SiteLight: Binding-site prediction using phage display libraries
Article first published online: 1 JAN 2009
Copyright © 2003 The Protein Society
Volume 12, Issue 7, pages 1344–1359, July 2003
How to Cite
Halperin, I., Wolfson, H. and Nussinov, R. (2003), SiteLight: Binding-site prediction using phage display libraries. Protein Science, 12: 1344–1359. doi: 10.1110/ps.0237103
- Issue published online: 1 JAN 2009
- Article first published online: 1 JAN 2009
- Manuscript Accepted: 17 APR 2003
- Manuscript Revised: 3 APR 2003
- Manuscript Received: 18 OCT 2002
- 1995. Characterization of phage that bind plastic from phage-displayed random peptide libraries. Gene 156: 27–31. , , , and
- 2001. Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol. 311: 395–408. , , , and
- 2001. ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogentic information. J. Mol. Biol. 307: 447–463. , , and
- 2000. The protein data bank. Nucleic Acids Res. 28: 235–242. , , , , , , , and
- 1999. Simple method for locating possible ligand binding sites on protein surfaces. J. Comp. Chem. 20: 983–988. and
- 2001. Predicting protein–protein interactions from primary structure. Bioinformatics 17: 455–460. and
- 1998. Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280: 1–9. and
- 1983a. Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709–713.
- 1983b. Analytical molecular surface calculation. J. Appl. Crystallogr. 16: 548–558.
- 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Biochem. Sci. 23: 324–328. , , , and
- 1999. Multiple alignment and sorting of peptides derived from phage-displayed random peptide libraries with polyclonal sera allows discrimination of relevant phagotopes. Mol. Immunol. 36: 659–667. , , , , , and
- 2002. Unraveling hot spots in binding interfaces: Progress and challenges. Curr. Opin. Struct. Biol. 12: 14–20.
- 2000. Convergent solutions to binding at a protein–protein interface. Science 287: 1279–1283. , , , and
- 1986. Docking flexible ligands to macromolecular receptors by molecular shape. J. Med. Chem. 29: 2149–2153. , , , , and
- 2001. The rational design of a ‘type 88’ genetically stable peptide display rector in the filamentous bacteriophage fd. Nucleic Acids Res. 29: E50, 1–13. , , and
- 2002. Prediction of protein–protein sites in heterocomplexes with neural networks. Eur. J. Biochem. 269: 1356–1361. , , , and
- 1999. Peptide ligands to human immunodeficiency virus type 1 gp120 identified from phage display libraries. J. Virol. 73: 5795–5802. and
- 1999. The propagation of binding interactions to remote sites in proteins: Analysis of the binding of the monoclonal antibody D1.3 to lysozyme. Proc. Natl. Acad. Sci. 96: 10118–10122.
- 1996. The automatic search for ligand binding sites in proteins of known three dimentional structure using onlygeometric criteria. J. Mol. Biol. 256: 201–213. , , and
- 1997. Modeling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 272: 106–120. , , and
- 1986. A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol. Immunol. 23: 709–715. , , and
- 1987. Calculation of electrostatic potentials in an enzyme active site. Nature 330: 84–86. and
- 2000. Co-evolution of proteins with their interaction partners. J. Mol. Biol. 299: 283–293. , , , , and
- 2002. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 47: 409–443. , , , and
- 1997. In vitro selection and evolution of functional proteins using ribosome display. Proc. Natl. Acad Sci. 94: 4937–4942. and
- 1997. Model-free methods of analyzing domain motions in proteins from simulations of lysozyme. Proteins 27: 425–437. , , and
- 1989. Graph algorithms. Computer Science Press, Technion—Israel Institue of Technology, Haifa, Israel.
- 2000. Conservation of polar residues as hot spots at protein–protein interfaces. Proteins 39: 331–342. , , , and
- 2001. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 44: 336–343. and
- 2001. Catalytic and binding poly-reactivities shared by two unrelated proteins: The potential role of promiscuity in enzyme evolution. Protein Sci. 10: 2600–2607. and
- 1999. Actin surface structure revealed by antibody imprints: Evaluation of phage-display analysis of anti-actin antibodies. Protein Sci. 8: 760–770. , , , , , and
- 1996. Phage display of peptides and proteins. Academic Press, New York. , , and
- 1995. A hypothetical structural role for proline residues in the flanking segments of protein–protein interaction sites. Biochem. Biophys. Res. Commun. 212: 1115–1124. and
- 2000. Analysis of antibody A6 binding to the extracellular interferon γ receptor α chain by alanine-scanning mutagenesis and random mutagenesis with phage display. Biochemistry 39: 15674–15685. , , , , , and
- 1995. SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph. 13: 323–330.
