-
1
-
-
0015222647
-
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
-
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
-
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
-
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
-
5
-
-
60149104606
-
Signatures of protein-DNA recognition in free DNA binding sites
-
Locasale JW, Napoli AA, Chen S, Berman HM, Lawson CL (2009) Signatures of protein-DNA recognition in free DNA binding sites. J Mol Biol 386: 1054-1065.
-
(2009)
J Mol Biol
, vol.386
, pp. 1054-1065
-
-
Locasale, J.W.1
Napoli, A.A.2
Chen, S.3
Berman, H.M.4
Lawson, C.L.5
-
6
-
-
0038174853
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
32
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
-
33
-
-
0032189626
-
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
-
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
|