-
1
-
-
0037335514
-
Human zinc fingers as building blocks in the construction of artificial transcription factors
-
Bae, K.H. et al. (2003) Human zinc fingers as building blocks in the construction of artificial transcription factors. Nat. Biotechnol., 21, 275-280.
-
(2003)
Nat. Biotechnol.
, vol.21
, pp. 275-280
-
-
Bae, K.H.1
-
2
-
-
0032475912
-
Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator
-
Bonvin, A.M. et al. (1998) Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator. J. Mol. Biol., 282, 859-873.
-
(1998)
J. Mol. Biol.
, vol.282
, pp. 859-873
-
-
Bonvin, A.M.1
-
3
-
-
36749066579
-
Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI
-
Bueno, M. and Camacho,C.J. (2007a) Acidic groups docked to well defined wetted pockets at the core of the binding interface: a tale of scoring and missing protein interactions in CAPRI. Proteins, 69, 786-792.
-
(2007)
Proteins
, vol.69
, pp. 786-792
-
-
Bueno, M.1
Camacho, C.J.2
-
4
-
-
34548746885
-
SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles
-
Bueno, M. et al. (2007b) SIMPLE estimate of the free energy change due to aliphatic mutations: superior predictions based on first principles. Proteins, 68, 850-862.
-
(2007)
Proteins
, vol.68
, pp. 850-862
-
-
Bueno, M.1
-
5
-
-
33646817694
-
Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions
-
Camacho, C.J. et al. (2006) Scoring a diverse set of high-quality docked conformations: a metascore based on electrostatic and desolvation interactions. Proteins, 63, 868-877.
-
(2006)
Proteins
, vol.63
, pp. 868-877
-
-
Camacho, C.J.1
-
6
-
-
46749149696
-
Critical parameters for genome editing using zinc finger nucleases
-
Camenisch, T.D. et al. (2008) Critical parameters for genome editing using zinc finger nucleases. Mini. Rev. Med. Chem., 8, 669-676.
-
(2008)
Mini. Rev. Med. Chem.
, vol.8
, pp. 669-676
-
-
Camenisch, T.D.1
-
7
-
-
0029011701
-
A 2Nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell, W.D. et al. (1995) A 2Nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J. Am. Chem. Soc., 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
-
8
-
-
0034141811
-
Continuum electrostatic analysis of preferred solvation sites around proteins in solution
-
Dennis, S. et al. (2000) Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins, 38, 176-188.
-
(2000)
Proteins
, vol.38
, pp. 176-188
-
-
Dennis, S.1
-
9
-
-
36549030301
-
Topology independent protein structural alignment
-
Dundas, J. et al. (2007) Topology independent protein structural alignment. BMC Bioinformatics, 8, 388.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 388
-
-
Dundas, J.1
-
10
-
-
0032522662
-
High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition
-
Elrod-Erickson, M. et al. (1998) High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure, 6, 451-464.
-
(1998)
Structure
, vol.6
, pp. 451-464
-
-
Elrod-Erickson, M.1
-
11
-
-
0030587774
-
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions
-
Elrod-Erickson, M. et al. (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure, 4, 1171-1180.
-
(1996)
Structure
, vol.4
, pp. 1171-1180
-
-
Elrod-Erickson, M.1
-
12
-
-
0028921999
-
Demonstration of positionally disordered water within a protein hydrophobic cavity by Nmr
-
Ernst, J.A. et al. (1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by Nmr. Science, 267, 1813-1817.
-
(1995)
Science
, vol.267
, pp. 1813-1817
-
-
Ernst, J.A.1
-
15
-
-
23944486752
-
Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in de novo protein design
-
Fung, H. et al. (2005) Computational comparison studies of quadratic assignment like formulations for the in silico sequence selection problem in de novo protein design. J. Comb. Optim., 10, 41-60.
-
(2005)
J. Comb. Optim.
, vol.10
, pp. 41-60
-
-
Fung, H.1
-
17
-
-
77949538571
-
-
ILOG CPLEX 11.0 User's Manual. ILOG CPLEX Division. Incline Village, NV
-
ILOG (2007) CPLEX 11.0 User's Manual. ILOG CPLEX Division. Incline Village, NV.
-
(2007)
-
-
-
18
-
-
34147132352
-
Correlation between functional and binding activities of designer zinc-finger proteins
-
Kang, J.S. (2007) Correlation between functional and binding activities of designer zinc-finger proteins. Biochem. J., 403, 177-182.
