-
1
-
-
34248155322
-
Function prediction of uncharacterized proteins
-
Hawkins, T.; Kihara, D. Function prediction of uncharacterized proteins. J. Bioinf. Comput. Biol. 2007, 5, 1-30.
-
(2007)
J. Bioinf. Comput. Biol
, vol.5
, pp. 1-30
-
-
Hawkins, T.1
Kihara, D.2
-
2
-
-
39449130713
-
New paradigm in protein function prediction for large scale omics analysis
-
Hawkins, T.; Chitale, M.; Kihara, D. New paradigm in protein function prediction for large scale omics analysis. Mol. BioSyst. 2008, 4, 223-231.
-
(2008)
Mol. BioSyst
, vol.4
, pp. 223-231
-
-
Hawkins, T.1
Chitale, M.2
Kihara, D.3
-
3
-
-
20444450051
-
Predicting protein function from sequence and structural data
-
Watson, J.D.; Laskowski, R.A.; Thornton, J.M. Predicting protein function from sequence and structural data. Curr. Opin. Struct. Biol. 2005, 15, 275-284.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 275-284
-
-
Watson, J.D.1
Laskowski, R.A.2
Thornton, J.M.3
-
4
-
-
20444456581
-
Automatic annotation of protein function
-
Valencia, A. Automatic annotation of protein function. Curr. Opin. Struct. Biol. 2005, 15, 267-74.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 267-274
-
-
Valencia, A.1
-
5
-
-
0033954256
-
The protein data bank
-
Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res. 2000, 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
6
-
-
31144467558
-
The impact of structural genomics: Expectations and outcomes
-
Chandonia, J.; Brenner, S.E. The impact of structural genomics: Expectations and outcomes. Science 2006, 311, 347-351.
-
(2006)
Science
, vol.311
, pp. 347-351
-
-
Chandonia, J.1
Brenner, S.E.2
-
7
-
-
67449108422
-
FINDSITE: A combined evolution/structure-based approach to protein function prediction
-
Skolnick, J.; Brylinski, M. FINDSITE: A combined evolution/structure-based approach to protein function prediction. Brief. Bioinform. 2009, 10, 378.
-
(2009)
Brief. Bioinform
, vol.10
, pp. 378
-
-
Skolnick, J.1
Brylinski, M.2
-
8
-
-
1842479856
-
Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q
-
Kihara, D.; Skolnick, J. Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins: Struct. Funct. Bioinf. 2004, 55, 464-473.
-
(2004)
Proteins: Struct. Funct. Bioinf
, vol.55
, pp. 464-473
-
-
Kihara, D.1
Skolnick, J.2
-
9
-
-
11844292002
-
Inference of protein function from protein structure
-
Pal, D.; Eisenberg, D. Inference of protein function from protein structure. Structure 2005, 13, 121-130.
-
(2005)
Structure
, vol.13
, pp. 121-130
-
-
Pal, D.1
Eisenberg, D.2
-
10
-
-
22244450719
-
Protein families and their evolution-A structural perspective
-
Orengo, C.A.; Thornton, J.M. Protein families and their evolution-A structural perspective. Biochemistry 2005, 74, 867-900.
-
(2005)
Biochemistry
, vol.74
, pp. 867-900
-
-
Orengo, C.A.1
Thornton, J.M.2
-
11
-
-
0028593509
-
Protein superfamilies and domain superfolds
-
Orengo, C.A.; Jones, D.T.; Thornton, J.M. Protein superfamilies and domain superfolds. Nature 1994, 372, 631-634.
-
(1994)
Nature
, vol.372
, pp. 631-634
-
-
Orengo, C.A.1
Jones, D.T.2
Thornton, J.M.3
-
12
-
-
34248185418
-
Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites
-
Ausiello, G.; Peluso, D.; Via, A.; Helmer-Citterish, M. Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics 2007, 8, S24.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 24
-
-
Ausiello, G.1
Peluso, D.2
Via, A.3
Helmer-Citterish, M.4
-
13
-
-
77953587057
-
Real-time ligand binding pocket database search using local surface descriptors
-
Chikhi, R.; Sael, L.; Kihara, D. Real-time ligand binding pocket database search using local surface descriptors. Proteins: Struct. Funct. Bioinf. 2010, 78, 2007-2028.
