A global optimization algorithm for protein surface alignment

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Bertolazzi, Paola ^a   Guerra, Concettina ^b,c   Liuzzi, Giampaolo ^a  

^a CNR   (Italy)

^b UNIVERSITY OF PADOVA   (Italy)

^c Georgia Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EFFICIENT GLOBAL OPTIMIZATION; GLOBAL OPTIMIZATION ALGORITHM; GLOBAL OPTIMIZATION TECHNIQUES; ISOMETRIC TRANSFORMATION; PROTEIN-LIGAND BINDING SITES; PROTEIN-PROTEIN INTERFACE; THREE DIMENSIONAL (3D) SHAPES; THREE-DIMENSIONAL STRUCTURE;

ALGORITHMS; ALIGNMENT; BIOCHEMISTRY; PROTEINS; THREE DIMENSIONAL;

GLOBAL OPTIMIZATION;

PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; DRUG DESIGN; METABOLISM; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; SURFACE PROPERTY;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DESIGN; PROTEIN CONFORMATION; PROTEINS; SURFACE PROPERTIES;

EID: 77957126449     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-488     Document Type: Article

References (43)

1. Shatsky M, Shulman-Peleg A, Nussinov R, Wolfson HJ. The multiple common point set problem and its application to molecule binding pattern detection. Journal of Computational Biology 2006, 13:407-428. 10.1089/cmb.2006.13.407, 16597249.
2. Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. Journal of Molecular Biology 2004, 339:607-633. 10.1016/j.jmb.2004.04.012, 15147845.
3. Artymiuk P, Spriggs R, Willett P. Graph theoretic methods for the analysis of structural relationships in biological macromolecules. Journal of the American Society for Information Science and Technology 2005, 56(5):518-528.
4. Chen B, Bryant D, Fofanov V, Kristensen D, Cruess A, Kimmel M, Lichtarge O, Kavraki L. Cavity-aware motifs reduce false positives in protein function pre-diction. Computational System Bioinformatics Conf 2005, 311-323.
5. Hofbauer C, Lohninger H, Aszodi A. Surfcomp: A novel graph-based approach to molecular surface comparison. Journal of Chemical Information and Computer Sciences 2004, 44(3):837-847.
6. Weskamp N, Kuhn D, Hullermeier E, Klebe G. Efficient similarity search in protein structure databases by k-clique hashing. Bioinformatics 2004, 20(10):1522-1526. 10.1093/bioinformatics/bth113, 15231546.
7. Ballester P, Richards W. Ultrafast shape recognition to search compound databases for similar molecular shapes. Journal of Computational Chemistry 2007, 28(10):1711-1723. 10.1002/jcc.20681, 17342716.
8. Sommer I, Müller O, Domingues F, Sander O, Weickert J, Lengauer T. Moment invariants as shape recognition technique for comparing protein binding sites. Bioinformatics 2007, 23:3139-3146. 10.1093/bioinformatics/btm503, 17977888.
9. Bock M, Garutti C, Guerra C. Discovery of similar regions on protein surfaces. Journal of Computational Biology 2007, 14(3):285-299. 10.1089/cmb.2006.0145, 17563312.
10. Bock M, Garutti C, Guerra C. Effective labeling of molecular surface points for cavity detection and location of putative binding sites. Proc of the VI Int Conf on Computational Systems Bioinformatics; San Diego 2007, 263-274.
11. Bock M, Garutti C, Guerra C. Cavity detection and matching for binding site recognition. Theoretical Computer Science 2008, 408(2-3):151-162.
12. Angaran S, Bock M, Garutti C, Guerra C. MolLoc: a web tool for the local structural alignment of molecular surfaces. Nucleic Acids Research 2009, (Web server). 2703929, 19465382.
13. Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M. Funclust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics 2008, 9(Suppl 2):S2. 10.1186/1471-2105-9-S2-S2, 2323665, 18387204.
14. Jambon M, Olivier A, Combet C, Deleage G, Delfaud F, Geourjon C. The SuMo server: 3D search for protein functional sites. Bioinformatics 2005, 21(20):3929-3930. 10.1093/bioinformatics/bti645, 16141250.
15. Kinoshita N, Furui J, Nakamura H. Identification of protein functions from a molecular surface database, ef-site. Journal of Structural and Functional Genomics 2001, 2:9-22.
16. Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Research 2008, (36 Web server).
17. Besl PJ, McKay ND. A method for registration of 3-D shapes. IEEE Trans. on Pattern Analysis and Mach. Intelligence 1992, 14:239-255.
