-
1
-
-
84863864586
-
Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences
-
Ahmadi Adl, A., Nowzari-Dalini, A., Xue, B., Uversky, V. N., & Qian, X. (2012). Accurate prediction of protein structural classes using functional domains and predicted secondary structure sequences. Journal of Biomolecular Structure & Dynamics, 29(6), 623-633.
-
(2012)
Journal of Biomolecular Structure & Dynamics
, vol.29
, Issue.6
, pp. 623-633
-
-
Ahmadi Adl, A.1
Nowzari-Dalini, A.2
Xue, B.3
Uversky, V.N.4
Qian, X.5
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Lipman, D. J., et al. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acid Research, 25(17), 3389-3402.
-
(1997)
Nucleic Acid Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Lipman, D.J.6
-
4
-
-
46249099576
-
Characterization and prediction of residues determining protein functional specificity
-
Capra, J. A., & Singh, M. (2008). Characterization and prediction of residues determining protein functional specificity. Bioinformatics, 24, 1473-1480.
-
(2008)
Bioinformatics
, vol.24
, pp. 1473-1480
-
-
Capra, J.A.1
Singh, M.2
-
5
-
-
0029587166
-
A method to predict functional residues in proteins
-
Casari, G., Sander, C., & Valencia, A. (1995). A method to predict functional residues in proteins. Nature Structural Biology, 2, 171-178.
-
(1995)
Nature Structural Biology
, vol.2
, pp. 171-178
-
-
Casari, G.1
Sander, C.2
Valencia, A.3
-
6
-
-
34748840163
-
Functional specificity lies within the properties and evolutionary changes of amino acids
-
Chakrabarti, S., Bryant, S.H., & Panchenko, A.R. (2007). Functional specificity lies within the properties and evolutionary changes of amino acids. Journal of Molecular Biology, 373, 801-810.
-
(2007)
Journal of Molecular Biology
, vol.373
, pp. 801-810
-
-
Chakrabarti, S.1
Bryant, S.H.2
Panchenko, A.R.3
-
7
-
-
65349142516
-
Computational tools for designing and engineering biocatalysts
-
Damborsky, J., & Brezovsky, J. (2009). Computational tools for designing and engineering biocatalysts. Current Opinion in Chemical Biology, 13, 26-34.
-
(2009)
Current Opinion in Chemical Biology
, vol.13
, pp. 26-34
-
-
Damborsky, J.1
Brezovsky, J.2
-
9
-
-
0037470597
-
Automated methods for predicting functionally important residues
-
del Sol Mesa, A., Pazos, F., & Valencia, A. (2003). Automated methods for predicting functionally important residues. Journal of Molecular Biology, 326, 1289-1302.
-
(2003)
Journal of Molecular Biology
, vol.326
, pp. 1289-1302
-
-
Del Sol-Mesa, A.1
Pazos, F.2
Valencia, A.3
-
10
-
-
77955501060
-
Evolution of substrate specificity within a diverse family of β/α-barrel-fold basic amino acid decarboxylases
-
Deng, X., Lee, J., Michael, A. J., Tomchick, D. R., Goldsmith, E. J., & Phillips, M. A. (2010). Evolution of substrate specificity within a diverse family of β/α-barrel-fold basic amino acid decarboxylases. Journal of Biological Chemistry, 285, 25708-25719.
-
(2010)
Journal of Biological Chemistry
, vol.285
, pp. 25708-25719
-
-
Deng, X.1
Lee, J.2
Michael, A.J.3
Tomchick, D.R.4
Goldsmith, E.J.5
Phillips, M.A.6
-
11
-
-
23344434599
-
Predicting specificity-determining residues in two large eukaryotic transcription factor families
-
Donald, J. E., & Shakhnovich, E. I. (2005). Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucleic Acid Research, 33, 4455-4465.
-
(2005)
Nucleic Acid Research
, vol.33
, pp. 4455-4465
-
-
Donald, J.E.1
Shakhnovich, E.I.2
-
12
-
-
77957371355
-
Promoting a structural view of biology for varied audiences: An overview of RCSB PDB resources and experiences
-
Dutta, S., Zardecki, C., Goodsell, D. S., & Berman, H. M. (2010). Promoting a structural view of biology for varied audiences: An overview of RCSB PDB resources and experiences. Journal of Applied Crystallography, 43, 1224-1229.
-
(2010)
Journal of Applied Crystallography
, vol.43
, pp. 1224-1229
-
-
Dutta, S.1
Zardecki, C.2
Goodsell, D.S.3
Berman, H.M.4
-
13
-
-
0019877271
-
Stereochemistry of the mammalian adenylate cyclase reaction
-
Eckstein, F., Romaniuk, P. J., Heideman, W., & Storm, D. R. (1981). Stereochemistry of the mammalian adenylate cyclase reaction. Journal of Biological Chemistry, 256, 9118-9120.
