Predicting surface properties of proteins on the Connolly molecular surface

Smart Materials and Structures

Volumn 11, Issue 5, 2002, Pages 772-777

  Cao, Jinan ^a   Pham, D K ^a   Tonge, L ^a   Nicolau, D V ^a  

^a SWINBURNE UNIVERSITY OF TECHNOLOGY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ELECTRONS; HYDROPHOBICITY; INTELLIGENT MATERIALS; POLYMERS; SURFACE PHENOMENA; SURFACE PROPERTIES;

MOLECULAR SURFACES;

PROTEINS;

EID: 0036803709     PISSN: 09641726     EISSN: None     Source Type: Journal    
DOI: 10.1088/0964-1726/11/5/323     Document Type: Article

References (42)

1. Norel R., Petry D., Wolfson H.J. and Nussinov R. 1999 Examination of shape complementarity in docking of unbound proteins Proteins: Struct., Funct., Genet. 36 307.
2. Kuntz I., Blaney J., Oatley S., Langridge R. and Ferrin T. 1982 A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 161 260.
3. 1 subunit interface Biopolymers 25 1229.
4. Norel R., Fischer D., Wolfson H.J. and Nussinov R. 1994 Molecular surface recognition by a computer vision-based technique Protein Eng. 7 39.
5. Norel R., Wolfson H.J. and Nussinov R. 1999 Small molecule recognition: solid angles surface representation and molecular shape complementarity Comb. Chem. High Throughput Screening 2 223.
6. Norel R., Lin S.L., Wolfson H. and Nussinov R. 1995 Shape complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse points in docking J. Mol. Biol. 252 263.
7. Jiang F. and Kim S. 1991 Soft docking: matching of molecular surface cubes J. Mol. Biol. 219 79.
8. Shoichet B. and Kuntz I. 1991 Protein docking and complementarity J. Mol. Biol. 219 327.
9. Bliznyuk A.A. and Gready J.E. 1999 Simple method for locating possible ligand binding sites on protein surface J. Comput. Chem. 20 983.
10. Gardiner E.J., Willett P. and Artymiuk P.J. 2001 Protein docking using a genetic algorithm Proteins: Struct. Funct. Genet. 44 44.
11. Majeux N., Scarsi M., Apostolakis J., Ehrhardt C. and Caflisch A. 1999 Exhaustive docking of molecular fragments with electrostatic solvation Proteins: Struct. Funct. Genet. 37 88.
12. Majeux N., Scarsi M. and Caflisch A. 2001 Efficient electrostatic solvation model for protein-fragment docking Proteins: Struct. Funct. Genet. 42 256.
13. Mitchell A.S. and Spackman M.A. 2000 Molecular surfaces from the promolecule: a comparison with Hartree-Fock ab initio electron density surfaces J. Comput. Chem. 11 933.
14. Novotny J., Bruccoleri R.E., Davis M. and Sharp K.A. 1997 Empirical free energy calculations: a blind test and further improvements to the method J. Mol. Biol. 268 401.
15. Camacho C.J., Weng Z., Vajda S. and DeLisi C. 1999 Free energy landscapes of encounter complexes in protein-protein association Biophys. J. 76 1166.
16. Connolly M.L. 1983 Solvent-accessible surfaces of proteins and nucleic acids Science 221 709.
17. Connolly M.L. 1983 Analytical molecular surface calculation J. Appl. Crystallogr. 16 548.
18. Connolly M.L. 1986 Measurement of protein surface shape by solid angles J. Mol. Graph. 4 3.
19. Via A., Ferre F., Brannetti B. and Helmer-Citterich M. 2000 Protein surface similarities: a survey of methods to describe and compare protein surfaces Cell. Mol. Life Sci. 57 1970.
20. Duncan B.S. and Olson A.J. 1993 Approximation and characterization of molecular surfaces Biopolymers 33 219.
21. Duncan B.S. and Olson A.J. 1993 Shape analysis of molecular surfaces Biopolymers 33 231.
22. Lin S.L., Nussinov R., Fischer D. and Wolfson H.J. 1994 Molecular surface representations by sparse critical points Proteins: Struct. Funct. Genet. 18 94.
23. Zauhar R.J. 1995 SMART - A solvent-accessible triangulated surface generator for molecular graphics and boundary element applications J. Comput. Aided Mol. Des. 9 149.
24. Bliznyuk A.A. and Gready J.E. 1996 Numerical calculation of molecular surface area: I. Assessment of errors J. Comput. Chem. 8 962.
25. Bliznyuk A.A. and Gready J.E. 1996 Numerical calculation of molecular surface area: II. Speed of calculation J. Comput. Chem. 8 970.
26. Bliznyuk A.A. and Rendell A.P. 1999 Faster gradients for semiempirical methods J. Comput. Chem. 6 629.
27. Totrov M. 1996 The contour-buildup algorithm to calculate the analytical molecular surface J. Struct. Biol. 116 138.
28. Pearl L.H. and Honegger A 1983 Generation of molecular surfaces for graphic display J. Mol. Graph. 1 9.
29. Meyer A.Y. 1988 Molecular mechanics and molecular shape: V. On the computation of the bare surface area of molecules J. Comput. Chem. 9 18.
30. Andrade J.D., Hlady V., Wei A.P., Ho C.H., Lea A.S., Jeon S.I., Lin Y.S. and Stroup E. 1992 Proteins at interface: principles, multivariate aspects, protein resistant surfaces, and direct imaging and manipulation of adsorbed proteins Clin. Mater. 11 67.
31. Feng L. and Andrade J.D. 1994 Protein adsorption on low-temperature isotropic carbon: 1. Protein conformational change probed by differential scanning calorimetry J. Biomed. Mater. Res. 28 735.
32. Feng L. and Andrade J.D. 1994 Protein adsorption on low-temperature isotropic carbon: 2. Effects of surface charge of solids J. Colloid interface Sci. 166 419.
33. Feng L. and Andrade J.D. 1994 Protein adsorption on low temperature isotropic carbon: 3. Isotherms, competitivity, desorption and exchange of human albumin and fibrinogen Biomaterials 15 323.
34. Nicolau D.V., Taguchi T., Taniguchi H. and Yoshikawa S. 1998 Micron-sized protein-protein patterning on diazonaphthoquinone/novolak thin polymeric films Langmuir 14 1927.
35. Nicolau D.V., Taguchi T., Taniguchi H. and Yoshikawa S. 1999 Negative and positive tone protein patterning on e-beam/deep-UV resists Langmuir 15 3845.
36. Nicolau D.V., Taguchi T., Taniguchi H. and Yoshikawa S. 1999 Protein patterning via radiation-assisted surface functionalization of conventional microlithographic materials Colloids Surf A 155 51.
37. Nicolau D.V. and Cross R. 2000 Protein profiled features patterned via confocal microscopy Biosens. Bioelectron. 15 85.
38. Kyte J. and Doolittle R.F. 1982 A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 157 105.
39. Hopp T.P. and Woods K.R. 1981 Prediction of protein antigenic determinants from amino acids sequences Proc. Natl Acad. Sci. USA 78 3824.
40. Cao J. 2000 Is the α-β transition a transition of α-helices to β-pleated sheets? Part I. In situ XRD studies J. Mol. Struct. 553 101.
41. Cao J. 2002 Is the α-β transition a transition of ́-helices to β-pleated sheets? Part II. Synchrotron investigation for stretched single specimens J. Mol. Struct. 607 69.
42. Branden C. and Tooze J. 1999 Introduction to Protein Structure 2nd edn (New York: Garland).