-
1
-
-
29144482496
-
Comprehensive identification of "druggable" protein ligand binding sites
-
An, J.H. et al. (2004) Comprehensive identification of "druggable" protein ligand binding sites. Genome Informatics, 15, 31-41.
-
(2004)
Genome Informatics
, vol.15
, pp. 31-41
-
-
An, J.H.1
-
2
-
-
22444434743
-
Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interface
-
Ben-Shimon, A. and Eisenstein, M. (2005) Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interface. J. Mol. Biol., 351, 309-326.
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 309-326
-
-
Ben-Shimon, A.1
Eisenstein, M.2
-
3
-
-
0024566942
-
New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
-
Boobbyer, D.N.A. et al. (1989) New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J. Med. Chem., 32, 1083-1094.
-
(1989)
J. Med. Chem.
, vol.32
, pp. 1083-1094
-
-
Boobbyer, D.N.A.1
-
4
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady, G.P. et al. (2000) Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aid. Mol. Des., 14, 383-401.
-
(2000)
J. Comput. Aid. Mol. Des.
, vol.14
, pp. 383-401
-
-
Brady, G.P.1
-
5
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly, M.L. (1983) Analytical molecular surface calculation. J. Appl. Cryst., 16, 548-558.
-
(1983)
J. Appl. Cryst.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
6
-
-
75249098178
-
-
PyMOL Molecular Graphics System
-
Delano, W. (2009) PyMOL Molecular Graphics System. http://www.pymol.org/.
-
(2009)
-
-
Delano, W.1
-
7
-
-
51249162203
-
The union of balls and its dual shape
-
Edelsbrunner, H. (1995) The union of balls and its dual shape. Discrete Comput. Geom., 3, 415-440.
-
(1995)
Discrete Comput. Geom.
, vol.3
, pp. 415-440
-
-
Edelsbrunner, H.1
-
8
-
-
0028259338
-
Three-dimensional alpha shapes
-
Edelsbrunner, H. and Mucke, E.P. (1994) Three-dimensional alpha shapes. ACM T Graphic, 13, 43-72.
-
(1994)
ACM T Graphic
, vol.13
, pp. 43-72
-
-
Edelsbrunner, H.1
Mucke, E.P.2
-
9
-
-
0000670028
-
Incremental topological flipping works for regular triangulations
-
Edelsbrunner, H. and Shah, N.R. (1996) Incremental topological flipping works for regular triangulations. Algorithmica, 15, 223-241.
-
(1996)
Algorithmica
, vol.15
, pp. 223-241
-
-
Edelsbrunner, H.1
Shah, N.R.2
-
11
-
-
0030310298
-
On the definition and the construction of pockets in macromolecules
-
Hunter, L. and Klein, T. (eds). World Scientific Publishing, Singapore
-
Edelsbrunner, H. et al. (1996) On the definition and the construction of pockets in macromolecules. In Hunter, L. and Klein, T. (eds). Biocomputing: Proceedings of the 1996 Pacific Symposium. World Scientific Publishing, Singapore, pp. 272-281.
-
(1996)
Biocomputing: Proceedings of the 1996 Pacific Symposium
, pp. 272-281
-
-
Edelsbrunner, H.1
-
12
-
-
12944257228
-
The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB Structures
-
Glaser, F. et al. (2005) The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB Structures. Proteins, 58, 610-617.
-
(2005)
Proteins
, vol.58
, pp. 610-617
-
-
Glaser, F.1
-
13
-
-
0021871375
-
Acomputational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford, P.J. (1985)Acomputational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med.. Chem., 28, 849-857.
-
(1985)
J. Med. Chem.
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
14
-
-
0031370977
-
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
-
Hendlich, M. et al. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model., 15, 359-363.
-
(1997)
J. Mol. Graph. Model.
, vol.15
, pp. 359-363
-
-
Hendlich, M.1
-
15
-
-
33750029942
-
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation
-
Huang, B.D. and Schroder, M. (2006) LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol., 6, 19-29.
-
(2006)
BMC Struct. Biol.
, vol.6
, pp. 19-29
-
-
Huang, B.D.1
Schroder, M.2
-
16
-
-
34250831648
-
Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
-
Kawabata, T. and Go, N. (2007) Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Proteins, 68, 516-529.
-
(2007)
Proteins
, vol.68
, pp. 516-529
-
-
Kawabata, T.1
Go, N.2
-
17
-
-
0028881975
-
SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions
-
Laskowski, R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions. J. Mol. Graph., 13, 323-330.
-
(1995)
J. Mol. Graph.
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
18
-
-
18744394070
-
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
-
Laurie, A.T.R. and Jackson, R.M. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-1916.
-
(2005)
Bioinformatics
, vol.21
, pp. 1908-1916
-
-
Laurie, A.T.R.1
Jackson, R.M.2
-
19
-
-
0027053611
-
POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
-
Levitt, D.J and Banaszak, L.G. (1992) POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph., 10, 229-234.
-
(1992)
J. Mol. Graph.
, vol.10
, pp. 229-234
-
-
Levitt, D.J.1
Banaszak, L.G.2
-
20
-
-
0031687653
-
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design
-
Liang, J. et al. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884-1897.
-
(1998)
Protein Sci.
, vol.7
, pp. 1884-1897
-
-
Liang, J.1
-
21
-
-
13444256512
-
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
-
Shin, J.M. and Cho, D.H. (2005) PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. Nucleic Acids Res, 33, 238-241.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 238-241
-
-
Shin, J.M.1
Cho, D.H.2
-
22
-
-
34247265436
-
Use of amino acid composition to predict ligand-binding sites
-
Soga, S. et al. (2007) Use of amino acid composition to predict ligand-binding sites. J. Chem. Inf. Model., 47, 400-406.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 400-406
-
-
Soga, S.1
-
23
-
-
0003557270
-
-
Chapter 5, Border tracing, 2nd edn. Pws Pub Co
-
Sonka, M. et al. (1998) Image Processing, Analysis, and Machine Vision. Chapter 5, Border tracing, 2nd edn. Pws Pub Co., pp. 142.
-
(1998)
Image Processing, Analysis, and Machine Vision
, pp. 142
-
-
Sonka, M.1
-
24
-
-
0037212102
-
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
-
Venkatachalam, C.M. et al. (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model., 21, 289-307.
-
(2003)
J. Mol. Graph. Model.
, vol.21
, pp. 289-307
-
-
Venkatachalam, C.M.1
-
25
-
-
0027510004
-
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
-
Wade, R.C. and Goodford, P.J. (1993) Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J. Med. Chem., 36, 148-156.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 148-156
-
-
Wade, R.C.1
Goodford, P.J.2
-
26
-
-
0027439587
-
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
-
Wade, R.C. et al. (1993). Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J. Med. Chem., 36, 140-147.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 140-147
-
-
Wade, R.C.1
-
27
-
-
34547341277
-
PocketPicker: analysis of ligand binding-sites with shape descriptors
-
Weisel, M. et al. (2007) PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem. Central J., 1, 7-23.
-
(2007)
Chem. Central J.
, vol.1
, pp. 7-23
-
-
Weisel, M.1
-
28
-
-
48449083056
-
MolAxis: a server for indentification of channels in macromolecules
-
Yaffe, E. et al. (2008) MolAxis: a server for indentification of channels in macromolecules. Nucleic Acids Res., 36, 210 215.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 210-215
-
-
Yaffe, E.1
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