-
(2010)
Proteins: Struct. Funct. Bioinf
, vol.78
, pp. 2007-2028
-
-
Chikhi, R.1
Sael, L.2
Kihara, D.3
-
14
-
-
33947420139
-
Shape variation in protein binding pockets and their ligands
-
Kahraman, A.; Morris, R.J.; Laskowski, R.A.; Thornton, J.M. Shape variation in protein binding pockets and their ligands. J. Mol. Biol. 2007, 368, 283-301.
-
(2007)
J. Mol. Biol
, vol.368
, pp. 283-301
-
-
Kahraman, A.1
Morris, R.J.2
Laskowski, R.A.3
Thornton, J.M.4
-
15
-
-
0028881975
-
SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski, R.A. SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graphics 1995, 13, 323-330.
-
(1995)
J. Mol. Graphics
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
16
-
-
0027053611
-
POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
-
Levitt, D.G.; Banaszak, L.J. POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graphics 1992, 10, 229-234.
-
(1992)
J. Mol. Graphics
, vol.10
, pp. 229-234
-
-
Levitt, D.G.1
Banaszak, L.J.2
-
17
-
-
34250831648
-
Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
-
Kawabata, T.; Go, N. Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites. Proteins: Struct. Funct. Bioinf. 2007, 68, 516-529.
-
(2007)
Proteins: Struct. Funct. Bioinf
, vol.68
, pp. 516-529
-
-
Kawabata, T.1
Go, N.2
-
18
-
-
34547341277
-
PocketPicker: Analysis of ligand binding-sites with shape descriptors
-
Weisel, M.; Proschak, E.; Schneider, G. PocketPicker: Analysis of ligand binding-sites with shape descriptors. Chem. Cent. J. 2007, 1, 1-17.
-
(2007)
Chem. Cent. J
, vol.1
, pp. 1-17
-
-
Weisel, M.1
Proschak, E.2
Schneider, G.3
-
19
-
-
41149093109
-
Characterization of local geometry of protein surfaces with the visibility criterion
-
Li, B.; Turuvekere, S.; Agrawal, M.; La, D.; Ramani, K.; Kihara, D. Characterization of local geometry of protein surfaces with the visibility criterion. Proteins: Struct. Funct. Bioinf. 2008, 71, 670-683.
-
(2008)
Proteins: Struct. Funct. Bioinf
, vol.71
, pp. 670-683
-
-
Li, B.1
Turuvekere, S.2
Agrawal, M.3
La, D.4
Ramani, K.5
Kihara, D.6
-
20
-
-
37349061824
-
PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins
-
Kalidas, Y.; Chandra, N. PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins. J. Struct. Biol. 2008, 161, 31-42.
-
(2008)
J. Struct. Biol
, vol.161
, pp. 31-42
-
-
Kalidas, Y.1
Chandra, N.2
-
21
-
-
0031687653
-
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
-
Liang, J.; Edelsbrunner, H.; Woodward, C. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Sci. 1998, 7, 1884-1897.
-
(1998)
Protein Sci
, vol.7
, pp. 1884-1897
-
-
Liang, J.1
Edelsbrunner, H.2
Woodward, C.3
-
22
-
-
33750029942
-
LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
-
Huang, B.; Schroeder, M. LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 2006, 6, 19.
-
(2006)
BMC Struct. Biol
, vol.6
, pp. 19
-
-
Huang, B.1
Schroeder, M.2
-
23
-
-
61649106689
-
Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns
-
Tseng, Y.Y.; Dundas, J.; Liang, J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J. Mol. Biol. 2009, 387, 451-464.
-
(2009)
J. Mol. Biol
, vol.387
, pp. 451-464
-
-
Tseng, Y.Y.1
Dundas, J.2
Liang, J.3
-
24
-
-
0035965145
-
Prediction of functionally important residues based solely on the computed energetics of protein structure
-
Elcock, A.H. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 2001, 312, 885-896.
-
(2001)
J. Mol. Biol
, vol.312
, pp. 885-896
-
-
Elcock, A.H.1
-
25
-
-
18744394070
-
Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
-
Laurie, A.T.; Jackson, R.M. Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21, 1908.
-
(2005)
Bioinformatics
, vol.21
, pp. 1908
-
-
Laurie, A.T.1
Jackson, R.M.2
-
26
-
-
21044444449
-
Pocketome via comprehensive identification and classification of ligand binding envelopes
-
An, J.; Totrov, M.; Abagyan, R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteomics 2005, 4, 752.
