-
1
-
-
33750247224
-
-
Bacardit,J. et al. (2004) Coordination number predication using learning classifier systems: Performance and interpretability In Proceedings of the 8th Anuual Conference on Genetic and Evolutionary Computation (GECCO 06). ACM Press, New York, pp. 247-254.
-
Bacardit,J. et al. (2004) Coordination number predication using learning classifier systems: Performance and interpretability In Proceedings of the 8th Anuual Conference on Genetic and Evolutionary Computation (GECCO 06). ACM Press, New York, pp. 247-254.
-
-
-
-
3
-
-
41349095151
-
-
Bacardit,J. (2004) Pittsburgh Genetics-Based Machine Learning in the Data mining era: Representations, generalization, and run-time. PhD Thesis. Ramon Llull University, Barcelona. Catalonia Spain.
-
Bacardit,J. (2004) Pittsburgh Genetics-Based Machine Learning in the Data mining era: Representations, generalization, and run-time. PhD Thesis. Ramon Llull University, Barcelona. Catalonia Spain.
-
-
-
-
4
-
-
0028500477
-
Iso-depth contour map of a molecular surface
-
Badel-chagnon,A. et al. (1994) "Iso-depth contour map" of a molecular surface. J. Mol. Graph, 12, 162-168, 193.
-
(1994)
J. Mol. Graph
, vol.12
, Issue.162-168
, pp. 193
-
-
Badel-chagnon, A.1
-
5
-
-
0036522644
-
A machine-learning strategy for protein analysis
-
Baldi,P. and Pollastri,G. (2002) A machine-learning strategy for protein analysis. IEEE Intel. Sys., 17, 28-35.
-
(2002)
IEEE Intel. Sys
, vol.17
, pp. 28-35
-
-
Baldi, P.1
Pollastri, G.2
-
6
-
-
0030381077
-
The quickhull algorithm for convex hulls
-
Barber,C.B. et al. (1996) The quickhull algorithm for convex hulls. ACM Trans. Math. Software, 22, 469-483.
-
(1996)
ACM Trans. Math. Software
, vol.22
, pp. 469-483
-
-
Barber, C.B.1
-
7
-
-
0347755642
-
-
Protherm, version 4.0: Thermodynamic database for proteins and mutants, Database issue, D120-D121
-
Bava,K.A. et al. (2004) Protherm, version 4.0: Thermodynamic database for proteins and mutants. Nucl. Acids Res., 32 (Database issue), D120-D121.
-
(2004)
Nucl. Acids Res
, vol.32
-
-
Bava, K.A.1
-
8
-
-
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 interfaces
-
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 interfaces. J. Mol. Biol., 351, 309-326.
-
(2005)
J. Mol. Biol
, vol.351
, pp. 309-326
-
-
Ben-shimon, A.1
Eisenstein, M.2
-
9
-
-
0033565815
-
Residue depth: A novel parameter for the analysis of protein structure and stability
-
Chakravarty,S. and Varadarajan,R. (1999) Residue depth: A novel parameter for the analysis of protein structure and stability. Structure, 7, 724-732.
-
(1999)
Structure
, vol.7
, pp. 724-732
-
-
Chakravarty, S.1
Varadarajan, R.2
-
10
-
-
34347406147
-
Cavity scaling: Automated refinement of cavity-aware motifs in protein function prediction
-
Chen,B.Y. et al. (2007) Cavity scaling: Automated refinement of cavity-aware motifs in protein function prediction. J. Bioinform. Comput. Biol., 5, 353-382.
-
(2007)
J. Bioinform. Comput. Biol
, vol.5
, pp. 353-382
-
-
Chen, B.Y.1
-
11
-
-
33748102999
-
Travel depth, a new shape descriptor for macromolecules: Application to ligand binding
-
Coleman,R.G. and Sharp,K.A. (2006) Travel depth, a new shape descriptor for macromolecules: Application to ligand binding. J. Mol. Biol., 362, 441-458.
-
(2006)
J. Mol. Biol
, vol.362
, pp. 441-458
-
-
Coleman, R.G.1
Sharp, K.A.2
-
13
-
-
33847073796
-
Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training
-
Dor,O. and Zhou,Y. (2007) Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins, 66, 838-845.
-
(2007)
Proteins
, vol.66
, pp. 838-845
-
-
Dor, O.1
Zhou, Y.2
-
15
-
-
33645312366
-
A consensus procedure improving solvent accessibility prediction
-
Gianese,G. and Pascarella,S. (2006) A consensus procedure improving solvent accessibility prediction. J. Comput. Chem., 27, 621-626.
-
(2006)
J. Comput. Chem
, vol.27
, pp. 621-626
-
-
Gianese, G.1
Pascarella, S.2
-
16
-
-
0032916868
-
Protherm: Thermodynamic database for proteins and mutants
-
Gromiha,M.M. et al. (1999) Protherm: Thermodynamic database for proteins and mutants. Nucl. Acids Res., 27, 286-288.
