-
1
-
-
34547127612
-
PDZ domain binding selectivity is optimized across the mouse proteome
-
Stiffler, M. A. et al. PDZ domain binding selectivity is optimized across the mouse proteome. Science 317, 364-369 (2007).
-
(2007)
Science
, vol.317
, pp. 364-369
-
-
Stiffler, M.A.1
-
2
-
-
30544449081
-
A quantitative protein interaction network for the ErbB receptors using protein microarrays
-
Jones, R. B., Gordus, A., Krall, J. A. & MacBeath, G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 439, 168-174 (2006).
-
(2006)
Nature
, vol.439
, pp. 168-174
-
-
Jones, R.B.1
Gordus, A.2
Krall, J.A.3
MacBeath, G.4
-
3
-
-
4744353840
-
Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides
-
Wiedemann, U. et al. Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J. Mol. Biol. 343, 703-718 (2004).
-
(2004)
J. Mol. Biol
, vol.343
, pp. 703-718
-
-
Wiedemann, U.1
-
4
-
-
0037595546
-
Comprehensive identification of human bZIP interactions with coiled-coil arrays
-
Newman, J. R. & Keating, A. E. Comprehensive identification of human bZIP interactions with coiled-coil arrays. Science 300, 2097-2101 (2003).
-
(2003)
Science
, vol.300
, pp. 2097-2101
-
-
Newman, J.R.1
Keating, A.E.2
-
5
-
-
19344377539
-
Protein interaction networks by proteome peptide scanning
-
Landgraf, C. et al. Protein interaction networks by proteome peptide scanning. PLoS Biol. 2, E14 (2004).
-
(2004)
PLoS Biol
, vol.2
-
-
Landgraf, C.1
-
6
-
-
26444481955
-
Twocomponent signal transduction pathways regulating growth and cell cycle progression in a bacterium: A system-level analysis
-
Skerker, J. M., Prasol, M. S., Perchuk, B. S., Biondi, E. G. & Laub, M. T. Twocomponent signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis, PLoS Biol. 3, e334 (2005).
-
(2005)
PLoS Biol
, vol.3
-
-
Skerker, J.M.1
Prasol, M.S.2
Perchuk, B.S.3
Biondi, E.G.4
Laub, M.T.5
-
7
-
-
0037217406
-
Automated design of specificity in molecular recognition
-
Havranek, J. J. & Harbury, P. B. Automated design of specificity in molecular recognition. Nature Struct. Biol. 10, 45-52 (2003).
-
(2003)
Nature Struct. Biol
, vol.10
, pp. 45-52
-
-
Havranek, J.J.1
Harbury, P.B.2
-
8
-
-
1842577654
-
Computational redesign of protein-protein interaction specificity
-
Kortemme, T. et al. Computational redesign of protein-protein interaction specificity. Nature Struct. Mol. Biol. 11, 371-379 (2004).
-
(2004)
Nature Struct. Mol. Biol
, vol.11
, pp. 371-379
-
-
Kortemme, T.1
-
9
-
-
13844297691
-
Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed α/β structure
-
All, M. H. et al. Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed α/β structure. Structure 13, 225-234 (2005).
-
(2005)
Structure
, vol.13
, pp. 225-234
-
-
All, M.H.1
-
10
-
-
33745056174
-
Designed tumor necrosis factor-related apoptoslsinducing ligand variants initiating apoptosis exclusively via the DR5 receptor
-
van der Sloot, A. M. et al. Designed tumor necrosis factor-related apoptoslsinducing ligand variants initiating apoptosis exclusively via the DR5 receptor. Proc. Natl Acad. Sci. USA 103, 8634-8639 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 8634-8639
-
-
van der Sloot, A.M.1
-
11
-
-
34147130190
-
Computational design of peptides that target transmembrane helices
-
Yin, H. et al. Computational design of peptides that target transmembrane helices. Science 315, 1817-1822 (2007).
-
(2007)
Science
, vol.315
, pp. 1817-1822
-
-
Yin, H.1
-
12
-
-
0036315558
-
Computer-aided design of a PDZ domain to recognize new target sequences
-
Reina, J. et al. Computer-aided design of a PDZ domain to recognize new target sequences. Nature Struct. Biol. 9, 621-627 (2002).
-
(2002)
Nature Struct. Biol
, vol.9
, pp. 621-627
-
-
Reina, J.1
-
13
-
-
0344392711
-
Exploring the origins of binding specificity through the computational redesign of calmodulin
-
Shifman, J. M. & Mayo, S. L. Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc. Natl Acad. Sci. USA 100, 13274-13279 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13274-13279
-
-
Shifman, J.M.1
Mayo, S.L.2
-
14
-
-
34547121250
-
Modeling backbone flexibility to achieve sequence diversity: The design of novel α-helical ligands for Bcl-xL
-
Fu, X., Apgar, J. R. & Keating, A. E. Modeling backbone flexibility to achieve sequence diversity: the design of novel α-helical ligands for Bcl-xL. J. Mol. Biol. 371, 1099-1117 (2007).