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 752
-
-
An, J.1
Totrov, M.2
Abagyan, R.3
-
27
-
-
84862297227
-
Protein surface representation and comparison: New approaches in structural proteomics
-
Chen, J.Y., Lonardi, S., Eds.; Chapman & Hall/CRC Press: Boca Raton, FL, USA
-
Sael, L.; Kihara, D. Protein surface representation and comparison: New approaches in structural proteomics. In Biological Data Mining; Chen, J.Y., Lonardi, S., Eds.; Chapman & Hall/CRC Press: Boca Raton, FL, USA, 2009aa; pp. 89-109.
-
(2009)
Biological Data Mining
, pp. 89-109
-
-
Sael, L.1
Kihara, D.2
-
28
-
-
0345864027
-
The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
-
Porter, C.T.; Bartlett, G.J.; Thornton, J.M. The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res. 2004, 32,D129-D133.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Porter, C.T.1
Bartlett, G.J.2
Thornton, J.M.3
-
29
-
-
2442677781
-
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
-
Arakaki, A.K.; Zhang, Y.; Skolnick, J. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics 2004, 20, 1087-1096.
-
(2004)
Bioinformatics
, vol.20
, pp. 1087-1096
-
-
Arakaki, A.K.1
Zhang, Y.2
Skolnick, J.3
-
30
-
-
0346494936
-
SURFACE: A database of protein surface regions for functional annotation
-
Ferrè, F.; Ausiello, G.; Zanzoni, A.; Helmer-Citterich, M. SURFACE: A database of protein surface regions for functional annotation. Nucleic Acids Res. 2004, 32, D240-D244.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Ferrè, F.1
Ausiello, G.2
Zanzoni, A.3
Helmer-Citterich, M.4
-
31
-
-
29444457054
-
Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships
-
Gold, N.D.; Jackson, R.M. Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships. J. Mol. Biol. 2006, 355, 1112-1124.
-
(2006)
J. Mol. Biol
, vol.355
, pp. 1112-1124
-
-
Gold, N.D.1
Jackson, R.M.2
-
32
-
-
34547587452
-
Ef-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
-
Kinoshita, K.; Murakami, Y.; Nakamura, H. eF-seek: Prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res. 2007, 35, W398-W402.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kinoshita, K.1
Murakami, Y.2
Nakamura, H.3
-
33
-
-
19544389524
-
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
-
Morris, R.J.; Najmanovich, R.J.; Kahraman, A.; Thornton, J.M. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 2005, 21, 2347-2355.
-
(2005)
Bioinformatics
, vol.21
, pp. 2347-2355
-
-
Morris, R.J.1
Najmanovich, R.J.2
Kahraman, A.3
Thornton, J.M.4
-
34
-
-
77950423796
-
A. new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: Application to ligand prediction
-
Hoffmann, B.; Zaslavskiy, M.; Vert, J.; Stoven, V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: Application to ligand prediction. BMC Bioinformatics 2010, 11, 99.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 99
-
-
Hoffmann, B.1
Zaslavskiy, M.2
Vert, J.3
Stoven, V.4
-
35
-
-
0037779312
-
3D Zernike moments and zernike affine invariants for 3D image analysis and recognition
-
Kangerlussuaq, Greenland, June
-
Canterakis, N. 3D Zernike moments and zernike affine invariants for 3D image analysis and recognition. In 11th Scandinavian Conference on Image Analysis, Kangerlussuaq, Greenland, 7-11 June 1999.
-
(1999)
11th Scandinavian Conference on Image Analysis
, pp. 7-11
-
-
Canterakis, N.1
-
36
-
-
0000486194
-
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems
-
Baker, N.; Holst, M.; Wang, F. Adaptive multilevel finite element solution of the Poisson- Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. J. Comput. Chem. 2000, 21, 1343-1352.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1343-1352
-
-
Baker, N.1
Holst, M.2
Wang, F.3
-
37
-
-
0038717852
-
Proceedings of the eighth ACM symposium on solid modeling and applications
-
Seattle, Washington, DC, USA, June
-
Novotni, M.; Klein, R. Proceedings of the eighth ACM symposium on solid modeling and applications. In Proceedings of the Eighth ACM Symposium on Solid Modeling and Applications, Seattle, Washington, DC, USA, 16-20 June 2003; pp. 216-225.
-
(2003)
Proceedings of the Eighth ACM Symposium On Solid Modeling and Applications
, pp. 16-20
-
-
Novotni, M.1
Klein, R.2
-
38
-
-
68549104171
-
Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors
-
Venkatraman, V.; Sael, L.; Kihara, D. Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors. Cell Biochem. Biophys. 2009, 54, 23-32.
