-
1
-
-
0022897983
-
A nonlinear measure of subalignment similarity and its significance levels
-
Altschul, S.F. and Erickson, B.W. 1986. A nonlinear measure of subalignment similarity and its significance levels. Bull. Math. Biol. 48: 617-632.
-
(1986)
Bull. Math. Biol.
, vol.48
, pp. 617-632
-
-
Altschul, S.F.1
Erickson, B.W.2
-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 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
-
3
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J.U., Luthy, R., and Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
4
-
-
84976668743
-
Finding all cliques of an undirected graph [H]
-
Bron, C. and Kerbosch, J. 1973. Finding all cliques of an undirected graph [H]. Commun. ACM. 16: 575-577.
-
(1973)
Commun. ACM
, vol.16
, pp. 575-577
-
-
Bron, C.1
Kerbosch, J.2
-
5
-
-
0030310317
-
Assessing the performance of fold recognition methods by means of a comprehensive benchmark
-
Fischer, D., Elofsson, A., Rice, D., and Eisenberg, D. 1996. Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac. Symp. Biocomput. 1996: 300-318.
-
(1996)
Pac. Symp. Biocomput.
, vol.1996
, pp. 300-318
-
-
Fischer, D.1
Elofsson, A.2
Rice, D.3
Eisenberg, D.4
-
6
-
-
0036840353
-
Analysis of protein sequence/structure similarity relationships
-
Gan, H.H., Perlow, R.A., Roy, S., Ko, J., Wu, M., Huang, J., Yan, S., Nicoletta, A., Vafai, J., Sun, D., et al. 2002. Analysis of protein sequence/structure similarity relationships. Biophys. J. 83: 2781-2791.
-
(2002)
Biophys. J.
, vol.83
, pp. 2781-2791
-
-
Gan, H.H.1
Perlow, R.A.2
Roy, S.3
Ko, J.4
Wu, M.5
Huang, J.6
Yan, S.7
Nicoletta, A.8
Vafai, J.9
Sun, D.10
-
7
-
-
0001969211
-
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
-
Gribskov, M. and Robinson, N.L. 1996. Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem. 20: 25-33.
-
(1996)
Comput. Chem.
, vol.20
, pp. 25-33
-
-
Gribskov, M.1
Robinson, N.L.2
-
8
-
-
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
-
9
-
-
0036081436
-
In search for more accurate alignments in the twilight zone
-
Jaroszewski, L., Li, W., and Godzik, A. 2002. In search for more accurate alignments in the twilight zone. Protein Sci. 11: 1702-1713.
-
(2002)
Protein Sci.
, vol.11
, pp. 1702-1713
-
-
Jaroszewski, L.1
Li, W.2
Godzik, A.3
-
10
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
11
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin, S. and Altschul, S.F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. 87: 2264-2268.
-
(1990)
Proc. Natl. Acad. Sci.
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
12
-
-
13444279981
-
Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
-
Kolodny, R., Koehl, P., and Levitt, M. 2005. Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J. Mol. Biol. 346: 1173-1188.
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 1173-1188
-
-
Kolodny, R.1
Koehl, P.2
Levitt, M.3
-
13
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14: 51-55.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wüthrich, K.3
-
14
-
-
0002192615
-
A combinatorial algorithm for calculating ligand-binding
-
Kuhl, F.S., Crippen, G.M., and Friesen, D.K. 1984. A combinatorial algorithm for calculating ligand-binding. J. Comp. Chem. 5: 24-34.
-
(1984)
J. Comp. Chem.
, vol.5
, pp. 24-34
-
-
Kuhl, F.S.1
Crippen, G.M.2
Friesen, D.K.3
-
15
-
-
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
-
16
-
-
0032568649
-
A unified statistical framework for sequence comparison and structure comparison
-
Levitt, M. and Gerstein, M. 1998. A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. 95: 5913-5920.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 5913-5920
-
-
Levitt, M.1
Gerstein, M.2
-
17
-
-
0029057126
-
Size-independent comparison of protein three-dimensional structures
-
Maiorov, V.N. and Crippen G.M. 1995. Size-independent comparison of protein three-dimensional structures. Proteins 22: 273-283.
