메뉴 건너뛰기




Volumn , Issue , 2009, Pages 259-270

A dynamic data structure for flexible molecular maintenance and informatics

Author keywords

Computer aided design; De novo drug design; Interactive software; Molecular docking; Protein folding; Shape modeling

Indexed keywords

BINDING AFFINITIES; CONTACT SURFACE; DE NOVO DRUG DESIGN; DRUG DESIGN; DYNAMIC DATA STRUCTURE; FAST ESTIMATION; FLEXIBLE MOLECULAR MODEL; FLEXIBLE MOLECULES; INFORMATICS; INTERACTIVE SOFTWARE; MOLECULAR DOCKING; MOLECULAR DYNAMICS CALCULATION; MOLECULAR PROPERTIES; MOLECULAR SURFACES; POLARIZATION ENERGY; SHAPE MODELING; SURFACE AREA; TIME BOUND; VAN DER WAALS; W-BIT WORDS;

EID: 70350623065     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1629255.1629287     Document Type: Conference Paper
Times cited : (4)

References (55)
  • 1
    • 70350631882 scopus 로고    scopus 로고
    • PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. http://pdb2pqr.sourceforge.net/.
    • PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. http://pdb2pqr.sourceforge.net/.
  • 2
    • 0033497571 scopus 로고    scopus 로고
    • A. A. and W. Z. VRDD: applying virtual reality visualization to protein docking and design. Journal of Molecular Graphics and Modelling, 17(7):180-186, 1999.
    • A. A. and W. Z. VRDD: applying virtual reality visualization to protein docking and design. Journal of Molecular Graphics and Modelling, 17(7):180-186, 1999.
  • 4
    • 33845381177 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
    • A. Arkhipov, P. L. Freddolino, K. Imada, K. Namba, and K. Schulten. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophy. J., 91:4589-4597, 2006.
    • (2006) Biophy. J , vol.91 , pp. 4589-4597
    • Arkhipov, A.1    Freddolino, P.L.2    Imada, K.3    Namba, K.4    Schulten, K.5
  • 5
    • 22544485999 scopus 로고    scopus 로고
    • C. Bajaj. A Laguerre Voronoi based scheme for meshing particle systems. Japan Journal of Industrial and Applied Mathematics, 22(2):167-177, June 2005.
    • C. Bajaj. A Laguerre Voronoi based scheme for meshing particle systems. Japan Journal of Industrial and Applied Mathematics, 22(2):167-177, June 2005.
  • 7
    • 0005532405 scopus 로고    scopus 로고
    • Multiresolution molecular shapes. Technical report, TICAM, Univ. of Texas at Austin
    • Dec
    • C. Bajaj, V. Pascucci, A. Shamir, R. Holt, and A. Netravali. Multiresolution molecular shapes. Technical report, TICAM, Univ. of Texas at Austin, Dec. 1999.
    • (1999)
    • Bajaj, C.1    Pascucci, V.2    Shamir, A.3    Holt, R.4    Netravali, A.5
  • 8
    • 0037375002 scopus 로고    scopus 로고
    • Dynamic maintenance and visualization of molecular surfaces
    • C. Bajaj, V. Pascucci, A. Shamir, R. Holt, and A. Netravali. Dynamic maintenance and visualization of molecular surfaces. Dis. App. Math., 127(1):23-51, 2003.
    • (2003) Dis. App. Math , vol.127 , Issue.1 , pp. 23-51
    • Bajaj, C.1    Pascucci, V.2    Shamir, A.3    Holt, R.4    Netravali, A.5
  • 9
    • 70350667888 scopus 로고    scopus 로고
    • C. Bajaj and W. Zhao. Fast molecular solvation energetics and forces computation. Technical Report ICES TR-08-20, The University University of Texas at Austin, 2008.
    • C. Bajaj and W. Zhao. Fast molecular solvation energetics and forces computation. Technical Report ICES TR-08-20, The University University of Texas at Austin, 2008.
  • 10
    • 0344436712 scopus 로고    scopus 로고
    • Van der Waals radii of elements
    • September
    • S. Batsanov. Van der Waals radii of elements. Inorganic Materials, 37:871-885(15), September 2001.
    • (2001) Inorganic Materials , vol.37 , Issue.15 , pp. 871-885
    • Batsanov, S.1
  • 12
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • M. Connolly. Analytical molecular surface calculation. Journal of Applied Crystallography, 16:548-558, 1983.
    • (1983) Journal of Applied Crystallography , vol.16 , pp. 548-558
