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Volumn 4, Issue 12, 2009, Pages 1-11

Generating triangulated macromolecular surfaces by euclidean distance transform

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; SOLVENT; CHAPERONIN;

EID: 77949504596     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008140     Document Type: Article
Times cited : (118)

References (34)
  • 1
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379-400.
    • (1971) J Mol Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 2
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • Zhang Y (2008) Progress and challenges in protein structure prediction. Curr Opin Struct Biol 18: 342-348.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 342-348
    • Zhang, Y.1
  • 3
    • 0038237369 scopus 로고    scopus 로고
    • Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking
    • Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, et al. (2003) Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins 52: 107-112.
    • (2003) Proteins , vol.52 , pp. 107-112
    • Schneidman-Duhovny, D.1    Inbar, Y.2    Polak, V.3    Shatsky, M.4    Halperin, I.5
  • 4
    • 36749002053 scopus 로고    scopus 로고
    • Docking of protein molecular surfaces with evolutionary trace analysis
    • Kanamori E, Murakami Y, Tsuchiya Y, Standley DM, Nakamura H, et al. (2007) Docking of protein molecular surfaces with evolutionary trace analysis. Proteins 69: 832-838.
    • (2007) Proteins , vol.69 , pp. 832-838
    • Kanamori, E.1    Murakami, Y.2    Tsuchiya, Y.3    Standley, D.M.4    Nakamura, H.5
  • 6
    • 0038174853 scopus 로고    scopus 로고
    • Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
    • Zavodszky MI, Sanschagrin PC, Korde RS, Kuhn LA (2002) Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des 16: 883-902.
    • (2002) J Comput Aided Mol Des , vol.16 , pp. 883-902
    • Zavodszky, M.I.1    Sanschagrin, P.C.2    Korde, R.S.3    Kuhn, L.A.4
  • 7
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221: 709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 8
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly ML (1983) Analytical molecular surface calculation. J Appl Crystallogr 16: 548-558.
    • (1983) J Appl Crystallogr , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 9
    • 0027159949 scopus 로고
    • The molecular surface package
    • Connolly ML (1993) The molecular surface package. J Mol Graph 11: 139-141.
    • (1993) J Mol Graph , vol.11 , pp. 139-141
    • Connolly, M.L.1
  • 10
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner JC (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38: 305-320.
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 12
    • 0001528720 scopus 로고    scopus 로고
    • Exact and efficient analytical calculation of the accessible surface area and their gradient for macromolecules
    • Fraczkiewicz R, Braun W (1998) Exact and efficient analytical calculation of the accessible surface area and their gradient for macromolecules. J Comput Chem 19: 319-333.
    • (1998) J Comput Chem , vol.19 , pp. 319-333
    • Fraczkiewicz, R.1    Braun, W.2
  • 13
    • 14744271380 scopus 로고    scopus 로고
    • A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients
    • Hayryan S, Hu CK, Skrivanek J, Hayryane E, Pokorny I (2005) A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients. J Comput Chem 26: 334-343.
    • (2005) J Comput Chem , vol.26 , pp. 334-343
    • Hayryan, S.1    Hu, C.K.2    Skrivanek, J.3    Hayryane, E.4    Pokorny, I.5
  • 14
    • 0032190305 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape
    • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S (1998) Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 33: 1-17.
    • (1998) Proteins , vol.33 , pp. 1-17
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 15
    • 84986462300 scopus 로고
    • MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives
    • Perrot G, Cheng B, Gibson KD, Vila J, Palmer KA, et al. (1992) MSEED: a program for the rapid analytical determination of accessible surface areas and their derivatives. J Comput Chem 13: 1-11.
    • (1992) J Comput Chem , vol.13 , pp. 1-11
    • Perrot, G.1    Cheng, B.2    Gibson, K.D.3    Vila, J.4    Palmer, K.A.5
  • 16
    • 0021755764 scopus 로고
    • Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect
    • Richmond TJ (1984) Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect. J Mol Biol 178: 63-89.
    • (1984) J Mol Biol , vol.178 , pp. 63-89
    • Richmond, T.J.1
  • 17
    • 34547336672 scopus 로고    scopus 로고
    • Joint neighbors approximation of macromo- lecular solvent accessible surface area
