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Journal of Computational Chemistry

Volumn 32, Issue 14, 2011, Pages 3023-3038

Geometric measures of large biomolecules: Surface, volume, and pockets

(2) MacH, Paul a Koehl, Patrice a

a UNIVERSITY OF CALIFORNIA (United States)

Author keywords

macromolecules; pockets; space filling diagrams; surface area; volume

Indexed keywords

ALPHA-SHAPES; GEOMETRIC MEASURES; IMPLICIT SOLVENT MODEL; LARGE BIOMOLECULES; MACROMOLECULAR SYSTEMS; OPEN-SOURCE SOFTWARES; POCKETS; ROBUST METHODS; SPACE-FILLING DIAGRAMS; SPEED-UPS; SURFACE AREA; VIRAL CAPSIDS; VOLUME;

ATOMS; BIOMOLECULES; CACHE MEMORY; MACROMOLECULES; MEMORY ARCHITECTURE; PERSONAL COMPUTERS;

GEOMETRY;

NUCLEIC ACID; PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; SURFACE PROPERTY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; NUCLEIC ACIDS; PROTEINS; SOFTWARE; SURFACE PROPERTIES;

EID: 80052035456 PISSN: 01928651 EISSN: 1096987X Source Type: Journal
DOI: 10.1002/jcc.21884 Document Type: Article

Times cited : (25)

References (78)

1
- 0022596727
- (London).
- D. Eisenberg, A. D. McLachlan, Nature (London) 1986, 319, 199.
- (1986) Nature , vol.319 , pp. 199
- Eisenberg, D.¹ McLachlan, A.D.²

2
- 0023338543
- T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga, Proc Natl Acad Sci USA 1987, 84, 3086.
- (1987) Proc Natl Acad Sci USA , vol.84 , pp. 3086
- Ooi, T.¹ Oobatake, M.² Nemethy, G.³ Scheraga, H.A.⁴

3
- 0032190305
- J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, S. Subramaniam, Proteins: Struct Funct Genet 1998, 33, 1.
- (1998) Proteins: Struct Funct Genet , vol.33 , pp. 1
- Liang, J.¹ Edelsbrunner, H.² Fu, P.³ Sudhakar, P.V.⁴ Subramaniam, S.⁵

4
- 0032189626
- J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, S. Subramaniam, Proteins: Struct Funct Genet 1998, 33, 18.
- (1998) Proteins: Struct Funct Genet , vol.33 , pp. 18
- Liang, J.¹ Edelsbrunner, H.² Fu, P.³ Sudhakar, P.V.⁴ Subramaniam, S.⁵

5
- 0015222647
- B. Lee, F. M. Richards, J Mol Biol 1971, 55, 379.
- (1971) J Mol Biol , vol.55 , pp. 379
- Lee, B.¹ Richards, F.M.²

6
- 0025017318
- R. H. Wood, P. T. Thompson, Proc Natl Acad Sci USA 1990, 87, 946.
- (1990) Proc Natl Acad Sci USA , vol.87 , pp. 946
- Wood, R.H.¹ Thompson, P.T.²

7
- 0027092952
- I. Tunon, E. Silla, J. L. Pascual-Ahuir, Protein Eng 1992, 5, 715.
- (1992) Protein Eng , vol.5 , pp. 715
- Tunon, I.¹ Silla, E.² Pascual-Ahuir, J.L.³

8
- 0000831520
- T. Simonson, A. T. Brünger, J Phys Chem 1994, 98, 4683.
- (1994) J Phys Chem , vol.98 , pp. 4683
- Simonson, T.¹ Brünger, A.T.²

9
- 0011960339
- K. Lum, D. Chandler, J. D. Weeks, J Phys Chem B 1999, 103, 4570.
- (1999) J Phys Chem B , vol.103 , pp. 4570
- Lum, K.¹ Chandler, D.² Weeks, J.D.³

10
- 33744822783
- J. Wagoner, N. Baker, Proc Natl Acad Sci (USA) 2006, 103, 8331.
- (2006) Proc Natl Acad Sci (USA) , vol.103 , pp. 8331
- Wagoner, J.¹ Baker, N.²

11
- 0015866154
- A. Shrake, J. A. Rupley, J Mol Biol 1973, 79, 351.
- (1973) J Mol Biol , vol.79 , pp. 351
- Shrake, A.¹ Rupley, J.A.²

12
- 84912079256
- S. M. Legrand, K. M. Merz, J Comp Chem 1993, 14, 349.
- (1993) J Comp Chem , vol.14 , pp. 349
- Legrand, S.M.¹ Merz, K.M.²