    • Connolly, M.1
  • 13
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • 19 August
    • M. Connolly. Solvent-accessible surfaces of proteins and nucleic acids. Science, 221(4612):709-713, 19 August 1983.
    • (1983) Science , vol.221 , Issue.4612 , pp. 709-713
    • Connolly, M.1
  • 16
    • 0027551946 scopus 로고
    • Approximation and characterization of molecular surfaces
    • February
    • B. Duncan and A. Olson. Approximation and characterization of molecular surfaces. Biopolymers, 33(2):219-229, February 1993.
    • (1993) Biopolymers , vol.33 , Issue.2 , pp. 219-229
    • Duncan, B.1    Olson, A.2
  • 20
    • 33646205091 scopus 로고    scopus 로고
    • Improved maintenance of molecular surfaces using dynamic graph connectivity
    • E. Eyal and D. Halperin. Improved maintenance of molecular surfaces using dynamic graph connectivity. Algorithms in Bioinformatics, pages 401-413, 2005.
    • (2005) Algorithms in Bioinformatics , pp. 401-413
    • Eyal, E.1    Halperin, D.2
  • 21
    • 0000743608 scopus 로고
    • Surpassing the information theoretic bound with fusion trees
    • M. L. Fredman and D. E. Willard. Surpassing the information theoretic bound with fusion trees. J. Comput. Syst. Sci., 47(3):424-436, 1993.
    • (1993) J. Comput. Syst. Sci , vol.47 , Issue.3 , pp. 424-436
    • Fredman, M.L.1    Willard, D.E.2
  • 22
    • 85183430449 scopus 로고
    • Smoothed particle hydrodynamics - theory and application to non-spherical stars
    • November
    • R. A. Gingold and J. J. Monaghan. Smoothed particle hydrodynamics - theory and application to non-spherical stars. Mon. Not. Roy. Astron. Soc., 181:375-389, November 1977.
    • (1977) Mon. Not. Roy. Astron. Soc , vol.181 , pp. 375-389
    • Gingold, R.A.1    Monaghan, J.J.2
  • 23
    • 0000747830 scopus 로고
    • A gaussian description of molecular shape
    • J. Grant and B. Pickup. A gaussian description of molecular shape. Journal of Physical Chemistry, 99:3503-3510, 1995.
    • (1995) Journal of Physical Chemistry , vol.99 , pp. 3503-3510
    • Grant, J.1    Pickup, B.2
  • 26
    • 0029878720 scopus 로고    scopus 로고
    • W. Humphrey, A. Dalke, and K. Schulten. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
    • W. Humphrey, A. Dalke, and K. Schulten. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
  • 27
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • February
    • R. M. Jackson, H. A. Gabba, and M. J. E. Sternberg. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. Journal of Molecular Biology, 276(1):265-285, February 1998.
    • (1998) Journal of Molecular Biology , vol.276 , Issue.1 , pp. 265-285
    • Jackson, R.M.1    Gabba, H.A.2    Sternberg, M.J.E.3
  • 30
    • 33646265008 scopus 로고    scopus 로고
    • The molecule evoluator. an interactive evolutionary algorithm for the design of drug-like molecules
    • E.-W. Lameijer, J. N. Kok, T. Bäck, and A. P. IJzerman. The molecule evoluator. an interactive evolutionary algorithm for the design of drug-like molecules. Journal of Chemical Information and Modeling, 46(2):545-552, 2006.
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.2 , pp. 545-552
    • Lameijer, E.-W.1    Kok, J.N.2    Bäck, T.3    IJzerman, A.P.4
  • 31
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • February
    • B. Lee and F. Richards. The interpretation of protein structures: estimation of static accessibility. Journal of Molecular Biology, 55(3):379-400, February 1971.
    • (1971) Journal of Molecular Biology , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.2
  • 32
    • 0033932839 scopus 로고    scopus 로고
    • Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
    • E. Lindahl and O. Edholm. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. Biophys. J., 79:426-433, 2000.
    • (2000) Biophys. J , vol.79 , pp. 426-433