-
(1981)
Journal of Biological Chemistry
, vol.256
, pp. 9118-9120
-
-
Eckstein, F.1
Romaniuk, P.J.2
Heideman, W.3
Storm, D.R.4
-
14
-
-
40049091146
-
Prediction of protein functional residues from sequence by probability density estimation
-
Fischer, J. D., Mayer, C. E., & Söding, J. (2008). Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics, 24, 613-620.
-
(2008)
Bioinformatics
, vol.24
, pp. 613-620
-
-
Fischer, J.D.1
Mayer, C.E.2
Söding, J.3
-
15
-
-
0018904273
-
Mechanism of the adenylate cyclase reaction. Stereochemistry of the reaction catalyzed by the enzyme from Brevibacterium liquefaciens
-
Gerlt, J. A., Coderre, J. A., & Wolin, M. S. (1980). Mechanism of the adenylate cyclase reaction. Stereochemistry of the reaction catalyzed by the enzyme from Brevibacterium liquefaciens. Journal of Biological Chemistry, 2552, 331-334.
-
(1980)
Journal of Biological Chemistry
, vol.2552
, pp. 331-334
-
-
Gerlt, J.A.1
Coderre, J.A.2
Wolin, M.S.3
-
16
-
-
0034644783
-
Analysis and prediction of functional sub-types from protein sequence alignments
-
Hannenhalli, S. S., & Russel, R. B. (2000). Analysis and prediction of functional sub-types from protein sequence alignments. Journal of Molecular Biology, 303, 61-76.
-
(2000)
Journal of Molecular Biology
, vol.303
, pp. 61-76
-
-
Hannenhalli, S.S.1
Russel, R.B.2
-
17
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S., & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. PNAS, 89, 10915-10919.
-
(1992)
PNAS
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences, 8, 275-282.
-
(1992)
Computer Applications in the Biosciences
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
20
-
-
1642452921
-
Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families
-
Kalinina, O. V., Mironov, A. A., Gelfand, M. S., & Rakhmaninova, A. B. (2004). Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Science, 13, 443-456.
-
(2004)
Protein Science
, vol.13
, pp. 443-456
-
-
Kalinina, O.V.1
Mironov, A.A.2
Gelfand, M.S.3
Rakhmaninova, A.B.4
-
22
-
-
13444307044
-
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
-
Krissinel, E., & Henrick, K. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica. Section D, Biological Crystallography, 60, 2256-2268.
-
(2004)
Acta Crystallographica. Section D, Biological Crystallography
, vol.60
, pp. 2256-2268
-
-
Krissinel, E.1
Henrick, K.2
-
23
-
-
44349084889
-
Simple is beautiful: A straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
-
Lee, M. M., Chan, M. K., & Bundschuh, R. (2008). Simple is beautiful: A straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches. Bioinformatics, 24, 1339-1343.
-
(2008)
Bioinformatics
, vol.24
, pp. 1339-1343
-
-
Lee, M.M.1
Chan, M.K.2
Bundschuh, R.3
-
24
-
-
34848893660
-
Phylogenetic diversity and the structural basis of substrate specificity in the β/α-barrel fold basic amino acid decarboxylases
-
Lee, J., Michael, A. J., Martynowski, D., Goldsmith, E. J., & Phillips, M. A. (2007). Phylogenetic diversity and the structural basis of substrate specificity in the β/α-barrel fold basic amino acid decarboxylases. Journal of Biological Chemistry, 282, 27115-27125.
-
(2007)
Journal of Biological Chemistry
, vol.282
, pp. 27115-27125
-
-
Lee, J.1
Michael, A.J.2
Martynowski, D.3
Goldsmith, E.J.4
Phillips, M.A.5
-
25
-
-
0029913807
-
An evolutionary trace method defines binding surfaces common to protein families
-
Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996). An evolutionary trace method defines binding surfaces common to protein families. Journal of Molecular Biology, 257, 342-358.
-
(1996)
Journal of Molecular Biology
, vol.257
, pp. 342-358
-
-
Lichtarge, O.1
Bourne, H.R.2
Cohen, F.E.3
-
26
-
-
29144504098
-
Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
-
Mayer, K. M., McCorkle, S. R., & Shanklin, J. (2005). Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality. BMC Bioinformatics, 6, 284-293.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 284-293
-
-
Mayer, K.M.1
McCorkle, S.R.2
Shanklin, J.3
-
27
-
-
77954554764
-
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies
-
Mazin, P. V., Gelfand, M. S., Mironov, A. A., Rakhmaninova, A. B., Rubinov, A. R., Russell, R. B., & Kalinina, O. V. (2010). An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms for Molecular Biology, 5, 29.
