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Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking

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Computational Methods for Macromolecules: Challenges and Applications

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 24))

Abstract

Efficient computational techniques provide advantageous solutions for complex problems in molecular modeling and related fields. These computational algorithms can come at hand where “wet biology” cannot be, or is too expensive to be carried out; they also help in solving computational bottlenecks caused when using the direct calculation. Here we illustrate these ideas by presenting two computational methods. The first algorithm provides a linear-complexity multiscale computation of the many-body problem of calculating long-range electrostatics in charge and dipolar systems [1,2]. The second method brings a Computer Vision approach to a biomolecular structural recognition problem, namely, an automated method for molecular docking [3–8]. We conclude by demonstrating a possible implementation of electrostatic docking, i.e., combining the use of our multiscale fast electrostatics method in molecular docking.

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References

  1. Sandak, B.: Multiscale Fast Summation of Long Range Charge and Dipolar Interactions. Journal of Computational Chemistry 22(7)(2001) 717–731

    Article  CAS  Google Scholar 

  2. Sandak, B. and Brandt, A: Multiscale Fast Summation of Long Range Charge and Dipolar Interactions. In: Multiscale Computational Methods in Chemistry and Physics; Eds., Brandt, A., Bernholc, J. and Binder, K. NATO Science Series: Computer and System Sciences. 177 (2000) 6–31

    Google Scholar 

  3. Sandak, B., Nussinov, R. and Wolfson, H.J.: A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility. Journal of Computational Biology. 5(4) (1998) 631–654

    Article  PubMed  CAS  Google Scholar 

  4. Sandak, B., Wolfson, H.J. and Nussinov, R.: Flexible Docking Allowing Induced Fit in Proteins: Insights from an Open to Closed Conformational Isomers Proteins: Struc, Func. & Genet. 32(2) (1998) 159–174

    Article  CAS  Google Scholar 

  5. Sandak, B. Nussinov, R. and Wolfson, H.J.: Docking of Conformationally Flexible Proteins. Seventh Symposium on Combinatorial Pattern Matching, Laguna Beach, California, USA. Springer Verlag. Lecture Notes in Computer Science, 1075 (1996) 271–287

    Article  Google Scholar 

  6. Sandak, B., Wolfson, H.J. and Nussinov, R: Hinge-bending at molecular interfaces: Automated docking of a dihydroxyethylene-containing inhibitor of the HIV-1 protease. Proceedings of the Ninth Conversation, Eds., R.H. Sarma and M.H. Sarma., Adenine Press. Journal of Biomolecular Structure & Dynamics 1 (1996) 233–252

    CAS  Google Scholar 

  7. Sandak, B., Nussinov, R. and Wolfson, H. J.: An automated Computer-Vision &Robotics based technique for 3-D flexible biomolecular docking and matching. Computer Applications in the Biosciences (CABIOS) 11 (1995) 87–99

    CAS  Google Scholar 

  8. Sandak, B., Nussinov, R. and Wolfson, H.J.: 3-D flexible docking of molecules. IEEE Proc. of the First International Workshop on Shape and Pattern Matching in Computational Biology. Seattle, Washington, USA (1994) 41–54

    Google Scholar 

  9. Brandt, A.: Guide to multigrid development. In: Multigrid Methods, edited by Hackbusch W. and Trottenberg U., Springer Verlag (1982) 220–312 (See §8.6)

    Google Scholar 

  10. Brandt, A. and Lubrecht, A.A.: Multilevel matrix multiplication and the fast solution of integral equations. J. Comp. Phys. 90 (1990) 348–370

    Article  Google Scholar 

  11. Brandt, A.: Multilevel computations of integral transforms and particle interactions with oscillatory kernels. Comp. Phys. Comm. 65 (1991) 24–38

    Article  Google Scholar 

  12. Brandt, A.: The Gauss Center research in multiscale scientific computation: six year summary. Report WI/GC-12. Weizmann Institute of Science (1999)

