-
1
-
-
0242720595
-
The PDB is a covering set of small protein structures
-
Kihara, D.; Skolnick, J. The PDB is a covering set of small protein structures. J. Mol. Biol., 2003, 334, 793-802.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 793-802
-
-
Kihara, D.1
Skolnick, J.2
-
2
-
-
0031715982
-
Protein structure alignment by in-cremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I.N.; Bourne, P.E. Protein structure alignment by in-cremental combinatorial extension (CE) of the optimal path. Prot. Eng., 1998, 11, 739-747.
-
(1998)
Prot. Eng
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
3
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm, L.; Sander, C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 1993, 233, 123-38.
-
(1993)
J. Mol. Biol
, vol.233
, pp. 123-38
-
-
Holm, L.1
Sander, C.2
-
4
-
-
0029061843
-
Comparison of spatial arrangements of secondary structural elements in proteins
-
Mizuguchi, K.; Go, N. Comparison of spatial arrangements of secondary structural elements in proteins. Prot. Eng., 1995, 8, 353-362.
-
(1995)
Prot. Eng
, vol.8
, pp. 353-362
-
-
Mizuguchi, K.1
Go, N.2
-
5
-
-
12944249776
-
A discussion of the solution for the best rotation to relate two sets of vectors
-
Kabsch, W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cryst., 1978, A34, 827-828.
-
(1978)
Acta Cryst
, vol.A34
, pp. 827-828
-
-
Kabsch, W.1
-
6
-
-
0029164708
-
Seeking significance in three-dimensional protein structure comparisons
-
Mizuguchi, K.; Go, N. Seeking significance in three-dimensional protein structure comparisons. Curr. Opin. Struct. Biol., 1995, 5, 377-382.
-
(1995)
Curr. Opin. Struct. Biol
, vol.5
, pp. 377-382
-
-
Mizuguchi, K.1
Go, N.2
-
7
-
-
33744805069
-
Protein structure comparison,implications for the nature of 'fold space', and structure and function prediction
-
Kolodny, R.; Petrey, D.; Honig, B. Protein structure comparison,implications for the nature of 'fold space', and structure and function prediction. Curr. Opin. Struct. Biol., 2006, 16, 393-398.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 393-398
-
-
Kolodny, R.1
Petrey, D.2
Honig, B.3
-
8
-
-
34250830250
-
Recent progress in measuring structural similarity be-tween proteins
-
Carugo, O. Recent progress in measuring structural similarity be-tween proteins. Curr. Prot. Pept. Sci., 2007, 8, 219-241.
-
(2007)
Curr. Prot. Pept. Sci
, vol.8
, pp. 219-241
-
-
Carugo, O.1
-
9
-
-
0037779312
-
3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition
-
Canterakis, N. 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. Proc.11th Scandinavian Conf. on Image Analysis, 1999, 85-93.
-
(1999)
Proc.11th Scandinavian Conf. On Image Analysis
, pp. 85-93
-
-
Canterakis, N.1
-
10
-
-
0038717852
-
3D Zernike descriptors for content based shape retrieval
-
Proceedings of the eighth ACM symposium on Solid modeling and applications
-
Novotni, M.; Klein, R.; 3D Zernike descriptors for content based shape retrieval. ACM Symposium on Solid and Physical Modeling, Proceedings of the eighth ACM symposium on Solid modeling and applications, 2003, 216-225.
-
(2003)
ACM Symposium On Solid and Physical Modeling
, pp. 216-225
-
-
Novotni, M.1
Klein, R.2
-
11
-
-
0015866154
-
Environment and exposure to solvent of protein atoms. Lysozyme and insulin
-
Shrake, A.; Rupley, J.A. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol., 1973, 79, 351-371.
-
(1973)
J. Mol. Biol
, vol.79
, pp. 351-371
-
-
Shrake, A.1
Rupley, J.A.2
-
12
-
-
0015222647
-
The interpretation of protein structures, estimation of static accessibility
-
Lee, B.; Richards, F.M. The interpretation of protein structures, estimation of static accessibility. J. Mol. Biol., 1971, 55, 379-400.
-
(1971)
J. Mol. Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
13
-
-
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
-
14
-
-
0021107965
-
Solvent-accessible surfaces of proteins and nucleic acids
-
Connolly, M.L. Solvent-accessible surfaces of proteins and nucleic acids. Science, 1983, 221, 709-713.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
15
-
-
0034969649
-
Rapid atomic density methods for molecular shape characterization
-
Mitchell, J.C.; Kerr, R.; Ten Eyck, L.F. Rapid atomic density methods for molecular shape characterization. J. Mol. Graph. Model., 2001, 19, 325-390.