-
(1999)
Nucl. Acids Res
, vol.27
, pp. 286-288
-
-
Gromiha, M.M.1
-
17
-
-
14644400399
-
An amino acid has two sides: A new 2d measure provides a different view of solvent exposure
-
Hamelryck,T. (2005) An amino acid has two sides: A new 2d measure provides a different view of solvent exposure. Proteins, 59, 38-48.
-
(2005)
Proteins
, vol.59
, pp. 38-48
-
-
Hamelryck, T.1
-
18
-
-
0003463297
-
-
MIT Press, Cambridge, MA, pp
-
Holland,J.H. (1975) Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control and Artificial Intelligence. MIT Press, Cambridge, MA, pp. 313-329.
-
(1975)
Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control and Artificial Intelligence
, pp. 313-329
-
-
Holland, J.H.1
-
19
-
-
27744538237
-
Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups
-
Holmes,J.B. and Tsai,J. (2005) Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups. J. Mol. Biol., 354, 706-721.
-
(2005)
J. Mol. Biol
, vol.354
, pp. 706-721
-
-
Holmes, J.B.1
Tsai, J.2
-
20
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
-
(1993)
J. Mol. Biol
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
22
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
-
(1999)
J. Mol. Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
23
-
-
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
-
24
-
-
10844226577
-
Predicting absolute contact numbers of native protein structure from amino acid sequence
-
Kinjo,A.R. et al. (2005) Predicting absolute contact numbers of native protein structure from amino acid sequence. Proteins, 58 158-165.
-
(2005)
Proteins
, vol.58
, pp. 158-165
-
-
Kinjo, A.R.1
-
25
-
-
85164392958
-
A study of cross-validation and bootstrap for accuracy estimation and model selection
-
Mellish,C.S, ed, Morgan Kaufmann, Sa Mateo, pp
-
Kohavi,R. (1995) A study of cross-validation and bootstrap for accuracy estimation and model selection. In Mellish,C.S. (ed.) Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence Morgan Kaufmann, Sa Mateo, pp. 1137-1145.
-
(1995)
Proceedings of the Fourteenth International Joint Conference on Artificial Intelligence
, pp. 1137-1145
-
-
Kohavi, R.1
-
26
-
-
33644874615
-
Protherm and pronit: Thermodynamic databases for proteins and protein-nucleic acid interactions
-
Database issue, D204-D206
-
Kumar,M.D. et al. (2006) Protherm and pronit: Thermodynamic databases for proteins and protein-nucleic acid interactions. Nucl. Acids Res., 34 (Database issue), D204-D206.
-
(2006)
Nucl. Acids Res
, vol.34
-
-
Kumar, M.D.1
-
27
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee,B. and Richards,F.M. (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
-
28
-
-
33745728310
-
Shapes of antibody binding sites: Qualitative and quantitative analyses based on a geomorphic classification scheme
-
Lee,M. et al. (2006) Shapes of antibody binding sites: Qualitative and quantitative analyses based on a geomorphic classification scheme. J Org Chem, 71, 5082-5092.
-
(2006)
J Org Chem
, vol.71
, pp. 5082-5092
-
-
Lee, M.1
-
29
-
-
0034901412
-
Are proteins well-packed?
-
Liang,J. and Dill,K.A. (2001) Are proteins well-packed? Biophys. J. 81, 751-766.
-
(2001)
Biophys. J
, vol.81
, pp. 751-766
-
-
Liang, J.1
Dill, K.A.2
-
30
-
-
0034742954
-
Three-dimensional quantitative structure-activity relationship for several bioactive peptides searched by a convex hull-comparative molecular field analysis approach
-
Lin,T.H. and Lin,J.J. (2001) Three-dimensional quantitative structure-activity relationship for several bioactive peptides searched by a convex hull-comparative molecular field analysis approach. Comput. Chem., 25, 489-498.
-
(2001)
Comput. Chem
, vol.25
, pp. 489-498
-
-
Lin, T.H.1
Lin, J.J.2
-
31
-
-
0032932918
-
A comparative molecular field analysis study on several bioactive peptides using the alignment rules derived from identification of commonly exposed groups
-
Lin,T.H. et al. (1999) A comparative molecular field analysis study on several bioactive peptides using the alignment rules derived from identification of commonly exposed groups. Biochim Biophys Acta 1429, 476-485.
-
(1999)
Biochim Biophys Acta
, vol.1429
, pp. 476-485
-
-
Lin, T.H.1
-
32
-
-
34447506573
-
Fold recognition by concurrent use of solvent accessibility and residue depth
-
Liu,S. et al. (2007) Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins, 68, 636-645.
-
(2007)
Proteins
, vol.68
, pp. 636-645
-
-
Liu, S.1
-
33
-
-
0029489424
-
Segmentation of molecular surfaces based on their convex hull
-
IEEE Computer Society, Washington DC
-
Meier,R. et al. (1995) Segmentation of molecular surfaces based on their convex hull. ICIP 95: Proceedings of the 1995 International Conference on Image Processing. IEEE Computer Society, Washington DC, Vol. 3, pp. 552-555.