-
(1995)
Proteins
, vol.22
, pp. 273-283
-
-
Maiorov, V.N.1
Crippen, G.M.2
-
18
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman, S.B. and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48: 443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
19
-
-
0033762915
-
Structural genomics programs at the US National Institute of General Medical Sciences
-
Norvell, J.C. and Machalek, A.Z. 2000. Structural genomics programs at the US National Institute of General Medical Sciences. Nat. Struct. Biol. S7: 931.
-
(2000)
Nat. Struct. Biol.
, vol.S7
, pp. 931
-
-
Norvell, J.C.1
Machalek, A.Z.2
-
20
-
-
0030777303
-
CATH: A hierarchic classification of protein domain structures
-
Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B., and Thornton, J.M. 1997. CATH: A hierarchic classification of protein domain structures. Structure 5: 1093-1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
21
-
-
0031564630
-
A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
-
Rice, D.W. and Eisenberg, D. 1997. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. J. Mol. Biol. 267: 1026-1038.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 1026-1038
-
-
Rice, D.W.1
Eisenberg, D.2
-
22
-
-
0025317502
-
Definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
-
Šali, A. and Blundell, T.L. 1990. Definition of general topological equivalence in protein structures: A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212: 403-428.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 403-428
-
-
Šali, A.1
Blundell, T.L.2
-
23
-
-
0347994105
-
FoldMiner: Structural motif discovery using an improved superposition algorithm
-
Shapiro, J. and Brutlag, D. 2004. FoldMiner: Structural motif discovery using an improved superposition algorithm. Protein Sci. 13: 278-294.
-
(2004)
Protein Sci.
, vol.13
, pp. 278-294
-
-
Shapiro, J.1
Brutlag, D.2
-
24
-
-
0035967880
-
FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
-
Shi, J., Blundell, T.L., and Mizuguchi, K. 2001. FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310: 243-257.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 243-257
-
-
Shi, J.1
Blundell, T.L.2
Mizuguchi, K.3
-
25
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I.N. and Bourne, P.E. 1998. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11: 739-747.
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
26
-
-
1342289274
-
Sensitivity and selectivity in protein structure comparison
-
Sierk, M.L. and Pearson, W.R. 2004. Sensitivity and selectivity in protein structure comparison. Protein Sci. 13: 773-785.
-
(2004)
Protein Sci.
, vol.13
, pp. 773-785
-
-
Sierk, M.L.1
Pearson, W.R.2
-
27
-
-
0031028657
-
Comparison of protein structures using 3D profile alignment
-
Suyama, M., Matsuo, Y., and Nishikawa, K. 1997. Comparison of protein structures using 3D profile alignment. J. Mol. Evol. 44S: 163-173.
-
(1997)
J. Mol. Evol.
, vol.44 S
, pp. 163-173
-
-
Suyama, M.1
Matsuo, Y.2
Nishikawa, K.3
-
28
-
-
0344873345
-
On the role of structural information in remote homology detection and sequence alignment: New methods using hybrid sequence profiles
-
Tang, C.L., Xie, L., Koh, I.Y., Posy, S., Alexov, E., and Honig, B. 2003. On the role of structural information in remote homology detection and sequence alignment: New methods using hybrid sequence profiles. J. Mol. Biol. 334: 1043-1062.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 1043-1062
-
-
Tang, C.L.1
Xie, L.2
Koh, I.Y.3
Posy, S.4
Alexov, E.5
Honig, B.6
-
29
-
-
0033011876
-
Protein structure comparison using iterated double dynamic programming
-
Taylor, W.R. 1999. Protein structure comparison using iterated double dynamic programming. Protein Sci. 8: 654-665.
-
(1999)
Protein Sci.
, vol.8
, pp. 654-665
-
-
Taylor, W.R.1
-
30
-
-
0034682851
-
An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments
-
Yang, A.S. and Honig, B. 2000. An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments. J. Mol. Biol. 301: 691-711.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 691-711
-
-
Yang, A.S.1
Honig, B.2
-
31
-
-
3042533398
-
Database searching by flexible protein structure alignment
-
Ye, Y. and Godzik, A. 2004. Database searching by flexible protein structure alignment. Protein Sci. 13: 1841-1850.
-
(2004)
Protein Sci.
, vol.13
, pp. 1841-1850
-
-
Ye, Y.1
Godzik, A.2
|