-
(2001)
J. Mol. Graph. Model
, vol.19
, pp. 325-390
-
-
Mitchell, J.C.1
Kerr, R.2
ten Eyck, L.F.3
-
16
-
-
14144254344
-
Identification of the ligand binding sites on the molecular surface of proteins
-
Kinoshita, K.; Nakamura, H. Identification of the ligand binding sites on the molecular surface of proteins. Prot. Sci., 2005, 14, 711-718.
-
(2005)
Prot. Sci
, vol.14
, pp. 711-718
-
-
Kinoshita, K.1
Nakamura, H.2
-
17
-
-
26444578248
-
Identifying similar surface patches on proteins using a spin-image surface representation
-
Identifying similar surface patches on proteins using a spin-image surface representation. Lecture Notes in Comp. Sci., 2005, 3537, 417-428.
-
(2005)
Lecture Notes In Comp. Sci
, vol.3537
, pp. 417-428
-
-
-
18
-
-
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, 2007, 71, 670-683.
-
(2007)
Proteins
, vol.71
, pp. 670-683
-
-
Li, B.1
Turuvekere, S.2
Agrawal, M.3
La, D.4
Ramani, K.5
Kihara, D.6
-
19
-
-
0034489092
-
Protein surface similarities, a survey of methods to describe and compare protein surfaces
-
Via, A.; Ferre, F.; Brannetti, B.; Helmer-Citterich, M. Protein surface similarities, a survey of methods to describe and compare protein surfaces. Cell Mol. Life Sci., 2000, 57, 1970-1977.
-
(2000)
Cell Mol. Life Sci
, vol.57
, pp. 1970-1977
-
-
Via, A.1
Ferre, F.2
Brannetti, B.3
Helmer-Citterich, M.4
-
20
-
-
84862297227
-
Protein surface representation and comparison, New approaches in structural proteomics
-
Edited by Chen J, Lonardi S. Boca Raton, Florida, USA, Chapman & Hall/CRC Press
-
Sael L.; Kihara, D. Protein surface representation and comparison, New approaches in structural proteomics. In Biological Data Mining. Edited by Chen J, Lonardi S. Boca Raton, Florida, USA, Chapman & Hall/CRC Press; 2009, 89-109.
-
(2009)
Biological Data Mining
, pp. 89-109
-
-
Sael, L.1
Kihara, D.2
-
21
-
-
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
-
22
-
-
70350697850
-
3D-SURFER, software for high-throughput protein surface comparison and analysis
-
La, D.; Esquivel-Rodriguez, 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-Rodriguez, J.2
Venkatraman, V.3
Li, B.4
Sael, L.5
Ueng, S.6
Ahrendt, S.7
Kihara, D.8
-
23
-
-
51349090017
-
Fast protein tertiary structure retrieval based on global surface shape similarity
-
Sael, L.; Li, B.; La, D.; Fang, Y.; Ramani, K.; Rustamov, R.; Ki-hara, D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins, 2008, 72, 1259-1273.
-
(2008)
Proteins
, vol.72
, pp. 1259-1273
-
-
Sael, L.1
Li, B.2
La, D.3
Fang, Y.4
Ramani, K.5
Rustamov, R.6
Ki-Hara, D.7
-
24
-
-
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. Protein, 2008, 73, 1-10.
-
(2008)
Protein
, vol.73
, pp. 1-10
-
-
Sael, L.1
La, D.2
Li, B.3
Rustamov, R.4
Kihara, D.5
-
25
-
-
40649089098
-
An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison
-
Mak, L.; Grandison, S.; Morris, R.J. An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. J. Mol. Graph. Model., 2007, 26, 1035-1045.
-
(2007)
J. Mol. Graph. Model
, vol.26
, pp. 1035-1045
-
-
Mak, L.1
Grandison, S.2
Morris, R.J.3
-
26
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol., 1990, 215, 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
27
-
-
0033824470
-
DaliLite workbench for protein structure comparison
-
Holm, L.; Park, J. DaliLite workbench for protein structure comparison. Bioinformatics, 2000, 16, 566-567.
