An algorithm for the protein docking problem

Bioinformatics: From Nucleic Acids and Proteins to Cell Metabolism

Volumn , Issue , 2007, Pages 125-139

  Lenhof, Hans Peter ^a  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION ALGORITHMS; ATOMS; LENNARD-JONES POTENTIAL; MOLECULES; VAN DER WAALS FORCES;

CONTACT AREAS; DOCKING ALGORITHMS; PARALLEL VERSION; POTENTIAL FUNCTION; PROTEIN DOCKING; SEQUENTIAL ALGORITHM; TEST EXAMPLES; VAN DER WAALS CONTACTS;

CONFORMATIONS;

EID: 84954327732     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527615193.ch10     Document Type: Chapter

References (15)

1. M.L. [Coni] M.L. Connolly: "Analytical Molecular Surface Calculation.", J. Appl. Cryst., vol. 16, 1983, pp. 548-558.
2. M.L. Connolly: "Solvent Accessible Surface of Proteins and Nucleic Add.", Science, vol. 221, 1983, pp. 709-713.
3. M.L. Connolly: "Shape Complementary at the Hemoglobin aifii Subunit Interface.", Biopolymers, vol. 25, 1986, pp. 1229-1247.
4. M. Ester, H.P. Kriegel, T. Seidl and X. Xu: "Formbasierte Suche nach kom- plementaren 3D-Oberflachen in einer Protein-Datenbank.", in Datenbanksysteme in Biiro, Technik und Wissenschaft, GI-Fachtagung 1995, Georg Lausen (Hrsg.), Springer Verlag, pp. 373-382.
5. D. Fischer, R. Norel, R. Nussinov and H.J. Wolfison: "3-D Docking of Protein Molecules." Combinatorial Pattern Matching, 1993, LNCS 684, Springer Verlag, pp. 20-43.
6. J. Foley, A. van Dam, S. Feiner and J. Hughes: "Computer Graphics: Principles and Practice." Addison Wesley, 1990.
7. M. Helmer-Citterich and A. Tramontano: "PUZZLE: A New Method for Automated Protein Docking Based on Surface Shape Complementarity.", J. Mol. Biol., vol. 235, 1994, pp. 1021-1031.
8. E. Katchalski-Katzir, I. Sharir, M. Eisenstein, A.A. Friesem, C. Aflalo and I.A. Vakser: "Molecular Surface Recognition: Determination of Geometric Fit between Protein and their Ligands by Correlation Techniques.", Proc. Natl. Acad. Sci. USA, 1992, vol. 89, pp. 2195-2199.
9. I.D. Kuntz, J.M. Blaney, S.J. Oatley, R. Langridge and T.E. Ferrin: "A Geometric Approach to Macromolecule-Ligand Interactions." J. Mol. Biol., vol. 161, 1982, pp. 269-288.
10. F.S. Kuhl, G.M. Crippen and D.K. Friesen: "A Combinatorial Algorithm for Calculating Ligand Binding.", J. Comp. Chem., vol. 5 (1), 1984, pp. 24-34.
11. R.A. Lewis: "Clefts and Binding Sites in Protein Receptors.", in Methods in Enzymology, Editor: J.J. Langone, vol. 202, 1991, pp. 126-156.
12. S.L. Lin, R. Nussinov, D. Fischer and H.J. Wolfson: "Molecular Surface Representations by Sparse Critical Points.", PROTEINS: Structure, Function, and Genetics, vol. 18, 1994, pp. 94-101.
13. Y. Lamdan and H.J. Wolfson:"Geometric Hashing: A General and Efficient Model-Based Recognition Scheme." In Proceedings of the IEEE Int. Conf. on Computer Vision, 1988, pp. 238-249.
14. R. Norel, S.L. Lin, H.J. Wolfson and R. Nussinov: "Shape Compementarity at Protein-Protein Interfaces.", Biopolymers, vol. 34, 1994, pp. 933-940.
15. V.S. Sunderam: "PVM: A Framework for Parallel Distributed Computing.", Concurrency: Practice & Experiment, vol. 2, 1990, pp. 315-339.