    • Rychkov G, Petukhov M (2007) Joint neighbors approximation of macromo- lecular solvent accessible surface area. J Comput Chem 28: 1974-1989.
    • (2007) J Comput Chem , vol.28 , pp. 1974-1989
    • Rychkov, G.1    Petukhov, M.2
  • 18
    • 2442595374 scopus 로고
    • Macromolecular shape and surface maps by solvent exclusion
    • Greer J, Bush BL (1978) Macromolecular shape and surface maps by solvent exclusion. Proc Natl Acad Sci U S A 75: 303-307.
    • (1978) Proc Natl Acad Sci U S A , vol.75 , pp. 303-307
    • Greer, J.1    Bush, B.L.2
  • 19
    • 0032059253 scopus 로고    scopus 로고
    • A flexible triangulation method to describe the solvent-accessible surface of biopolymers
    • Juffer AH, Vogel HJ (1998) A flexible triangulation method to describe the solvent-accessible surface of biopolymers. J Comput Aided Mol Des 12: 289-299.
    • (1998) J Comput Aided Mol Des , vol.12 , pp. 289-299
    • Juffer, A.H.1    Vogel, H.J.2
  • 20
    • 33750517742 scopus 로고    scopus 로고
    • Efficient molecular surface generation using level-set methods
    • Can T, Chen CI, Wang YF (2006) Efficient molecular surface generation using level-set methods. J Mol Graph Model 25: 442-454.
    • (2006) J Mol Graph Model , vol.25 , pp. 442-454
    • Can, T.1    Chen, C.I.2    Wang, Y.F.3
  • 21
    • 33745587012 scopus 로고    scopus 로고
    • Quality meshing of implicit solvation models of biomolecular structures
    • Zhang Y, Xu G, Bajaj C (2006) Quality meshing of implicit solvation models of biomolecular structures. Comput Aided Geom Des 23: 510-530.
    • (2006) Comput Aided Geom Des , vol.23 , pp. 510-530
    • Zhang, Y.1    Xu, G.2    Bajaj, C.3
  • 22
    • 0027551946 scopus 로고
    • Approximation and characterization of molecular surfaces
    • Duncan BS, Olson AJ (1993) Approximation and characterization of molecular surfaces. Biopolymers 33: 219-229.
    • (1993) Biopolymers , vol.33 , pp. 219-229
    • Duncan, B.S.1    Olson, A.J.2
  • 23
    • 0001309005 scopus 로고
    • Molecular surface triangulation
    • Connolly ML (1985) Molecular surface triangulation. J Appl Crystallogr 18: 499-505.
    • (1985) J Appl Crystallogr , vol.18 , pp. 499-505
    • Connolly, M.L.1
  • 24
    • 0023381475 scopus 로고
    • Marching cubes: A high resolution 3d surface construction algorithm
    • Lorensen WE, Cline HE (1987) Marching cubes: a high resolution 3d surface construction algorithm. Comput Graph 21: 163-169.
    • (1987) Comput Graph , vol.21 , pp. 163-169
    • Lorensen, W.E.1    Cline, H.E.2
  • 25
    • 84986487007 scopus 로고
    • Calculating the electric potential of macromolecules: A simple method for molecular surface triangulation
    • Xiang Z, Shi Y, Xu YJ (1995) Calculating the electric potential of macromolecules: A simple method for molecular surface triangulation. J Comput Chem 16: 512-516.
    • (1995) J Comput Chem , vol.16 , pp. 512-516
    • Xiang, Z.1    Shi, Y.2    Xu, Y.J.3
  • 26
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards FM (1977) Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 6: 151-176.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 28
    • 0028405361 scopus 로고
    • A Euclidean distance transform using grayscale morphology decomposition
    • Huang CT, Mitchell QR (1994) A Euclidean distance transform using grayscale morphology decomposition. IEEE Trans PAMI 16: 443-448.
    • (1994) IEEE Trans PAMI , vol.16 , pp. 443-448
    • Huang, C.T.1    Mitchell, Q.R.2
  • 30
    • 33845269582 scopus 로고    scopus 로고
    • Euclidean distance transform of digital images in arbitrary dimensions
    • Xu D, Li H (2006) Euclidean distance transform of digital images in arbitrary dimensions. LNCS 4261: 72-79.
    • (2006) LNCS , vol.4261 , pp. 72-79
    • Xu, D.1    Li, H.2
  • 31
    • 0030819133 scopus 로고    scopus 로고
    • Computation of molecular electrostatics with boundary element methods
    • Liang J, Subramaniam S (1997) Computation of molecular electrostatics with boundary element methods. Biophys J 73: 1830-1841.
    • (1997) Biophys J , vol.73 , pp. 1830-1841
    • Liang, J.1    Subramaniam, S.2
  • 33
    • 0032189626 scopus 로고    scopus 로고
    • Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
    • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S (1998) Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins 33: 18-29.
    • (1998) Proteins , vol.33 , pp. 18-29
    • Liang, J.1    Edelsbrunner, H.2    Fu, P.3    Sudhakar, P.V.4    Subramaniam, S.5
  • 34
    • 46449123146 scopus 로고    scopus 로고
    • MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
    • Wu S, Zhang Y (2008) MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72: 547-556.
    • (2008) Proteins , vol.72 , pp. 547-556
    • Wu, S.1    Zhang, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.