- 1996. Protein clefts in molecular recognition and function. Protein Sci. 5: 2438–2452. , , , and
- 2001. Phage randomization in a charybdotoxin scaffold leads to CD4-mimetic recognition motifs that bind HIV-1 envelope through non-aromatic sequences. J. Peptide Res. 57: 507–518. Direct Link:, , , and
- 1996a. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257: 342–358. , , and
- 1996b. Evolutionarily conserved Gαβγ binding surfaces support a model of the G protein-receptor complex. Proc. Natl. Acad. Sci. 93: 7505–7511. , , and
- 1997. Identification of functional surfaces of the binding domains of intracellular receptors. J. Mol. Biol. 274: 325–337. , , and
- 1994. Molecular surface representation by sparse critical points. Proteins 18: 94–101. , , , and
- 2000. Structural stability of binding sites: Consequences for binding affinity and allosteric effects. Proteins Suppl. 4: 63–71. and
- 2002. Multiple ligands binding at a single site: A matter of pre-existing conformations. Protein Sci. 11: 184–197. , , , and
- 1999. Detecting protein function and protein–protein interactions from genome sequences. Science 285: 751–753. , , , , , and
- 1972. Repeating sequences and gene duplication in proteins. J. Mol. Biol. 64: 417–437.
- 1997. Correlated mutations contain information about protein–protein interaction. J. Mol. Biol. 271: 511–523. , , , and
- 1999. Protein surface roughness and small molecular binding sites. J. Mol. Biol. 285: 1377–1382. and
- 2000. Alignment of flexible protein structures. In Proceedings of the 8th conference on intelligent systems in molecular biology (ISMB) (eds. R.Altman et al.), pp. 329–343. AAAI Press, Menlo Park, CA. , , , and
- 2002. Flexible protein alignment and hinge-bending detection. Proteins 48: 242–256. , , and
- 2003. Exploring protein–protein interactions with phage display. Chem. BioChem. 14: 14–25. , , and
- 2001. Structure of a Bag/Hsc70 complex: Convergent functional evolution of Hsp70 nucleotide exchange factors. Science 291: 1553–1557. , , , , , and
- 2001. Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nat. Struct. Biol. 8: 234–237. , , , , and
- 1995. Hsc70-binding peptides selected from a phage display peptide library that resemble organellar targeting sequences. J. Biol. Chem. 270: 19839–19844. , , , , and
- 1999. The effect of inhibitor binding on the structural stability and cooperativity of the HIV protease. Proteins 36: 147–156. and
- 1998. The structural stability of the HIV-1 protease. J. Mol. Biol. 283: 475–488. , , and
- 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321–324. , , , , , , , , , , et al.
- 1997. Studies of protein–protein interfaces: A statistical analysis of the hydrophobic effect. Protein Sci. 6: 53–64. , , , and
- 2001. Conservation helps to identify biological relevant crystal contacts. J. Mol. Biol. 313: 399–416. and
- 2002. ASPD (Artificially Selected Proteins/Peptides Database): A database of proteins and peptides evolved in vitro. Nucleic Acids Res. 30: 200–202. , , , , and
- 2000. Peptide display on bacterial flagella: Principles and applications. Int. J. Med. Microbiol. 290: 223–230.
- 1999. Randomization of the receptor α chain recruitment epitope reveals a functional interleukin-5 with charge depletion in the CD loop. J. Biol. Chem. 274: 20479–20488. , , , , , , , and
- 2000. Epitope randomization redefines the functional role of glutamic acid 110 in interleukin-5 receptor activation. J. Biol. Chem. 275: 7351–7358. , , , , , and
- 2000. A fast method to predict protein interaction sites from sequences. J. Mol. Biol. 302: 917–926. , , , and