-
(2000)
Bioinformatics
, vol.16
, pp. 566-567
-
-
Holm, L.1
Park, J.2
-
28
-
-
85089921422
-
Rotation invariant spherical harmonic representation of 3D shape descriptors
-
Kazhdan, M.; Funkhouser, T.; Rusinkiewicz, S. Rotation invariant spherical harmonic representation of 3D shape descriptors. Proc.of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing, 2003, 43, 156-164.
-
(2003)
Proc.of the 2003 Eurographics/ACM SIGGRAPH Symposium On Geometry Processing
, vol.43
, pp. 156-164
-
-
Kazhdan, M.1
Funkhouser, T.2
Rusinkiewicz, S.3
-
29
-
-
25144499619
-
A 3D Model Retrieval Method Using 2D Freehand Sketches
-
Berlin/Heidelberg, Springer
-
Jiantao, P.; Ramani, K. A 3D Model Retrieval Method Using 2D Freehand Sketches. In Computational Science -- ICCS 2005. Berlin/Heidelberg, Springer; 2005, 343-346.
-
(2005)
Computational Science -- ICCS 2005
, pp. 343-346
-
-
Jiantao, P.1
Ramani, K.2
-
30
-
-
84943377867
-
Effective similarity search on voxelized CAD objects
-
Kriegel, H.-P.; Kroger, P.; Mashael, Z.; Pfeifle, M.; Potke, M.; Seidl, S. Effective similarity search on voxelized CAD objects. Proc.of 8th international conference on database systems for advanced applications, 2003, 27-36.
-
(2003)
Proc.of 8th International Conference On Database Systems For Advanced Applications
, pp. 27-36
-
-
Kriegel, H.-P.1
Kroger, P.2
Mashael, Z.3
Pfeifle, M.4
Potke, M.5
Seidl, S.6
-
31
-
-
78650810394
-
Protein surface representation for application to comparing low-resolution protein structure data
-
Sael, L.; Kihara, D. Protein surface representation for application to comparing low-resolution protein structure data. BMC Bioinformatics, 2010, 11, S2.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Sael, L.1
Kihara, D.2
-
32
-
-
58149187899
-
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies
-
Cuff, A.L.; Sillitoe, I.; Lewis, T.; Redfern, O.C.; Garratt, R.; Thornton, J.; Orengo, C.A. The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res., 2009, 37, D310-D314.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cuff, A.L.1
Sillitoe, I.2
Lewis, T.3
Redfern, O.C.4
Garratt, R.5
Thornton, J.6
Orengo, C.A.7
-
33
-
-
38949092920
-
Protein structure fitting and refinement guided by cryo-EM density
-
Topf, M.; Lasker, K.; Webb, B.; Wolfson, H.; Chiu, W.; Sali, A. Protein structure fitting and refinement guided by cryo-EM density. Structure, 2008, 16, 295-307.
-
(2008)
Structure
, vol.16
, pp. 295-307
-
-
Topf, M.1
Lasker, K.2
Webb, B.3
Wolfson, H.4
Chiu, W.5
Sali, A.6
-
34
-
-
1942521664
-
Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization
-
Ceulemans, H.; Russell, R.B. Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. J. Mol. Biol., 2004, 338, 783-793.
-
(2004)
J. Mol. Biol
, vol.338
, pp. 783-793
-
-
Ceulemans, H.1
Russell, R.B.2
-
35
-
-
0033377664
-
EMAN, semiautomated software for high-resolution single-particle reconstructions
-
Ludtke, S.J.; Baldwin, P.R.; Chiu, W. EMAN, semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol., 1999, 128, 82-97.
-
(1999)
J. Struct. Biol
, vol.128
, pp. 82-97
-
-
Ludtke, S.J.1
Baldwin, P.R.2
Chiu, W.3
-
36
-
-
61749091910
-
The application of 3D Zernike moments for the description of model-free molecular structure, functional motion, and structural reliability
-
Grandison, S.; Roberts, C.; Morris, R.J. The application of 3D Zernike moments for the description of model-free molecular structure, functional motion, and structural reliability. J. Comput. Biol., 2009, 16, 487-500.
-
(2009)
J. Comput. Biol
, vol.16
, pp. 487-500
-
-
Grandison, S.1
Roberts, C.2
Morris, R.J.3
-
37
-
-
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, 2010, 78, 2007-2028.
-
(2010)
Proteins
, vol.78
, pp. 2007-2028
-
-
Chikhi, R.1
Sael, L.2
Kihara, D.3
-
38
-
-
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. Prot. Sci., 1998, 7, 1884-1897.