    • Lindahl, E.1    Edholm, O.2
  • 34
    • 0035812110 scopus 로고    scopus 로고
    • Effect of undulations on surface tension in simulated bilayers
    • S. J. Marrink and A. E. Mark. Effect of undulations on surface tension in simulated bilayers. J. Phys. Chem. B, 105:6122-6127, 2001.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6122-6127
    • Marrink, S.J.1    Mark, A.E.2
  • 40
    • 2442420008 scopus 로고    scopus 로고
    • Cuckoo hashing
    • R. Pagh and F. Rodler. Cuckoo hashing. J. Algorithms, 51(2):122-144, 2004.
    • (2004) J. Algorithms , vol.51 , Issue.2 , pp. 122-144
    • Pagh, R.1    Rodler, F.2
  • 43
    • 0032147007 scopus 로고    scopus 로고
    • Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
    • December
    • B. Sandak, H. J. Wolfson, and R. Nussinov. Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers. Proteins: Structure, Function, and Genetics, 32(2):159-174, December 1998.
    • (1998) Proteins: Structure, Function, and Genetics , vol.32 , Issue.2 , pp. 159-174
    • Sandak, B.1    Wolfson, H.J.2    Nussinov, R.3
  • 45
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • March
    • M. Sanner, A. Olson, and J. Spehner. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers, 38(3):305-320, March 1996.
    • (1996) Biopolymers , vol.38 , Issue.3 , pp. 305-320
    • Sanner, M.1    Olson, A.2    Spehner, J.3
  • 46
    • 55749110069 scopus 로고    scopus 로고
    • Techniques for the design of molecules and combinatorial chemical libraries
    • A. N. Sedwell and I. C. Parmee. Techniques for the design of molecules and combinatorial chemical libraries. In 2007 IEEE Congress on Evolutionary Computation, pages 2435-2442, 2007.
    • (2007) 2007 IEEE Congress on Evolutionary Computation , pp. 2435-2442
    • Sedwell, A.N.1    Parmee, I.C.2
  • 47
    • 11244346546 scopus 로고    scopus 로고
    • Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins
    • A. Y. Shih, I. G. Denisov, J. C. Phillips, S. G. Sligar, and K. Schulten. Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins. Biophys. J., 88:548-556, 2005.
    • (2005) Biophys. J , vol.88 , pp. 548-556
    • Shih, A.Y.1    Denisov, I.G.2    Phillips, J.C.3    Sligar, S.G.4    Schulten, K.5
  • 48
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc, 112:6127-6129, 1990.
    • (1990) J. Am. Chem. Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 49
    • 0035013784 scopus 로고    scopus 로고
    • A system for interactive molecular dynamics simulation
    • J. F. Hughes and C. H. Séquin, editors, New York, ACM SIGGRAPH
    • J. Stone, J. Gullingsrud, P. Grayson, and K. Schulten. A system for interactive molecular dynamics simulation. In J. F. Hughes and C. H. Séquin, editors, 2001 ACM Symposium on Interactive 3D Graphics, pages 191-194, New York, 2001. ACM SIGGRAPH.
    • (2001) 2001 ACM Symposium on Interactive 3D Graphics , pp. 191-194
    • Stone, J.1    Gullingsrud, J.2    Grayson, P.3    Schulten, K.4
  • 53
  • 54
    • 0020802573 scopus 로고
    • Log-logarithmic worst-case range queries are possible in space n
    • D. Willard. Log-logarithmic worst-case range queries are possible in space n. Information Processing Letters, 17(2):81-84, 1983.
    • (1983) Information Processing Letters , vol.17 , Issue.2 , pp. 81-84
    • Willard, D.1
  • 55
    • 84986431462 scopus 로고
    • An analytical algorithm for the rapid determination of the solvent accessibility of points in a three-dimensional lattice around a solute molecule
    • T. You and D. Bashford. An analytical algorithm for the rapid determination of the solvent accessibility of points in a three-dimensional lattice around a solute molecule. Journal of Computational Chemistry, 16(6):743-757, 1995.
    • (1995) Journal of Computational Chemistry , vol.16 , Issue.6 , pp. 743-757
    • You, T.1    Bashford, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.