-
(2007)
J. Mol. Biol
, vol.371
, pp. 1099-1117
-
-
Fu, X.1
Apgar, J.R.2
Keating, A.E.3
-
15
-
-
24644472964
-
Specificity versus stability in computational protein design
-
Bolon, D. N., Grant, R. A., Baker, T. A. & Sauer, R. T. Specificity versus stability in computational protein design. Proc. NatlAcad. Sci. USA 102, 12724-12729 (2005).
-
(2005)
Proc. NatlAcad. Sci. USA
, vol.102
, pp. 12724-12729
-
-
Bolon, D.N.1
Grant, R.A.2
Baker, T.A.3
Sauer, R.T.4
-
16
-
-
0001192934
-
Electrostatic specificity in molecular ligand design
-
Kangas, E. & Tidor, B. Electrostatic specificity in molecular ligand design. J. Comput. Phys. 112, 9120-9131 (2000).
-
(2000)
J. Comput. Phys
, vol.112
, pp. 9120-9131
-
-
Kangas, E.1
Tidor, B.2
-
17
-
-
4243719017
-
New algorithm for protein design
-
Deutsch, J. M. & Kurosky, T. New algorithm for protein design. Phys. Rev. Lett. 76, 323-326 (1996).
-
(1996)
Phys. Rev. Lett
, vol.76
, pp. 323-326
-
-
Deutsch, J.M.1
Kurosky, T.2
-
18
-
-
33745164260
-
Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for eucine zipper prediction and design
-
Mason, J. M., Schmitz, M. A., Muller, K. M. & Arndt, K. M. Semirational design of Jun-Fos coiled coils with increased affinity: universal implications for eucine zipper prediction and design. Proc. Natl Acad. Sci. USA 103, 8989-8994 (2006).
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 8989-8994
-
-
Mason, J.M.1
Schmitz, M.A.2
Muller, K.M.3
Arndt, K.M.4
-
19
-
-
33646157076
-
Deciphering B-ZIP transcription factor interactions in vitro and in vivo
-
Vinson, C., Acharya, A. & Taparowsky, E. J. Deciphering B-ZIP transcription factor interactions in vitro and in vivo. Biochim. Biophys. Acta 1759, 4-12 (2006).
-
(2006)
Biochim. Biophys. Acta
, vol.1759
, pp. 4-12
-
-
Vinson, C.1
Acharya, A.2
Taparowsky, E.J.3
-
20
-
-
33747875862
-
Activator proteln-1 activity regulates epithelial tumor eel identity
-
Gerdes, M. J ef at. Activator proteln-1 activity regulates epithelial tumor eel identity. Cancer Res. 66, 7578-7588 (2006).
-
(2006)
Cancer Res
, vol.66
, pp. 7578-7588
-
-
Gerdes, M.J.1
ef at2
-
21
-
-
0028786167
-
Extending dimerizatlon interfaces: The bZIP basic region can form a coiled coil
-
Krylov, D., Olive, M. & Vinson, C. Extending dimerizatlon interfaces: the bZIP basic region can form a coiled coil. EMBO J. 14, 5329-5337 (1995).
-
(1995)
EMBO J
, vol.14
, pp. 5329-5337
-
-
Krylov, D.1
Olive, M.2
Vinson, C.3
-
22
-
-
33749025290
-
Stability of 100 homo and heterotypic coiledcoi a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R)
-
Acharya, A., Rishi, V. & Vinson, C. Stability of 100 homo and heterotypic coiledcoi a-a' pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R). Biochemistry 45, 11324-11332 (2006).
-
(2006)
Biochemistry
, vol.45
, pp. 11324-11332
-
-
Acharya, A.1
Rishi, V.2
Vinson, C.3
-
23
-
-
0032546758
-
Inter-helical interactions in the leucine zipper coiled coil dimer: PH and salt dependence of coupling energy between charged amino acids
-
Krylov, D., Barchi, J. & Vinson, C. Inter-helical interactions in the leucine zipper coiled coil dimer: pH and salt dependence of coupling energy between charged amino acids. J. Mol. Biol. 279, 959-972 (1998).
-
(1998)
J. Mol. Biol
, vol.279
, pp. 959-972
-
-
Krylov, D.1
Barchi, J.2
Vinson, C.3
-
24
-
-
17444424974
-
The structure of α-helica coiled coils
-
Lupas, A. N. & Gruber, M. The structure of α-helica coiled coils. Adv. Protein Chem. 70, 37-78 (2005).
-
(2005)
Adv. Protein Chem
, vol.70
, pp. 37-78
-
-
Lupas, A.N.1
Gruber, M.2
-
25
-
-
4143058720
-
Predicting specificity in bZIP coi ed-coi protein interactions
-
Fong, J. H., Keating, A. E. & Singh, M. Predicting specificity in bZIP coi ed-coi protein interactions. Genome Biol. 5, R11 (2004).