-
(2007)
Biochem. J.
, vol.403
, pp. 177-182
-
-
Kang, J.S.1
-
19
-
-
0035253047
-
Zinc finger proteins: new insights into structural and functional diversity
-
Laity, J.H. et al. (2001) Zinc finger proteins: new insights into structural and functional diversity. Curr. Opin. Struct. Biol., 11, 39-46.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 39-46
-
-
Laity, J.H.1
-
20
-
-
25444480735
-
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein
-
Liu, J. and Stormo,G.D. (2005) Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics, 6, 176.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 176
-
-
Liu, J.1
Stormo, G.D.2
-
21
-
-
50549103329
-
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
-
Liu, J. and Stormo, G.D. (2008) Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors, Bioinformatics, 24, 1850-1857.
-
(2008)
Bioinformatics
, vol.24
, pp. 1850-1857
-
-
Liu, J.1
Stormo, G.D.2
-
22
-
-
21644469377
-
Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
-
Mendez, R. et al. (2005) Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins, 60, 150-169.
-
(2005)
Proteins
, vol.60
, pp. 150-169
-
-
Mendez, R.1
-
23
-
-
27244460904
-
Protein-DNA binding specificity predictions with structural models
-
Morozov, A.V. et al. (2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res., 33, 5781-5798.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5781-5798
-
-
Morozov, A.V.1
-
25
-
-
0034923498
-
Design and selection of novel Cys2His2 zinc finger proteins
-
Pabo, C.O. et al. (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu. Rev. Biochem., 70, 313-340.
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 313-340
-
-
Pabo, C.O.1
-
27
-
-
0025773296
-
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A
-
Pavletich, N.P. and Pabo, C.O. (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science, 252, 809-817.
-
(1991)
Science
, vol.252
, pp. 809-817
-
-
Pavletich, N.P.1
Pabo, C.O.2
-
28
-
-
0027423758
-
Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers
-
Pavletich, N.P. and Pabo, C.O. (1993) Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science, 261, 1701-1707.
-
(1993)
Science
, vol.261
, pp. 1701-1707
-
-
Pavletich, N.P.1
Pabo, C.O.2
-
29
-
-
0141738776
-
Consensus alignment for reliable framework prediction in homology modeling
-
Prasad, J.C. et al. (2003) Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics, 19, 1682-1691.
-
(2003)
Bioinformatics
, vol.19
, pp. 1682-1691
-
-
Prasad, J.C.1
-
30
-
-
33645424495
-
On multiple-ratio hyperbolic 0-1 programming problems
-
Prokopyev, O. et al. (2005) On multiple-ratio hyperbolic 0-1 programming problems. Pac. J. Optim. 1/2, 327-345.
-
(2005)
Pac. J. Optim.
, vol.1-2
, pp. 327-345
-
-
Prokopyev, O.1
-
31
-
-
33749155924
-
Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA
-
Segal, D.J. et al. (2006) Structure of Aart, a designed six-finger zinc finger peptide, bound to DNA. J. Mol. Biol., 363, 405-421.
-
(2006)
J. Mol. Biol.
, vol.363
, pp. 405-421
-
-
Segal, D.J.1
-
32
-
-
0032981699
-
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences
-
Segal, D.J. et al. (1999) Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences. Proc. Natl Acad. Sci. USA, 96, 2758-2763.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 2758-2763
-
-
Segal, D.J.1
-
33
-
-
11844279783
-
Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity
-
Siggers, T.W. et al. (2005) Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity. J. Mol. Biol., 345, 1027-1045.
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 1027-1045
-
-
Siggers, T.W.1
-
34
-
-
67651173036
-
Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface
-
Temiz, N.A. and Camacho, C.J. (2009) Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface. Nucleic Acids Res., 37, 4076-4088.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4076-4088
-
-
Temiz, N.A.1
Camacho, C.J.2
-
36
-
-
0033624684
-
DNArecognition by Cys2His2 zinc finger proteins
-
Wolfe, S.A. et al. (2000) DNArecognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct., 29, 183-212.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 183-212
-
-
Wolfe, S.A.1
-
37
-
-
0031197655
-
A note on a global approach for general 0-1 fractional programming
-
Wu, T.-H. (1997) A note on a global approach for general 0-1 fractional programming. Eur. J. Oper. Res., 101, 220-223.
-
(1997)
Eur. J. Oper. Res.
, vol.101
, pp. 220-223
-
-
Wu, T.-H.1
|