13
- 84986519265
- H. Wang, C. Levinthal, J Comp Chem 1991, 12, 868.
- (1991) J Comp Chem , vol.12 , pp. 868
- Wang, H.¹ Levinthal, C.²

14
- 0036612947
- N. Futamura, S. Alura, D. Ranjan, B. Hariharan, IEEE Trans Parallel Dist Syst 2004, 13, 544.
- (2004) IEEE Trans Parallel Dist Syst , vol.13 , pp. 544
- Futamura, N.¹ Alura, S.² Ranjan, D.³ Hariharan, B.⁴

15
- 0345268014
- J. S. Rowlinson, Mol Phys 1963, 6, 517.
- (1963) Mol Phys , vol.6 , pp. 517
- Rowlinson, J.S.¹

16
- 0345699551
- R. Pavani, G. Ranghino, Comput Chem 1982, 6, 133.
- (1982) Comput Chem , vol.6 , pp. 133
- Pavani, R.¹ Ranghino, G.²

17
- 0020799931
- A. Gavezzotti, J Am Chem Soc 1983, 105, 5220.
- (1983) J Am Chem Soc , vol.105 , pp. 5220
- Gavezzotti, A.¹

18
- 77951214658
- M. Till, G. M. Ullmann, J Mol Model 2010, 16, 419.
- (2010) J Mol Model , vol.16 , pp. 419
- Till, M.¹ Ullmann, G.M.²

19
- 0001018540
- S. J. Wodak, J. Janin, Proc Natl Acad Sci USA 1980, 77, 1736.
- (1980) Proc Natl Acad Sci USA , vol.77 , pp. 1736
- Wodak, S.J.¹ Janin, J.²

20
- 0001308921
- W. Hasel, T. F. Hendrikson, W. C. Still, Tetrahed Comp Method 1988, 1, 103.
- (1988) Tetrahed Comp Method , vol.1 , pp. 103
- Hasel, W.¹ Hendrikson, T.F.² Still, W.C.³

21
- 0042121261
- L. Cavallo, J. K., F. Fraternali, Nucl Acids Res 2003, 31, 3364.
- (2003) Nucl Acids Res , vol.31 , pp. 3364
- Cavallo, L.¹ Fraternali, F.²

22
- 85171394526
- A. G. Street, S. L. Mayo, Folding Des 1998, 3, 253.
- (1998) Folding des , vol.3 , pp. 253
- Street, A.G.¹ Mayo, S.L.²

23
- 0000408363
- J. Weiser, P. S. Shenkin, W. C. Still, J Comp Chem 1999, 20, 217.
- (1999) J Comp Chem , vol.20 , pp. 217
- Weiser, J.¹ Shenkin, P.S.² Still, W.C.³

24
- 64749108343
- D. Dynerman, E. Butzlaff, J. Mitchell, J Comput Biol 2009, 16, 523.
- (2009) J Comput Biol , vol.16 , pp. 523
- Dynerman, D.¹ Butzlaff, E.² Mitchell, J.³

25
- 0021755764
- T. J. Richmond, J Mol Biol 1984, 178, 63.
- (1984) J Mol Biol , vol.178 , pp. 63
- Richmond, T.J.¹

26
- 33845377446
- M. L. Connolly, J Am Chem Soc 1985, 107, 1118.
- (1985) J Am Chem Soc , vol.107 , pp. 1118
- Connolly, M.L.¹

27
- 22544446558
- L. R. Dodd, D. N. Theodorou, Mol Phys 1991, 72, 1313.
- (1991) Mol Phys , vol.72 , pp. 1313
- Dodd, L.R.¹ Theodorou, D.N.²

28
- 84986431702
- M. Petitjean, J Comp Chem 1994, 15, 507.
- (1994) J Comp Chem , vol.15 , pp. 507
- Petitjean, M.¹

29
- 0030289081
- M. Irisa, Comp Phys Comm 1996, 98, 317.
- (1996) Comp Phys Comm , vol.98 , pp. 317
- Irisa, M.¹

30
- 0000280208
- K. D. Gibson, H. A. Scheraga, Mol Phys 1987, 62, 1247.
- (1987) Mol Phys , vol.62 , pp. 1247
- Gibson, K.D.¹ Scheraga, H.A.²

31
- 0000410978
- K. W. Kratky, J Phys A: Math Gen 1978, 11, 1017.
- (1978) J Phys A: Math Gen , vol.11 , pp. 1017
- Kratky, K.W.¹

32
- 51249162203
- H. Edelsbrunner, Discr Comput Geom, 1995, 13, 415.
- (1995) Discr Comput Geom , vol.13 , pp. 415
- Edelsbrunner, H.¹

