An intuitive approach to measuring protein surface curvature

Proteins: Structure, Function and Genetics

Volumn 61, Issue 4, 2005, Pages 1068-1074

  Coleman, Ryan G ^a,b,c   Burr, Michael A ^b   Souvaine, Diane L ^b   Cheng, Alan C ^a  

^a PFIZER INC   (United States)

^b Tufts University   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Computational geometry; Curvature; Molecular surface; Peptide binding sites

Indexed keywords

PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; GEOMETRY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; BINDING SITES; IMAGE PROCESSING, COMPUTER-ASSISTED; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOLVENTS; SURFACE PROPERTIES;

EID: 28644438570     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20680     Document Type: Article

References (39)

1. Laskowski RA, Luscombe NM, Swindells MB, Thornton JM. Protein clefts in molecular recognition and function. Prot Sci 1996;5:2438-2452.
2. Cheng AC, Calabro V, Frankel AD. Design of RNA-binding proteins and ligands. Curr Opin Struct Biol 2001;11:478-84.
3. Brady GP Jr, Stouten PF. Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 2000;14:383-401.
4. Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities; Measurement of binding site geometry and implications for ligand design. Prot Sci 1998;7:1884-1897.
5. Laskowski RA. SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995;13:323-330.
6. Sharp KA, Nicholls A, Fine RF, Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 1991;252:106-109.
7. Chan HS, Dill KA. Solvation: Effects of molecular size and shape. J Chem Phys 1994;101:7007-7026.
8. Southall NT, Dill KA. The mechanism of hydrophobic solvation depends on solute radius. J Phys Chem B 2000;104:1326-1331.
9. Ferre F, Ausiello G, Zanzoni A, Helmer-Citterich M. SURFACE: A database of protein surface regions for functional annotation. Nucleic Acids Res 2004;32:D240-244.
10. Richards FM. Areas, volumes, packing, and protein structure. Annual Rev Biophys Bioeng 1977;6:151-76.
11. Connolly ML. Measurement of protein surface shape by solid angles. J Mol Graphics 1986;4:3-6.
12. Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991;11:281-296.
13. Sridharan S, Nicholls A, Honig B. A new vertex algorithm to calculate solvent accessible surface area. Biophys J 1992;61:A174.
14. Duncan BS, Olson AJ. Shape analysis of molecular surfaces. Biopolymers 1993;33:231-238.
15. Tsodikov OV, Record MT Jr, Sergeev YV. Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J Comput Chem 2002;23:600-609.
16. Zachmann C-D, Heiden W, Schlenkrich M, Brickmann J. Topological analysis of complex molecular surfaces. J Comp Chem 1992;13:76-84.
17. Pearson K. On lines and planes of closest fit to systems of points in space. The Philosophical Magazine 1901;2:559-572.
18. Shakarji CM. Least squares fitting algorithms of the NIST algorithm testing system. J Res Natl Inst Stand Technol 1998;103:633-641.
19. Eberly D. Least squares fitting of data. http://www. magic-software.com/ Documentation/LeastSquaresFitting.pdf; 2001.
20. Ahn SJ, Rauh W, Warnecke H-J. Least-squares orthogonal distances fitting of circle, sphere, ellipse, hyperbola, and parabola. Pattern Recog 2001;34:2283-303.
21. Ahn SJ, Rauh W, Cho HS. Orthogonal distance fitting of implicit curves and surfaces. IEEE Trans Pattern Anal Mach Intell 2002;24:620-638.
22. Atieg A, Watson GA. A class of methods for fitting a curve or surface to data by minimizing the sum of squares of orthogonal distances. J Comput Appl Math 2003;158:277-296.
23. Edelsbrunner H, Mucke EP. Three-dimensional alpha shapes. ACM Trans Graph 1994;13:43-72.
24. Koehl P. ProShape. http://csb.stanford.edu/koehl/ProShape; 2003.
25. Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 1998;33:1-17.
26. O'Rourke J. Computational geometry column 18. Int J Comput Geom Appl 1993;3:107-113.
27. Saff EB, Kuijlaars A. Distributing many points on a sphere. Math Intell 1997;19:5-11.
28. Connolly ML. Plotting protein surfaces. J Mol Graphics 1986;4:93-96.
29. Brannan DA, Esplen MF, Gray JJ. Geometry. Cambridge University Press, Cambridge UK; 1999. 510 p.
30. Dobkin DP, Souvaine DL. Advances in robotics 1: algorithmic and geometric aspects of robotics. In: Schwartz T, Yap CK, editors. Computational geometry: a user's guide. Mahwah, NJ: Lawrence Erlbaum Associates; 1997. p 43-93.
31. Yeates TO. Algorithms for evaluating the long-range accessibility of protein surfaces. J Mol Biol 1995;249:804-815.
32. Barford D, Flint AJ, Tonks NK. Crystal structure of human protein tyrosine phosphatase IB. Science 1994;263:1397-1404.
33. Puius YA, Zhao Y, Sullivan M, Lawrence DS, Almo SC, Zhang ZY. Identification of a second aryl phosphate-binding site in protein-tyrosine phosphatase 1B: a paradigm for inhibitor design. Proc Natl Acad Sci USA 1997;94:13420-13425.
34. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
35. Coleman RG, Burr MA, Souvaine DL, Cheng AC. Transformations and algorithms for least sum of squares hypersphere fitting. Proc Can Conf Comp Geometry 2004;16:104-107.
36. Strandlie A, Wroldsen J, Fruhwirth R, Lillekjendlie B. Particle tracks fitted on the Riemann sphere. Comp Phys Comm 2000;131:905-908.
37. Tsuchiya Y, Kinoshita K, Nakamura H. Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. Proteins 2004;55:885-894.
38. Joughin BA, Tidor B, Yaffe MB. A computational method for the analysis and prediction of protein:phosphopeptide-binding sites. Prot Sci 2005;14:131-139.
39. Meyer M, Desbrun M, Schröder P, Barr AH. Discrete differential-geometry operators for triangulated 2-manifolds. In: Visualization and mathematics III. Springer Verlag, Heidelberg, Germany; 2003. p 34-58.