-
(1995)
ICIP 95: Proceedings of the 1995 International Conference on Image Processing
, vol.3
, pp. 552-555
-
-
Meier, R.1
-
34
-
-
0004146487
-
Simultaneous Statistical Inference
-
Springer-Verlag Inc, New York
-
Miller,R.G. (1981) Simultaneous Statistical Inference (Springer Series in Statistics). Springer-Verlag Inc., New York.
-
(1981)
Springer Series in Statistics
-
-
Miller, R.G.1
-
35
-
-
0035172128
-
Pdb-reprdb: A database of representative protein chains from the protein data bank (pdb)
-
Noguchi,T. et al. (2001) Pdb-reprdb: A database of representative protein chains from the protein data bank (pdb). Nuct. Acids Res, 29, 219-220.
-
(2001)
Nuct. Acids Res
, vol.29
, pp. 219-220
-
-
Noguchi, T.1
-
36
-
-
0037316590
-
Dpx: For the analysis of the protein core
-
Pintar,A. et al. (2003) Dpx: For the analysis of the protein core. Bionformatics, 19, 313-314.
-
(2003)
Bionformatics
, vol.19
, pp. 313-314
-
-
Pintar, A.1
-
37
-
-
0017453547
-
Convex hulls of finite sets of points in two and three dimensions
-
Preparata,F.P. and Hong,S.J. (1977) Convex hulls of finite sets of points in two and three dimensions. Commun. ACM, 20, 87-93.
-
(1977)
Commun. ACM
, vol.20
, pp. 87-93
-
-
Preparata, F.P.1
Hong, S.J.2
-
39
-
-
0028109886
-
Conservation and prediction of solvent accessibility in protein families
-
Rost,B. and Sander,C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226.
-
(1994)
Proteins
, vol.20
, pp. 216-226
-
-
Rost, B.1
Sander, C.2
-
40
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander,C. and Schneider,R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
41
-
-
41349102674
-
Prediction of topological contacts in proteins using learning classifier systems. Soft Computing, Special Issue on Evolutionary and Metaheuristic-based Data Mining (EMBDM)
-
in press
-
Stout,M. et al. (2008) Prediction of topological contacts in proteins using learning classifier systems. Soft Computing, Special Issue on Evolutionary and Metaheuristic-based Data Mining (EMBDM), (in press).
-
(2008)
-
-
Stout, M.1
-
42
-
-
16344394781
-
Sabmark - a benchmark for sequence alignment that covers the entire known fold space
-
Van Walle,I. et al. (2005) Sabmark - a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
-
(2005)
Bioinformatics
, vol.21
, pp. 1267-1268
-
-
Van Walle, I.1
-
43
-
-
23144454480
-
Cx, dpx and pride: www servers for the analysis and comparison of protein 3d structures
-
Web Server issue, W252-W254
-
Vlahovicek,K. et al. (2005) Cx, dpx and pride: www servers for the analysis and comparison of protein 3d structures. Nucl. Acids Res. 33 (Web Server issue), W252-W254.
-
(2005)
Nucl. Acids Res
, vol.33
-
-
Vlahovicek, K.1
-
44
-
-
33745858035
-
Automatic classification of protein structures based on convex hull representation by integrated neural network
-
Theory and Applications of Models of Computation, Third International Conference, TAMC} 2006, Beijing, China, May 15-20, Springer
-
Wang,Y. et al. (2006) Automatic classification of protein structures based on convex hull representation by integrated neural network. Theory and Applications of Models of Computation, Third International Conference, {TAMC} 2006, Beijing, China, May 15-20, 2006. Lecture Notes in Computer Science. Springer, Vol. 3959. pp. 505-514.
-
(2006)
Lecture Notes in Computer Science
, vol.3959
, pp. 505-514
-
-
Wang, Y.1
-
45
-
-
0003957032
-
Data Mining: Practical Machine Learning Tools and Techniques
-
Second Edition: , Morgan Kaufmann, Amsterdam, Boston, MA
-
Witten,I.H. and Frank,E. (2005) Data Mining: Practical Machine Learning Tools and Techniques. Second Edition: (The Morgan Kaufmann Series in Data Management Systems). Morgan Kaufmann, Amsterdam, Boston, MA.
-
(2005)
The Morgan Kaufmann Series in Data Management Systems
-
-
Witten, I.H.1
Frank, E.2
-
46
-
-
17844373552
-
Protein secondary structure prediction with dihedral angles
-
Wood,M.J. and Hirst,J.D. (2005) Protein secondary structure prediction with dihedral angles. Proteins, 59, 476-481.
-
(2005)
Proteins
, vol.59
, pp. 476-481
-
-
Wood, M.J.1
Hirst, J.D.2
|