-
(2010)
Algorithms for Molecular Biology
, vol.5
, pp. 29
-
-
Mazin, P.V.1
Gelfand, M.S.2
Mironov, A.A.3
Rakhmaninova, A.B.4
Rubinov, A.R.5
Russell, R.B.6
Kalinina, O.V.7
-
28
-
-
38949150854
-
Matt: Local flexibility aids protein multiple structure alignment
-
Menke, M., Berger, B., & Cowen, L. (2008). Matt: Local flexibility aids protein multiple structure alignment. PLoS Computational Biology, 4, e10.
-
(2008)
PLoS Computational Biology
, vol.4
-
-
Menke, M.1
Berger, B.2
Cowen, L.3
-
29
-
-
0036352010
-
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
-
Mirny, L., & Gelfand, M. (2002). Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. Journal of Molecular Biology, 321, 7-20.
-
(2002)
Journal of Molecular Biology
, vol.321
, pp. 7-20
-
-
Mirny, L.1
Gelfand, M.2
-
30
-
-
18144403554
-
Improve enzyme properties: When are closer mutations better
-
Morley, K., & Kazlauskas, R. J. (2005). Improve enzyme properties: When are closer mutations better. TRENDS in Biotechnology, 23, 231-237.
-
(2005)
TRENDS in Biotechnology
, vol.23
, pp. 231-237
-
-
Morley, K.1
Kazlauskas, R.J.2
-
31
-
-
14644429634
-
A ligand-centric analysis of the diversity and evolution of protein-ligand relationship in E. Coli
-
Nobeli, I., Spriggs, R. V., George, R. A., & Thornton, J. M. (2005). A ligand-centric analysis of the diversity and evolution of protein-ligand relationship in E.coli. Journal of Molecular Biology, 347, 415-436.
-
(2005)
Journal of Molecular Biology
, vol.347
, pp. 415-436
-
-
Nobeli, I.1
Spriggs, R.V.2
George, R.A.3
Thornton, J.M.4
-
32
-
-
0034623005
-
T-coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D. G., & Heringa, J. (2000). T-coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302, 205-217.
-
(2000)
Journal of Molecular Biology
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
33
-
-
0026540411
-
The alpha/beta hydrolase fold
-
Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., ..., Goldman, A. (1992). The alpha/beta hydrolase fold. Protein Engineering, 5(3), 197-211.
-
(1992)
Protein Engineering
, vol.5
, Issue.3
, pp. 197-211
-
-
Ollis, D.L.1
Cheah, E.2
Cygler, M.3
Dijkstra, B.4
Frolow, F.5
Franken, S.M.6
Goldman, A.7
-
34
-
-
22244450719
-
Protein families and their evolution - A structural perspective
-
Orengo, C. A., & Thornton, J. M. (2005). Protein families and their evolution - a structural perspective. Annual Review of Biochemistry, 74, 867-900.
-
(2005)
Annual Review of Biochemistry
, vol.74
, pp. 867-900
-
-
Orengo, C.A.1
Thornton, J.M.2
-
35
-
-
33846220351
-
Computational prediction of functionally important regions in proteins
-
Pazos, F., & Bang, J.-W. (2006). Computational prediction of functionally important regions in proteins. Current Bioinformatics, 1, 15-23.
-
(2006)
Current Bioinformatics
, vol.1
, pp. 15-23
-
-
Pazos, F.1
Bang, J.-W.2
-
36
-
-
33745599119
-
Phylogeny-independent detection of functional residues
-
Pazos, F., Rausell, A., & Valencia, A. (2006). Phylogeny-independent detection of functional residues. Bioinformatics, 22, 1440-1448.
-
(2006)
Bioinformatics
, vol.22
, pp. 1440-1448
-
-
Pazos, F.1
Rausell, A.2
Valencia, A.3
-
37
-
-
32144442848
-
Prediction of functional specificity determinants from protein sequences using log likelihood ratios
-
Pei, J., Cai, W., Kinch, L. N., & Grishin, N. V. (2006). Prediction of functional specificity determinants from protein sequences using log likelihood ratios. Bioinformatics, 22, 164-171.
-
(2006)
Bioinformatics
, vol.22
, pp. 164-171
-
-
Pei, J.1
Cai, W.2
Kinch, L.N.3
Grishin, N.V.4
-
38
-
-
33845882991
-
Sequence comparison by sequence harmony identifies subtype-specific functional sites
-
Pirovano, W., Feenstra, K. A., & Heringa, J. (2006). Sequence comparison by sequence harmony identifies subtype-specific functional sites. Nucleic Acids Research, 34, 6540-6548.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 6540-6548
-
-
Pirovano, W.1
Feenstra, K.A.2
Heringa, J.3
-
39
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut, A., & Grassly, N. C. (1997). Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences, 13(3), 235-238.