-
(2004)
Genome Biol
, vol.5
-
-
Fong, J.H.1
Keating, A.E.2
Singh, M.3
-
26
-
-
29444447288
-
Structure-based prediction of bZIP partnering specificity
-
Grigoryan, G. & Keating, A. E. Structure-based prediction of bZIP partnering specificity. J. Mol. Biol. 355, 1125-1142 (2006).
-
(2006)
J. Mol. Biol
, vol.355
, pp. 1125-1142
-
-
Grigoryan, G.1
Keating, A.E.2
-
27
-
-
16344382546
-
Solving and analyzing side-chain positioning problems using linear and integer programming
-
Kingsford, C. L., Chazelle, B. & Singh, M. Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformaties 21, 1028-1036 (2005).
-
(2005)
Bioinformaties
, vol.21
, pp. 1028-1036
-
-
Kingsford, C.L.1
Chazelle, B.2
Singh, M.3
-
28
-
-
33745620457
-
Ultra-fast evaluation of protein energies directly from sequence
-
Grlgoryan, G. et al. Ultra-fast evaluation of protein energies directly from sequence. PLOS Comput. Biol. 2, e63 (2006).
-
(2006)
PLOS Comput. Biol
, vol.2
-
-
Grlgoryan, G.1
-
29
-
-
28844499162
-
Coarse-graining protein energetics in sequence variab es
-
Zhou, F. et al. Coarse-graining protein energetics in sequence variab es. Phys. Rev. Lett. 95, 148103 (2005).
-
(2005)
Phys. Rev. Lett
, vol.95
, pp. 148103
-
-
Zhou, F.1
-
30
-
-
34247500390
-
Positive aspects of negative design: Simultaneous selection of specificity and interaction stability
-
Mason, J. M., Muller, K. M. & Arndt, K. M. Positive aspects of negative design: simultaneous selection of specificity and interaction stability. Biochemistry 46, 4804-4814 (2007).
-
(2007)
Biochemistry
, vol.46
, pp. 4804-4814
-
-
Mason, J.M.1
Muller, K.M.2
Arndt, K.M.3
-
31
-
-
38649087300
-
Preferred side-chain constellations at antiparallel coiled-coil interfaces
-
Hadley, E. B., Testa, O. D., Woolfson, D. N. & Gellman, S. H. Preferred side-chain constellations at antiparallel coiled-coil interfaces. Proc. Natl Acad. Sci. USA 105, 530-535 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 530-535
-
-
Hadley, E.B.1
Testa, O.D.2
Woolfson, D.N.3
Gellman, S.H.4
-
32
-
-
65249141494
-
Cluster-expansion models flexible-backbone protein energetics
-
in the press
-
Apgar, J. R., Hahn, S., Grigoryan, G. & Keating, A. E. Cluster-expansion models flexible-backbone protein energetics, J. Comput. Chem. (in the press).
-
J. Comput. Chem
-
-
Apgar, J.R.1
Hahn, S.2
Grigoryan, G.3
Keating, A.E.4
-
33
-
-
42949092832
-
-
Sanchez, I. E. et al. Genome-wide prediction of SH2 domain targets using structura information and the FoldX algorithm. PLOS Comput. Biol. 4, e1000052 (2008).
-
Sanchez, I. E. et al. Genome-wide prediction of SH2 domain targets using structura information and the FoldX algorithm. PLOS Comput. Biol. 4, e1000052 (2008).
-
-
-
-
34
-
-
29444434700
-
Ab initio prediction of transcription factor targets using structural knowledge
-
el
-
Kaplan, T., Friedman, N. & Margalit, H. Ab initio prediction of transcription factor targets using structural knowledge. PLOS Comput. Biol. 1, el (2005).
-
(2005)
PLOS Comput. Biol
, vol.1
-
-
Kaplan, T.1
Friedman, N.2
Margalit, H.3
-
35
-
-
34147169516
-
Potential energy functions for protein design
-
Boas, F. E. & Harbury, P. B. Potential energy functions for protein design. Curr. Opin. Struct. Biol. 17, 199-204 (2007).
-
(2007)
Curr. Opin. Struct. Biol
, vol.17
, pp. 199-204
-
-
Boas, F.E.1
Harbury, P.B.2
-
36
-
-
50649095790
-
Macromolecular modeling with ROSETTA
-
Das, R. & Baker, D. Macromolecular modeling with ROSETTA. Annu. Rev. Biochem. 77, 363-382 (2008).
-
(2008)
Annu. Rev. Biochem
, vol.77
, pp. 363-382
-
-
Das, R.1
Baker, D.2
-
37
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou, H. & Zhou, Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11, 2714-2726 (2002).
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
38
-
-
0037095730
-
DNAWorks: An automated method for designing oligonucleotides for PCR-based gene synthesis
-
Hoover, D. M. & Lubkowski, J. DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis, Nucleic Acids Res. 30, e43 (2002).
-
(2002)
Nucleic Acids Res
, vol.30
-
-
Hoover, D.M.1
Lubkowski, J.2
|