affinity of Binding to Antigen

Hawkins, R. E., Russell, S. J., Baier, M., & Winter, G. P. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1650 · Cited by 128

Alanine Point-Mutations in the Reactive Region of Bovine Pancreatic Trypsin Inhibitor: Effects on the Kinetics and Thermodynamics of Binding to β-Trypsin and α-Chymotrypsin

Castro, M. J. M., & Anderson, S. (1996) · Biochemistry · doi:10.1021/bi960515w · Cited by 114

Localization in human interleukin 2 of the binding site to the alpha chain (p55) of the interleukin 2 receptor.

Sauvé, K., Nachman-Clewner, M., Spence, C. L., Bailon, P., Campbell, E., Tsien, W. H., Kondas, J. A., Hakimi, J., & Ju, G. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.11.4636 · Cited by 100

Affinity and Specificity of Serine Endopeptidase-Protein Inhibitor Interactions

Krystek, S. R., Stouch, T. R., & Novotný, J. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1619 · Cited by 98

A mixed-charge pair in human interleukin 4 dominates high-affinity interaction with the receptor α chain

Wang, Y., Shen, B., & Sebald, W. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.5.1657 · Cited by 95

Analysis of the Factor VIIa Binding Site on Human Tissue Factor: Effects of Tissue Factor Mutations on the Kinetics and Thermodynamics of Binding

Kelley, R. F., Costas, K. E., O'Connell, M. P., & Lazarus, R. A. (1995) · Biochemistry · doi:10.1021/bi00033a009 · Cited by 80

Dissecting the energetics of an antibody‐antigen interface by alanine shaving and molecular grafting

Jin, L., & Wells, J. A. (1994) · Protein Science · doi:10.1002/pro.5560031219 · Cited by 79

Identification of functional arginines in human angiogenin by site-directed mutagenesis

Shapiro, R., & Vallée, B. L. (1992) · Biochemistry · doi:10.1021/bi00164a026 · Cited by 71

Role of Tyr Residues in the Contact Region of Anti-lysozyme Monoclonal Antibody HyHEL10 for Antigen Binding

Tsumoto, K., Ogasahara, K., Ueda, Y., Watanabe, K., Yutani, K., & Kumagai, I. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.31.18551 · Cited by 70

Mutational Mapping of Functional Residues in Tissue Factor: Identification of Factor VII Recognition Determinants in Both Structural Modules of the Predicted Cytokine Receptor Homology Domain

Ruf, W., Schullek, J. R., Stone, M. J., & Edgington, T. S. (1994) · Biochemistry · doi:10.1021/bi00172a037 · Cited by 69

Analysis of Binding Interactions in an Idiotope−Antiidiotope Protein−Protein Complex by Double Mutant Cycles

Goldman, E. R., Dall’Acqua, W. F., Braden, B. C., & Mariuzza, R. A. (1997) · Biochemistry · doi:10.1021/bi961769k · Cited by 67

Use of X-Ray Crystallography in the Design of Antiviral Agents

(1990) · Elsevier eBooks · doi:10.1016/b978-0-12-438745-4.x5001-0 · Cited by 58

High-resolution mapping of the HyHEL-10 epitope of chicken lysozyme by site-directed mutagenesis.

Kam-Morgan, L. N. W., Smith‐Gill, S. J., Taylor, M. G., Zhang, L., Wilson, A. C., & Kirsch, J. F. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.9.3958 · Cited by 54

Identification of Residues Critical to the Activity of Human Granulocyte Colony-Stimulating Factor

Reidhaar-Olson, J. F., Souza-Hart, J. A. D., & Selick, H. E. (1996) · Biochemistry · doi:10.1021/bi952705x · Cited by 45

Site-specific mutagenesis reveals differences in the structural bases for tight binding of RNase inhibitor to angiogenin and RNase A

Chen, C., & Shapiro, R. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.5.1761 · Cited by 44

Characterization of the receptor binding determinants of granulocyte colony stimulating factor

Young, D. C., Cheng, Q., Hou, J., Matthews, D. J., & Zhan, H. (1997) · Protein Science · doi:10.1002/pro.5560060611 · Cited by 41

Energetic Contributions and Topographical Organization of Ligand Binding Residues of Tissue Factor

Ruf, W., Kelly, C. R., Schullek, J. R., Martin, D. M. A., Polikarpov, I., Boys, C., Tuddenham, E. G. D., & Edgington, T. S. (1995) · Biochemistry · doi:10.1021/bi00019a008 · Cited by 36

Identification of the Factor VIIa Binding Site on Tissue Factor by Homologous Loop Swap and Alanine Scanning Mutagenesis

Gibbs, C. S., McCurdy, S. N., Leung, L. L. K., & Paborsky, L. R. (1994) · Biochemistry · doi:10.1021/bi00251a007 · Cited by 34

Glu-96 of Basic Fibroblast Growth Factor Is Essential for High Affinity Receptor Binding

Zhu, H., Ramnarayan, K., Anchin, J. M., Miao, W. Y., Sereno, A., Millman, L., Zheng, J., Balaji, V., & Wolff, M. E. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.37.21869 · Cited by 27

Knowledge-based modeling of a bacterial dichloromethane dehalogenase

and, A. M., & Ferguson, D. M. (1997) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(199706)28:2 · Cited by 27

Analysis of Antibody-Protein Interactions Utilizing Site-Directed Mutagenesis and a New Evolutionary Variant of Lysozyme

Lavoie, T., Kam-Morgan, L. N. W., Mallett, C. P., Schilling, J. W., Prager, E. M., Wilson, A. C., & Smith‐Gill, S. J. (1990) · Elsevier eBooks · doi:10.1016/b978-0-12-438745-4.50022-7 · Cited by 13

Water as an active constituent in cell biology

Ball, P. (2008) · Chemical Reviews · doi:10.1021/cr068037a · Cited by 2,177

The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht

Conte, L. L., Chothia, C., & Janin, J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2439 · Cited by 1,967

Small-molecule inhibitors of protein–protein interactions: progressing towards the dream

Arkin, M. R., & Wells, J. A. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1343 · Cited by 1,705

Principles of docking: An overview of search algorithms and a guide to scoring functions

Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294

Insights into Protein–Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras–Raf and Ras–RalGDS Complexes

Gohlke, H., Kiel, C., & Case, D. A. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00610-7 · Cited by 1,205

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)