-
(1998)
Prot. Sci
, vol.7
, pp. 1884-1897
-
-
Liang, J.1
Edelsbrunner, H.2
Woodward, C.3
-
39
-
-
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
-
40
-
-
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
-
42
-
-
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
-
43
-
-
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
-
44
-
-
44949110143
-
Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions
-
Minai, R.; Matsuo, Y.; Onuki, H.; Hirota, H. Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions. Proteins, 2008, 72, 367-381.
-
(2008)
Proteins
, vol.72
, pp. 367-381
-
-
Minai, R.1
Matsuo, Y.2
Onuki, H.3
Hirota, H.4
-
45
-
-
77249086225
-
BSSF, a fingerprint based ultrafast binding site similarity search and function analysis server
-
Xiong, B.; Wu, J.; Burk, D.; Xue, M.; Jiang, H.; Shen, J. BSSF, a fingerprint based ultrafast binding site similarity search and function analysis server. BMC Bioinformatics, 2010, 11, 47.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 47
-
-
Xiong, B.1
Wu, J.2
Burk, D.3
Xue, M.4
Jiang, H.5
Shen, J.6
-
46
-
-
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. Discovery Bioinform. (IJKDB), 2010, 1, 32-47.
-
(2010)
Int. J. Knowl. Discovery Bioinform. (IJKDB)
, vol.1
, pp. 32-47
-
-
Sael, L.1
Kihara, D.2
-
47
-
-
33745890364
-
ESOM-Maps, tools for clustering, visualization, and classification with Emergent SOM
-
Dept.of Mathematics and Computer Sciece, Univeristy of Marburg
-
Ultsch, A. ESOM-Maps, tools for clustering, visualization, and classification with Emergent SOM. Technical report. Dept.of Mathematics and Computer Sciece, Univeristy of Marburg. 2005.
-
(2005)
Technical Report
-
-
Ultsch, A.1
-
48
-
-
24944572401
-
Maps for the visualization of high-dimensional data spaces
-
Ultsch, A. Maps for the visualization of high-dimensional data spaces. Proc.WSOM'03, 2003, 225-230.
-
(2003)
Proc.WSOM'03
, pp. 225-230
-
-
Ultsch, A.1
-
49
-
-
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 Bioin-formatics, 2009, 10, 407.
-
(2009)
BMC Bioin-formatics
, vol.10
, pp. 407
-
-
Venkatraman, V.1
Yang, Y.D.2
Sael, L.3
Kihara, D.4
-
50
-
-
0031247975
-
Geometric hashing, an overview
-
Wolfson, H.; Rigoutsos, I. Geometric hashing, an overview. IEEE Comput. Sci. Eng., 1997, 4, 10-21.
-
(1997)
IEEE Comput. Sci. Eng
, vol.4
, pp. 10-21
-
-
Wolfson, H.1
Rigoutsos, I.2
-
51
-
-
21644480883
-
Protein-Protein Docking Benchmark 2.0, an update
-
Mintseris, J.; Wiehe, K.; Pierce, B.; Anderson, R.; Chen, R.; Janin, J.; Weng, Z. Protein-Protein Docking Benchmark 2.0, an update. Proteins, 2005, 60, 214-216.
-
(2005)
Proteins
, vol.60
, pp. 214-216
-
-
Mintseris, J.1
Wiehe, K.2
Pierce, B.3
Anderson, R.4
Chen, R.5
Janin, J.6
Weng, Z.7
-
52
-
-
0038237369
-
Taking geometry to its edge, fast unbound rigid (and hinge-bent) docking
-
Schneidman-Duhovny, D.; Inbar, Y.; Polak, V.; Shatsky, M.; Halperin, I.; Benyamini, H.; Barzilai, A.; Dror, O.; Haspel, N.; Nussinov, R.; Wolfson, H.J. Taking geometry to its edge, fast unbound rigid (and hinge-bent) docking. Proteins, 2003, 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
Benyamini, H.6
Barzilai, A.7
Dror, O.8
Haspel, N.9
Nussinov, R.10
Wolfson, H.J.11
-
53
-
-
38549107118
-
Context shapes, Efficient complementary shape matching for protein-protein docking
-
Shentu, Z.; Al, H.M.; Bystroff, C.; Zaki, M.J. Context shapes, Efficient complementary shape matching for protein-protein docking. Proteins, 2008, 70, 1056-1073.
-
(2008)
Proteins
, vol.70
, pp. 1056-1073
-
-
Shentu, Z.1
Al, H.M.2
Bystroff, C.3
Zaki, M.J.4
|