33
- 84986533794
- C. E. Kundrot, J. W. Ponder, F. M. Richards, J Comp Chem 1991, 12, 402.
- (1991) J Comp Chem , vol.12 , pp. 402
- Kundrot, C.E.¹ Ponder, J.W.² Richards, F.M.³

34
- 84986523908
- V. Gogonea, E. Osawa, J Mol Struct 1994, 311, 305.
- (1994) J Mol Struct , vol.311 , pp. 305
- Gogonea, V.¹ Osawa, E.²

35
- 84986531697
- V. Gogonea, E. Osawa, J Comp Chem 1995, 16, 817.
- (1995) J Comp Chem , vol.16 , pp. 817
- Gogonea, V.¹ Osawa, E.²

36
- 84962430704
- M. Cossi, B. Mennucci, R. Cammi, J Comp Chem 1996, 17, 57.
- (1996) J Comp Chem , vol.17 , pp. 57
- Cossi, M.¹ Mennucci, B.² Cammi, R.³

37
- 84986462300
- G. Perrot, B. Cheng, K. D. Gibson, J. Vila, K. A. Palmer, A. Nayeem, B. Maigret, H. A. Scheraga, J Comp Chem 1992, 13, 1.
- (1992) J Comp Chem , vol.13 , pp. 1
- Perrot, G.¹ Cheng, B.² Gibson, K.D.³ Vila, J.⁴ Palmer, K.A.⁵ Nayeem, A.⁶ Maigret, B.⁷ Scheraga, H.A.⁸

38
- 84986534141
- S. Sridharan, A. Nicholls, K. A. Sharp, J Comp Chem 1994, 16, 1038.
- (1994) J Comp Chem , vol.16 , pp. 1038
- Sridharan, S.¹ Nicholls, A.² Sharp, K.A.³

39
- 21344481461
- R. J. Wawak, K. D. Gibson, H. A. Scheraga, J Math Chem 1994, 15, 207.
- (1994) J Math Chem , vol.15 , pp. 207
- Wawak, R.J.¹ Gibson, K.D.² Scheraga, H.A.³

40
- 0000747830
- J. A. Grant, B. T. Pickup, J Phys Chem 1995, 99, 3503.
- (1995) J Phys Chem , vol.99 , pp. 3503
- Grant, J.A.¹ Pickup, B.T.²

41
- 0009581180
- J. Weiser, P. S. Shenkin, W. C. Still, J Comp Chem 1999, 20, 688.
- (1999) J Comp Chem , vol.20 , pp. 688
- Weiser, J.¹ Shenkin, P.S.² Still, W.C.³

42
- 0033482642
- H. Edelsbrunner, Discr Comput Geom 1999, 21, 87.
- (1999) Discr Comput Geom , vol.21 , pp. 87
- Edelsbrunner, H.¹

43
- 0027053611
- D. Levitt, L. Banaszak, J Mol Graph 1992, 10, 229.
- (1992) J Mol Graph , vol.10 , pp. 229
- Levitt, D.¹ Banaszak, L.²

44
- 0031370977
- M. Hendlich, F. Rippmann, G. Barnickel, J Mol Graph Model 1997, 15, 359.
- (1997) J Mol Graph Model , vol.15 , pp. 359
- Hendlich, M.¹ Rippmann, F.² Barnickel, G.³

45
- 0037212102
- C. Venkatachalam, X. Jiang, T. Oldfield, M. Waldman, J Mol Graph Model 2003, 21, 289.
- (2003) J Mol Graph Model , vol.21 , pp. 289
- Venkatachalam, C.¹ Jiang, X.² Oldfield, T.³ Waldman, M.⁴

46
- 34547341277
- M. Weisel, E. Proschak, G. Schneider, Chem Central J 2007, 1, 7.
- (2007) Chem Central J , vol.1 , pp. 7
- Weisel, M.¹ Proschak, E.² Schneider, G.³

47
- 0028881975
- R. Laskowski, J Mol Graph 1995, 13, 323.
- (1995) J Mol Graph , vol.13 , pp. 323
- Laskowski, R.¹

48
- 0342424187
- G. Brady, P. Stouten, J Comput Aided Mol Des 2000, 14, 383.
- (2000) J Comput Aided Mol des , vol.14 , pp. 383
- Brady, G.¹ Stouten, P.²

49
- 34250831648
- T. Kawabata, N. Go, Proteins: Struct Funct Genet 2007, 68, 516.
- (2007) Proteins: Struct Funct Genet , vol.68 , pp. 516
- Kawabata, T.¹ Go, N.²