    Google Scholar 

  13. Hockney, R.W. and Eastwood, J.W.: Computer Simulation Using Particles. McGraw-Hill. (1981)

    Google Scholar 

  14. Appel, A.W.: An efficient program for many-body simulation. SIAM J. Sci. Stat. Comp. 6 (1985) 85–103

    Article  Google Scholar 

  15. Barnes, J. and Hut, P.: A hierarchical 0(N ln N) force calculation algorithm. Nature 324 (1986) 446–449

    Article  Google Scholar 

  16. Greengard, L.: Fast algorithm for classical physics. Science 265 (1994) 909–914

    Article  PubMed  CAS  Google Scholar 

  17. Greengard, L. and Rokhlin, V.: A fast algorithm for particle simulations. J. Comp. Phys. 73 (1987) 325–348

    Article  Google Scholar 

  18. Kutteh, R. and Nicholas, J.B.: Implementing the cell multipole method for dipolar and a charged dipolar systems. Comp. Phys. Comm. 86 (1995) 236–254

    Article  CAS  Google Scholar 

  19. Brandt, A. and Venner, C.H.: Multilevel evaluation of integral transforms with asymptotically smooth kernels. SIAM J. Sci. Comput. 19 (1998) 468–492

    Article  Google Scholar 

  20. Wolfson, H.J.: Generalizing the generalized Hough transform. Pattern Recognition Letters 12(9) (1991) 565–573

    Article  Google Scholar 

  21. Kuntz, I.D. et al.: A Geometric Approach to Macromolecule-Ligand Interactions. J. Mol. Biol. 161 (1982) 269–288

    Article  PubMed  CAS  Google Scholar 

  22. DesJarlais, R.L. et al.: Docking flexible ligands to macromolecular receptors by molecular shape. J. Med. Chem. 29 (1986) 2149–2153

    Article  PubMed  CAS  Google Scholar 

  23. Rarey et al.: A fast flexible docking method using incremental construction algorithm. J. Mol. Biol. 261 (1996) 470–489

    Article  PubMed  CAS  Google Scholar 

  24. Leach, A.R.: Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235 (1994) 345–356

    Article  PubMed  CAS  Google Scholar 

  25. Jones, G., Willet, P. and Glen, R.C.: Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 245 (1995) 43–53

    Article  PubMed  CAS  Google Scholar 

  26. Bernstein, F.C. et al.: The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures. J. Mol. Biol. 112 (1977) 535–542

    Article  PubMed  CAS  Google Scholar 

  27. Meador, W.E., Means, A.R. and Quiocho, F.A.: Target enzyme recognition by calmodulin: 2.4Å structure of a calmodulin-peptide complex. Science 257 (1992) 1251–1255

    Article  PubMed  CAS  Google Scholar 

  28. Sharff, A.J. et al.: Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and Chemotaxis. Biochemistry 31 (1992) 10657–10663

    Article  PubMed  CAS  Google Scholar 

  29. Spurlino, J.C. and Lu, G.Y. and Quiocho, F.A.: The 2.3Å resolution structure of the maltose or maltodextrin binding protein, a primary receptor of bacterial transport and Chemotaxis. J. Bio. Chem. 266 (1991) 5202–5219

    CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    B. Sandak

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  1. B. Sandak
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Editor information

Editors and Affiliations

  1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

  2. Howard Hughes Medical Institute, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

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© 2002 Springer-Verlag Berlin Heidelberg

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Sandak, B. (2002). Efficient Computational Algorithms for Fast Electrostatics and Molecular Docking. In: Schlick, T., Gan, H.H. (eds) Computational Methods for Macromolecules: Challenges and Applications. Lecture Notes in Computational Science and Engineering, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56080-4_17

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  • DOI: https://doi.org/10.1007/978-3-642-56080-4_17

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43756-7

  • Online ISBN: 978-3-642-56080-4

  • eBook Packages: Springer Book Archive

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