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
40
-
-
0023453329
-
Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
-
Rousseeuw, P. J. (1987). Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics, 20, 53-65.
-
(1987)
Journal of Computational and Applied Mathematics
, vol.20
, pp. 53-65
-
-
Rousseeuw, P.J.1
-
41
-
-
33947222410
-
X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: Insight into the structural basis for substrate specificity
-
Shah, R., Akella, R., Goldsmith, E. J., & Phillips, M. A. (2007). X-ray structure of Paramecium bursaria Chlorella virus arginine decarboxylase: Insight into the structural basis for substrate specificity. Biochemistry, 46(10), 2831-2841.
-
(2007)
Biochemistry
, vol.46
, Issue.10
, pp. 2831-2841
-
-
Shah, R.1
Akella, R.2
Goldsmith, E.J.3
Phillips, M.A.4
-
42
-
-
0037026230
-
Predicting amino acid residues responsible for enzyme specificity solely from protein sequences
-
Shaw, E., & Dordick, J. S. (2002). Predicting amino acid residues responsible for enzyme specificity solely from protein sequences. Biotechnology and Bioengineering, 79(3), 295-300.
-
(2002)
Biotechnology and Bioengineering
, vol.79
, Issue.3
, pp. 295-300
-
-
Shaw, E.1
Dordick, J.S.2
-
43
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., Koonin, E. V., & Lipman, D. J. (1997). A genomic perspective on protein families. Science, 278(5338), 631-637.
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
44
-
-
0035815113
-
Evolution of function in protein superfamilies, from a structural perspective
-
Todd, A. E., Orengo, C. A., & Thornton, J. M. (2001). Evolution of function in protein superfamilies, from a structural perspective. Journal of Molecular Biology, 307, 1113-1143.
-
(2001)
Journal of Molecular Biology
, vol.307
, pp. 1113-1143
-
-
Todd, A.E.1
Orengo, C.A.2
Thornton, J.M.3
-
45
-
-
0032568549
-
Two amino acid substitutions convert a guanylyl cyclase, RetGC-1, into an adenylyl cyclase
-
Tucker, C. L., Hurley, J. H., Miller, T. R., & Hurley, J. B. (1998). Two amino acid substitutions convert a guanylyl cyclase, RetGC-1, into an adenylyl cyclase. In Proceedings of the National Academy of Sciences of the USA, 5993-5997.
-
(1998)
Proceedings of the National Academy of Sciences of the USA
, pp. 5993-5997
-
-
Tucker, C.L.1
Hurley, J.H.2
Miller, T.R.3
Hurley, J.B.4
-
46
-
-
0035178383
-
Protein-protein interfaces: Analysis of amino acid conservation in homodimes
-
Valdar, W. S. J., & Thornton, J. M. (2001). Protein-protein interfaces: Analysis of amino acid conservation in homodimes. Proteins, 42, 108-124.
-
(2001)
Proteins
, vol.42
, pp. 108-124
-
-
Valdar, W.S.J.1
Thornton, J.M.2
-
47
-
-
0035542305
-
Enzyme active sites: Bioinformatics, architecture, and mechanisms of action
-
Varfolomeev, S. D., & Gurevich, K. G. (2001). Enzyme active sites: Bioinformatics, architecture, and mechanisms of action. Russian Chemical Bulletin, 50, 1709-1717.
-
(2001)
Russian Chemical Bulletin
, vol.50
, pp. 1709-1717
-
-
Varfolomeev, S.D.1
Gurevich, K.G.2
-
48
-
-
0024544755
-
A fast and sensitive multiple sequence alignment algorithm
-
Vingron, M., & Argos, P. (1989). A fast and sensitive multiple sequence alignment algorithm. Computer Applications in the Biosciences, 5, 115-121.
-
(1989)
Computer Applications in the Biosciences
, vol.5
, pp. 115-121
-
-
Vingron, M.1
Argos, P.2
-
49
-
-
33747614282
-
Siteprob: Yet another algorithm to find regulatory signals in nucleotide sequences
-
Novosibirsk, Russia, July 1
-
Vinogradov, D. V., & Mironov, A. A. (2002). Siteprob: Yet another algorithm to find regulatory signals in nucleotide sequences. In Proceedings 3rd International Conference On Bioinformatics of Genome Regulation and Structure BGRS'2002. Novosibirsk, Russia, July 1, 1, 30-32.
-
(2002)
Proceedings 3rd International Conference on Bioinformatics of Genome Regulation and Structure BGRS'2002
, vol.1
, pp. 30-32
-
-
Vinogradov, D.V.1
Mironov, A.A.2
|