50
- 75249088440
- J. Yu, Y. Zhou, I. Tanaka, M. Yao, Bioinformatics 2010, 26, 46.
- (2010) Bioinformatics , vol.26 , pp. 46
- Yu, J.¹ Zhou, Y.² Tanaka, I.³ Yao, M.⁴

51
- 0002052671
- H. Edelsbrunner, M. A. Facello, J. Liang, Discr Appl Math 1998, 88, 83.
- (1998) Discr Appl Math , vol.88 , pp. 83
- Edelsbrunner, H.¹ Facello, M.A.² Liang, J.³

52
- 0031687653
- J. Liang, H. Edelsbrunner, C. Woodward, Prot Sci 1998, 7, 1884.
- (1998) Prot Sci , vol.7 , pp. 1884
- Liang, J.¹ Edelsbrunner, H.² Woodward, C.³

53
- 48449083056
- E. Yaffe, D. Fishelovitch, H. Wolfson, D. Halperin, R. Nussinov, Nucl Acids Res 2008, 36, W210.
- (2008) Nucl Acids Res , vol.36
- Yaffe, E.¹ Fishelovitch, D.² Wolfson, H.³ Halperin, D.⁴ Nussinov, R.⁵

54
- 59849101376
- J. Busa, S. Hayryan, C.-K. Hu, J. Skrivanek, M.-C. Wu, J Comp Chem 2009, 30, 346.
- (2009) J Comp Chem , vol.30 , pp. 346
- Busa, J.¹ Hayryan, S.² Hu, C.-K.³ Skrivanek, J.⁴ Wu, M.-C.⁵

55
- 0037418171
- H. Edelsbrunner, P. Koehl, Proc Natl Acad Sci USA 2003, 100, 2203.
- (2003) Proc Natl Acad Sci USA , vol.100 , pp. 2203
- Edelsbrunner, H.¹ Koehl, P.²

56
- 80052027313
- R. Bryant, H. Edelsbrunner, P. Koehl, M. Levitt, Discr Comput Geom 2004.
- (2004) Discr Comput Geom
- Bryant, R.¹ Edelsbrunner, H.² Koehl, P.³ Levitt, M.⁴

57
- 39749166769
- H. Edelsbrunner, P. Koehl, Discr Comput Geom 2005, 52, 243.
- (2005) Discr Comput Geom , vol.52 , pp. 243
- Edelsbrunner, H.¹ Koehl, P.²

58
- 33747818007
- J. Dundas, Z. Ouyang, J. Tseng, A. Binkowski, Y. Turpaz, J. Liang, Nucl Acids Res 2006, 34, W116.
- (2006) Nucl Acids Res , vol.34
- Dundas, J.¹ Ouyang, Z.² Tseng, J.³ Binkowski, A.⁴ Turpaz, Y.⁵ Liang, J.⁶

59
- 0001805469
- D. Naiman, H. Wynn, Ann Stat 1992, 43.
- (1992) Ann Stat , pp. 43
- Naiman, D.¹ Wynn, H.²

60
- 0025214884
- H. Edelsbrunner, E. P. Mücke, ACM Trans Graphics, 1990, 9, 66.
- (1990) ACM Trans Graphics , vol.9 , pp. 66
- Edelsbrunner, H.¹ Mücke, E.P.²

61
- 33846798193
- D. Attali, H. Edelsbrunner, Discr Comput Geom 2007, 37, 59.
- (2007) Discr Comput Geom , vol.37 , pp. 59
- Attali, D.¹ Edelsbrunner, H.²

62
- 0028259338
- H. Edelsbrunner, E. P. Mücke, ACM Trans Graphics 1994, 13, 43.
- (1994) ACM Trans Graphics , vol.13 , pp. 43
- Edelsbrunner, H.¹ Mücke, E.P.²

63
- 0000670028
- H. Edelsbrunner, N. R. Shah, Algorithmica 1996, 15, 223.
- (1996) Algorithmica , vol.15 , pp. 223
- Edelsbrunner, H.¹ Shah, N.R.²

64
- 0005904188
- University of Illinois, Urbana, Illinois.
- H. Edelsbrunner, Weighted alpha shapes, Technical Report UIUC-CS-R-92-1760, University of Illinois, Urbana, Illinois, 1992.
- (1992) Weighted Alpha Shapes, Technical Report UIUC-CS-R-92-1760
- Edelsbrunner, H.¹