-
(2009)
Cell Biochem. Biophys
, vol.54
, pp. 23-32
-
-
Venkatraman, V.1
Sael, L.2
Kihara, D.3
-
39
-
-
78650849574
-
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking
-
accepted
-
Kihara, D.; Sael, L.; Chikhi, R.; Esquivel-Rodriguez, J. Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking. Curr. Protein Peptide Sci. 2010, accepted.
-
(2010)
Curr. Protein Peptide Sci
-
-
Kihara, D.1
Sael, L.2
Chikhi, R.3
Esquivel-Rodriguez, J.4
-
40
-
-
51349090017
-
Fast protein tertiary structure retrieval based on global surface shape similarity
-
Sael, L.; Li, B.; La, D.; Fang, Y.; Ramani, K.; Rustamov, R.; Kihara, D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins: Struct. Funct. Bioinf. 2008, 72, 1259-1273.
-
(2008)
Proteins: Struct. Funct. Bioinf
, vol.72
, pp. 1259-1273
-
-
Sael, L.1
Li, B.2
La, D.3
Fang, Y.4
Ramani, K.5
Rustamov, R.6
Kihara, D.7
-
41
-
-
70350697850
-
3D-SURFER: Software for high-throughput protein surface comparison and analysis
-
La, D.; Esquivel-Rodríguez, J.; Venkatraman, V.; Li, B.; Sael, L.; Ueng, S.; Ahrendt, S.; Kihara, D. 3D-SURFER: Software for high-throughput protein surface comparison and analysis. Bioinformatics 2009, 25, 2843-2844.
-
(2009)
Bioinformatics
, vol.25
, pp. 2843-2844
-
-
La, D.1
Esquivel-Rodríguez, J.2
Venkatraman, V.3
Li, B.4
Sael, L.5
Ueng, S.6
Ahrendt, S.7
Kihara, D.8
-
42
-
-
50849126111
-
Rapid comparison of properties on protein surface
-
Sael, L.; La, D.; Li, B.; Rustamov, R.; Kihara, D. Rapid comparison of properties on protein surface. Proteins: Struct. Funct. Bioinf. 2008, 73, 1-10.
-
(2008)
Proteins: Struct. Funct. Bioinf
, vol.73
, pp. 1-10
-
-
Sael, L.1
La, D.2
Li, B.3
Rustamov, R.4
Kihara, D.5
-
43
-
-
76749110379
-
Application of 3D Zernike descriptors to shape-based ligand similarity searching
-
Venkatraman, V.; Chakravarthy, P.R.; Kihara, D. Application of 3D Zernike descriptors to shape-based ligand similarity searching. J. Cheminformatics 2009, 1, 19.
-
(2009)
J. Cheminformatics
, vol.1
, pp. 19
-
-
Venkatraman, V.1
Chakravarthy, P.R.2
Kihara, D.3
-
44
-
-
74049092313
-
Protein-protein docking using region-based 3D Zernike descriptors
-
Venkatraman, V.; Yang, Y.D.; Sael, L.; Kihara, D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics 2009, 10, 407.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 407
-
-
Venkatraman, V.1
Yang, Y.D.2
Sael, L.3
Kihara, D.4
-
45
-
-
78650810394
-
Protein surface representation for application to comparing low-resolution protein structure data
-
in press
-
Sael, L.; Kihara, D. Protein surface representation for application to comparing low-resolution protein structure data. BMC Bioinformatics (GIW 2010 issue) 2010, in press.
-
(2010)
BMC Bioinformatics (GIW 2010 Issue)
-
-
Sael, L.1
Kihara, D.2
-
46
-
-
84934453083
-
Multi-item auctions
-
Demange, G.; Gale, D.; Sotomayor, M. Multi-item auctions. J. Polit. Economy 1986, 94,863-872.
-
(1986)
J. Polit. Economy
, vol.94
, pp. 863-872
-
-
Demange, G.1
Gale, D.2
Sotomayor, M.3
-
47
-
-
74049098905
-
Characterization and classification of local protein surfaces using self-organizing map
-
Sael, L.; Kihara, D. Characterization and classification of local protein surfaces using self-organizing map. Int. J. Knowl. Discov. Bioinformatics 2010, 1, 32-47.
-
(2010)
Int. J. Knowl. Discov. Bioinformatics
, vol.1
, pp. 32-47
-
-
Sael, L.1
Kihara, D.2
|