18. Goodrich MT, Mitchell JSB, Orletsky MW. Practical methods for approximate geometric pettern matching under rigid motions. Proc of the 10th Ann Symp on Computational Geometry 1994, 103-112. Press A.
19. Efrat A, Itai A, Katz MJ. Geometry helps in bottle-neck matching and related problems. Algorithmica 2001, 31:1-28.
20. Connolly ML. Analytical molecular surface calculation. Journal of Applied Crystallography 1983, 16:548-558.
21. Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and caviteis: measurement of binding site geometry and implications for ligand design. Protein Science 1998, 7:1884-1897. 10.1002/pro.5560070905, 2144175, 9761470.
22. Xu D, Li H, Gu T. Protein Structure Superposition by Curve Moment Invariants and Iterative Closest Point. The 1st Int Conf on Bioinformatics and Biomedical Engineering 2007, 6:25-28.
23. Brachetti P, De Felice Ciccoli M, Di Pillo G, Lucidi S. A new version of the Price's algorithm for global optimization. Journal of Global Optimization 1997, 10:165-184.
24. Cirio L, Lucidi S, Parasiliti F, Villani M. A global optimization approach for the synchronous motors design by finite element analysis. Journal of Applied Electromagnetics and Mechanics 2002, 16:13-27.
25. Price WL. A controlled random search procedure for global optimization. Towards Global Optimization 2 1978, Amsterdam: North-Holland, Dixon L, Szego G.
26. Daidone A, Parasiliti F, Villani M, Lucidi S. A new method for the design optimization of three-phase induction motors. IEEE Trans. on Magnetics 1998, 34:2932-2935.
27. Liuzzi G, Lucidi S, Piccialli V, Sotgiu A. A magnetic resonance device designed via global optimization techniques. Mathematical Programming 2004, 101:339-364.
28. Liuzzi G, Lucidi S, Parasiliti F, Villani M. Multi-objective Optimization Techniques for the Design of Induction Motors. IEEE Transactions on Magnetics 2003, 39:1261-1264.
29. Price WL. Global optimization by controlled random search. Journal of Optimization Theory and Applications 1983, 40:333-348.
30. Price WL. Global optimization algorithms for a CAD workstation. Journal of Optimization Theory and Applications 1983, 55:133-146.
31. Price WL, Woodhams F. Optimising accelerator for CAD workstations. IEEE proceedings 1988, 135:214-221.
32. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research 2000, 28:235-242. 10.1093/nar/28.1.235, 102472, 10592235.
33. Horn BKP. Closed-form solution of absolute orientation using unit quaternions. Journal of the Optical Society of America 1987, 4:629-642.
34. Goldberg AV, Kennedy R. An Efficient Cost Scaling Algorithm for the Assignment Problem. Mathematical Programming 1995, 71:153-178.
35. Schmitt S, Kuhn D, Klebe G. A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology. Journal of Molecular Biology 2002, 323:387-406. 10.1016/S0022-2836(02)00811-2, 12381328.
36. Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Shape Variation in Protein Binding Pockets and their Ligands. Journal of Molecular Biology 2007, 368:283-301. 10.1016/j.jmb.2007.01.086, 17337005.
37. Stockwell GR, Thornton JM. Conformational diversity of ligands bound to proteins. Journal of Molecular Biology 2006, 356:928-944. 10.1016/j.jmb.2005.12.012, 16405908.
38. Kolodny R, Koehl P, Levitt M. Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures. Journal of Molecular Biology 2005, 346:1173-1188. 10.1016/j.jmb.2004.12.032, 2692023, 15701525.
39. Connolly ML. Analytical molecular surface calculation. Journal of Applied Crystallography 1983, 16:548-558.
40. Subbiah S, Laurents D, Levitt M. Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core. Current Biology 1993, 3(3):141-148. 10.1016/0960-9822(93)90255-M, 15335781.
41. Gerstein M, Levitt M. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Science 1998, 7(2):445-456. 10.1002/pro.5560070226, 2143933, 9521122.
42. Comin M, Guerra C, Dellaert F. Binding Balls: Fast detection of Binding Sites using a property of Spherical Fourier Transform. Journal of Computational Biology 2009, 16(11):1577-1591. 10.1089/cmb.2009.0045, 19958084.
43. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995, 247:536-540.