Predictive docking of protein-protein and protein-DNA complexes

Current Opinion in Structural Biology

Volumn 8, Issue 2, 1998, Pages 250-256

  Sternberg, Michael Je ^a   Gabb, Henry A ^a   Jackson, Richard M ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CONFORMATIONAL TRANSITION; DNA PROTEIN COMPLEX; MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW;

EID: 0032054715     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80047-X     Document Type: Article

References (46)

1. Cherfils J, Janin J. Protein docking algorithms: simulating molecular recognition. Curr Opin Struct Biol. 3:1993;265-269.
2. Janin J. Protein - protein recognition. Prog Biophys Mol Biol. 64:1995;145-166.
3. Shoicnet BK, Kuntz ID. Predicting the structure of protein complexes: a step in the right direction. Chem Biol. 3:1996;151-156.
4. Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struct Biol. 6:1996;402-406.
5. Bamborough P, Cohen FE. Modeling protein - ligand complexes. Curr Opin Struct Biol. 6:1996;236-241.
6. Shoichet BK, Kuntz ID. Protein docking and complementarity. J Mol Biol. 221:1991;327-346.
7. Janin J. Principles of protein - protein recognition from structure to thermodynamics. Biochimie. 77:1995;497-505.
8. Janin J. Elusive affinities. Proteins. 21:1997;30-39.
9. Strynadka NCJ, Eisenstein M, Katchalski-Katzir E, Shoichet B, Kuntz I, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, et al. Molecular docking programs sucessfully determine the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. of outstanding interest Nat Struct Biol. 3:1996;233-238 The report of the first blind trial of protein docking (the Alberta challenge). The results showed that for an enzyme - inhibitor complex, predictive docking can identify solutions close to the native state, even though local structural changes were poorly predicted.
10. Dixon JS. Evaluation of the CASP2 docking section. of outstanding interest Proteins Suppl. 1997;198-204 The report of the second blind trial of docking (CASP2). The study highlights the problem of tackling a large complex without a determined binding site. Nevertheless there were entries that reproduced some of the stereochemical features of the complex.
11. Horton N, Lewis M. Calculation of the free energy of association for protein complexes. Protein Sci. 1:1992;169-181.
12. Cherfils J, Duquerroy S, Janin J. Protein - protein recognition analyzed by docking simulation. Proteins. 11:1991;271-280.
13. Cherfils J, Bizebard T, Knossow M, Janin J. Rigid-body docking with mutant constraints of influenza hemagglutin in with antibody HC19. Proteins. 18:1994;8-18.
14. Duncan BS, Olson AJ. Shape analysis of molecular surfaces. Biopolymers. 33:1993;231-238.
15. Webster DM, Rees AR. Macromolecular recognition: antibody - antigen complexes. Protein Eng. 1993;65-94.
16. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA. 89:1992;2195-2199.
17. Vakser IA, Aflalo C. Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins. 20:1994;320-329.
18. Vakser IA. Protein docking for low-resolution structures. Protein Eng. 8:1995;371-377.
19. Vakser IA. Long-distance potentials: an approach to the multiple-minima problem in ligand - receptor interaction. of outstanding interest Protein Eng. 9:1996;37-41 The author describes the application of Fourier correlation using a simplified potential function to smooth the energy profile. The method uses uniform long distance atom - atom potentials modelled using a step function. This method was used in the CASP2 docking competition.
20. Gabb HA, Jackson RM, Sternberg MJE. Modelling protein docking using shape complementarity, electrostatics and biochemical information. of outstanding interest J Mol Biol. 272:1997;106-120 The application of a Fourier correlation including an additional electrostatic component is presented. The method has been applied to available unbound protein - protein complexes including enzyme - inhibitor and antibody - antigen systems, in an attempt to develop a predictive docking algorithm. This method was used in the CASP2 docking competition.
21. Meyer M, Wilson P, Schomburg D. Hydrogen bonding and molecular surface shape complementaririty as a basis for protein docking. J Mol Biol. 264:1996;199-210.
22. Fischer D, Lin SL, Wolfson HJ, Nussinov R. A suite of molecular docking processes. J Mol Biol. 248:1995;459-477.
23. Norel R, Lin SL, Wolfson HL, Nussinov R. Molecular surface complementarity at protein - protein interfaces: the critical role played by surface normals at well placed sparse points in docking. J Mol Biol. 252:1995;263-273.
24. Wallqvist A, Covell DG. Docking enzyme - inhibitor complexes using a preference-based free-energy surface. Proteins. 25:1996;403-419.