65
- 58149182734
- M. Carrillo-Tripp, C. Shephered, I. Borelli, S. Venkataram, G. Lander, P. Natarajan, J. Johnson, III, C. B., and, V. Reddy, Nucl Acids Res 2009, 37, D436.
- (2009) Nucl Acids Res , vol.37
- Carrillo-Tripp, M.¹ Shephered, C.² Borelli, I.³ Venkataram, S.⁴ Lander, G.⁵ Natarajan, P.⁶ Reddy, V.⁷

66
- 0036827856
- W. Zhang, S. Mukhopadhyay, S. Pletnev, T. Baker, R. Kuhn, M. Rossmann, J Virol 2002, 76, 11645.
- (2002) J Virol , vol.76 , pp. 11645
- Zhang, W.¹ Mukhopadhyay, S.² Pletnev, S.³ Baker, T.⁴ Kuhn, R.⁵ Rossmann, M.⁶

67
- 0038714810
- In.
- N. Amenta, S. Choi, G. Rote, In Proceedings of the 19th ACM Symposium Computational Geometry, 211, 2003.
- (2003) Proceedings of the 19th ACM Symposium Computational Geometry , pp. 211
- Amenta, N.¹ Choi, S.² Rote, G.³

68
- 47849083143
- Y. Liu, J. Snoeyink, Discr Comput Geom 2005, 52, 439.
- (2005) Discr Comput Geom , vol.52 , pp. 439
- Liu, Y.¹ Snoeyink, J.²

69
- 0030188659
- S. Fortune, C. J. VanWyk, ACM Trans Graph 1996, 15, 223.
- (1996) ACM Trans Graph , vol.15 , pp. 223
- Fortune, S.¹ Vanwyk, C.J.²

70
- 0035827346
- P. Cramer, D. A. Bushnell, R. D. Kornberg, Science 2001, 292, 1863.
- (2001) Science , vol.292 , pp. 1863
- Cramer, P.¹ Bushnell, D.A.² Kornberg, R.D.³

71
- 0034699518
- B. T. Wimberly, D. E. Brodersen, W. M. Clemons Jr., R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T. Hartsch, V. Ramakrishnan, Nature (London) 2000, 407, 327.
- (2000) Nature (London) , vol.407 , pp. 327
- Wimberly, B.T.¹ Brodersen, D.E.² Clemons Jr., W.M.³ Morgan-Warren, R.J.⁴ Carter, A.P.⁵ Vonrhein, C.⁶ Hartsch, T.⁷ Ramakrishnan, V.⁸

72
- 0034637111
- N. Ban, P. Nissen, J. Hansen, P. B. Moore, T. A. Steitz, Science 2002, 289, 905.
- (2002) Science , vol.289 , pp. 905
- Ban, N.¹ Nissen, P.² Hansen, J.³ Moore, P.B.⁴ Steitz, T.A.⁵

73
- 0031623775
- In.
- J. Shewchuk, In Proceedings of the 14th Annual Symposiun Computational Geometry, 1998, 86.
- (1998) Proceedings of the 14th Annual Symposiun Computational Geometry , pp. 86
- Shewchuk, J.¹

74
- 5244231127
- K. D. Gibson, H. A. Scheraga, Mol Phys 1988, 64, 641.
- (1988) Mol Phys , vol.64 , pp. 641
- Gibson, K.D.¹ Scheraga, H.A.²

75
- 85045620777
- University of Illinois, Urbana, Illinois.
- H. Edelsbrunner, P. Fu, Measuring space filling diagrams and voids, Technical Report UIUC-BI-MB-94-01, University of Illinois, Urbana, Illinois, 1994.
- (1994) Measuring Space Filling Diagrams and Voids, Technical Report UIUC-BI-MB-94-01
- Edelsbrunner, H.¹ Fu, P.²

76
- 0344752604
- J. Lee, J Korea Soc Math Educ Ser B: Pure Appl Math, 1997, 4, 1.
- (1997) J Korea Soc Math Educ ser B: Pure Appl Math , vol.4 , pp. 1
- Lee, J.¹

77
- 80052029795
- International Center for Theoretical Physics, Trieste, Italy.
- L. Yang, J. Zhang, Metric equations in geometry and their applications, Technical Report IC/89/281, International Center for Theoretical Physics, Trieste, Italy, 1989.
- (1989) Metric Equations in Geometry and Their Applications, Technical Report IC/89/281
- Yang, L.¹ Zhang, J.²

78
- 38549121758
- In.
- L. Yang, Z. Zeng, In, F. Botana, T. Recio, Proc. ADG2006, LNAI 4869, 2007, 203.
- (2007) Proc. ADG2006, LNAI 4869 , pp. 203
- Yang, L.¹ Zeng, Z.² Botana, F.³ Recio, T.⁴

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