25. Wallqvist A, Jernigan RL, Cowell DG. A preference-based free-energy parameterization of enzyme-inhibitor binding. Application to HIV-1 protease inhibitor design. Protein Sci. 4:1995;1881-1903.
26. Ausiello G, Cesareni G, Helmer-Citterich M. ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. of special interest Proteins. 28:1997;556-567 A new docking program that has been benchmarked on some unbound protein - protein complexes.
27. Jackson RM, Sternberg MJE. A continuum model for protein - protein interactions: application to the docking problem. J Mol Biol. 250:1995;258-275.
28. Hart TN, Read RJ. A multiple-start Monte Carlo docking method. Proteins. 13:1992;206-222.
29. Stoddard BL, Koshland DE. Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli. Proc Natl Acad Sci USA. 90:1993;1146-1153.
30. Goodsell DS, Olson AJ. Automated docking of substrates to proteins by simulated annealing. Proteins. 8:1990;195-202.
31. Cummings M, Hart T, Read R. Atomic solvation parameters in the analysis of protein - protein docking results. Protein Sci. 4:1995;2087-2099.
32. Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
33. Weng Z, Vajda S, DeLisi C. Prediction of protein complexes using empirical free energy functions. of outstanding interest Protein Sci. 5:1996;614-626 An approach for the screening and refinement of docked complexes using a comprehensive treatment of energy components and sidechain refinement. Applied in the CASP2 competition.
34. Totrov M, Abagyan R. Detailed ab initio prediction of lysozyme - antibody complex with 1.6 Å accuracy. Nat Struct Biol. 1:1994;259-263.
35. Jackson RM, Gabb HA, Sternberg MJE. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. of outstanding interest J Mol Biol. 276:1997;265-285 A method for the refinement of sidechain conformations and relative positions of the subunits is described. The method was developed for the screening of a large data set of putative docked complexes and was tested on the five enzyme - inhibitor and four antibody - lysozyme data sets generated by Gabb et al. [20], and used in the CASP2 docking competition.
36. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. of special interest J Mol Biol. 257:1996;342-358 A method of predicting binding or functional sites from aligned sequences mapped onto a protein structure is presented.
37. Pazos F, Helmercitterich M, Ausiello G, Valencia A. Correlated mutations contain information about protein - protein interactions. of special interest J Mol Biol. 271:1997;511-523 The authors present a method of predicting modes of docking from aligned sequences mapped onto the structures of two proteins.
38. Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein - protein recognition. Protein Sci. 3:1994;717-729.
39. McCoy AJ, Epa VC, Colman PM. Electrostatic complementarity at protein/protein interaces. J Mol Biol. 268:1997;570-584.
40. Laskowski RA, Luscombe NM, Swindells MB, Thornton JM. Protein clefts in molecular recognition and function. of special interest Protein Sci. 5:1996;2438-2452 An approach to predicting binding sites from coordinates only is described. The active site of an enzyme can usually be predicted using purely geometric criteria, as it is likely to be the largest cleft on the protein. Such knowledge would be useful where restricted search methods are being used.
41. Jones S, Thornton JM. Analysis of protein - protein interaction sites using surface patches. of special interest J Mol Biol. 272:1997;121-132 A study of the stereochemical and physiochemical features of surface patches that mediate protein docking.
42. Jones S, Thornton JM. Prediction of protein - protein interaction sites using patch analysis. of special interest J Mol Biol. 272:1997;133-143 An algorithm to predict potential sites for protein docking exploiting the analysis in [41].
43. Vakser IA. Evaluation of GRAMm low-resolution docking methodology on the hemagglutinin - antibody complex. of outstanding interest Proteins Suppl. 1997;226-230 A description of the low resolution Fourier correlation approach using long distance potentials to overcome the multiple-minima problem as applied in the CASP2 docking challenge. The method obtained the lowest average rmsd.
44. Knegtel RMA, Boelens R, Kaptein R. Monte Carlo docking of protein - DNA complexes: incorporation of DNA flexibility and experimental data. Protein Eng. 7:1994;761-767.
45. Knegtel RMA, Antoon J, Rullmann C, Boelens R, Kaptein R. MONTY: a Monte Carlo approach to protein - DNA recognition. J Mol Biol. 235:1994;318-324.
46. Database for covalent binding on World Wide Web URL: http://dbncb.sdsc.edu.