-
1
-
-
37249004920
-
Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
-
Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450:1001-1009.
-
(2007)
Nature
, vol.450
, pp. 1001-1009
-
-
Wells, J.A.1
McClendon, C.L.2
-
2
-
-
49649114605
-
-
Humana, Totowa, NJ, pp
-
Eswar N, Eramian D, Webb B, Shen M-Y, Sali A (2008) in Methods in Molecular Biology (Humana, Totowa, NJ), pp 145-159.
-
(2008)
Methods in Molecular Biology
, pp. 145-159
-
-
Eswar, N.1
Eramian, D.2
Webb, B.3
Shen, M.-Y.4
Sali, A.5
-
4
-
-
5244260010
-
Prediction of peptide conformations by multicanonical algorithm-New approach to the multiple-minima problem
-
Hansmann UHE, Okamoto Y (1993) Prediction of peptide conformations by multicanonical algorithm-New approach to the multiple-minima problem. J Comput Chem 14:1333-1338.
-
(1993)
J Comput Chem
, vol.14
, pp. 1333-1338
-
-
Hansmann, U.H.E.1
Okamoto, Y.2
-
5
-
-
0642285282
-
Reproducible protein folding with the stochastic tunneling method
-
Schug A, Herges T, Wenzel W(2003) Reproducible protein folding with the stochastic tunneling method. Phys Rev Lett 91:158102.
-
(2003)
Phys Rev Lett
, vol.91
, pp. 158102
-
-
Schug, A.1
Herges, T.2
Wenzel, W.3
-
6
-
-
46749127364
-
Are current molecular dynamics force fields too helical?
-
Best RB, Buchete NV, Hummer G(2008) Are current molecular dynamics force fields too helical? Biophys J 95:07-09.
-
(2008)
Biophys J
, vol.95
, pp. 07-09
-
-
Best, R.B.1
Buchete, N.V.2
Hummer, G.3
-
7
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731-1737.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
8
-
-
0034035586
-
Two-component and phosphorelay signal transduction
-
Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3:165-170.
-
(2000)
Curr Opin Microbiol
, vol.3
, pp. 165-170
-
-
Hoch, J.A.1
-
9
-
-
70349541000
-
Biological insights from structures of two-component proteins
-
Gao R, Stock AM(2009) Biological insights from structures of two-component proteins. Annu Rev Microbiol 63:133-154.
-
(2009)
Annu Rev Microbiol
, vol.63
, pp. 133-154
-
-
Gao, R.1
Stock, A.M.2
-
10
-
-
36549003158
-
Sensor complexes regulating two-component signal transduction
-
Szurmant H, White RA, Hoch JA (2007) Sensor complexes regulating two-component signal transduction. Curr Opin Struct Biol 17:706-715.
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 706-715
-
-
Szurmant, H.1
White, R.A.2
Hoch, J.A.3
-
11
-
-
0034662751
-
A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction
-
Zapf J, Sen U, Madhusudan, Hoch JA, Varughese KI (2000) A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Structure (London) 8:851-862.
-
(2000)
Structure (London)
, vol.8
, pp. 851-862
-
-
Zapf, J.1
Sen, U.2
Madhusudan3
Hoch, J.A.4
Varughese, K.I.5
-
12
-
-
16544381695
-
Metals in the sporulation phosphorelay: Manganese binding by the response regulator Spo0F
-
Mukhopadhyay D, Sen U, Zapf J, Varughese KI (2004) Metals in the sporulation phosphorelay: Manganese binding by the response regulator Spo0F. Acta Crystallogr D 60:638-645.
-
(2004)
Acta Crystallogr D
, vol.60
, pp. 638-645
-
-
Mukhopadhyay, D.1
Sen, U.2
Zapf, J.3
Varughese, K.I.4
-
13
-
-
0032184886
-
Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase
-
Varughese KI, Madhusudan, Zhou XZ, Whiteley JM, Hoch JA (1998) Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase. Mol Cell 2:485-493.
-
(1998)
Mol Cell
, vol.2
, pp. 485-493
-
-
Varughese, K.I.1
Madhusudan2
Zhou, X.Z.3
Whiteley, J.M.4
Hoch, J.A.5
-
14
-
-
48249148736
-
Co-evolving motions at protein-protein interfaces of twocomponent signaling systems identified by covariance analysis
-
Szurmant H, et al. (2008) Co-evolving motions at protein-protein interfaces of twocomponent signaling systems identified by covariance analysis. Biochemistry 47:7782-7784.
-
(2008)
Biochemistry
, vol.47
, pp. 7782-7784
-
-
Szurmant, H.1
-
15
-
-
34447104524
-
Features of protein-protein interactions in two-component signaling deduced from genomic libraries
-
White RA, Szurmant H, Hoch JA, Hwa T (2007) Features of protein-protein interactions in two-component signaling deduced from genomic libraries. Methods Enzymol 422:75-101.
-
(2007)
Methods Enzymol
, vol.422
, pp. 75-101
-
-
White, R.A.1
Szurmant, H.2
Hoch, J.A.3
Hwa, T.4
-
16
-
-
58549114185
-
Identification of direct residue contacts in protein-protein interaction by message passing
-
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 106:67-72.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 67-72
-
-
Weigt, M.1
White, R.A.2
Szurmant, H.3
Hoch, J.A.4
Hwa, T.5
-
17
-
-
39149114704
-
Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
-
Burger L, van Nimwegen E (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol 4:165.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 165
-
-
Burger, L.1
van Nimwegen, E.2
-
18
-
-
44649153450
-
Rewiring the specificity of two-component signal transduction systems
-
Skerker JM, et al. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133:1043-1054.
-
(2008)
Cell
, vol.133
, pp. 1043-1054
-
-
Skerker, J.M.1
-
20
-
-
63449135082
-
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
-
Whitford PC, et al. (2009) An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Proteins Struct Funct Bioinf 75:430-441.
-
(2009)
Proteins Struct Funct Bioinf
, vol.75
, pp. 430-441
-
-
Whitford, P.C.1
-
21
-
-
36749023459
-
Mutations as trapdoors to two competing native conformations of the Rop-dimer
-
Schug A, Whitford PC, Levy Y, Onuchic JN (2007) Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proc Natl Acad Sci USA 104:17674-17679.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 17674-17679
-
-
Schug, A.1
Whitford, P.C.2
Levy, Y.3
Onuchic, J.N.4
-
22
-
-
44949216600
-
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: A detailed investigation of several reduced models
-
Oliveira LC, Schug A, Onuchic JN (2008) Geometrical features of the protein folding mechanism are a robust property of the energy landscape: A detailed investigation of several reduced models. J Phys Chem B 112:6131-6136.
-
(2008)
J Phys Chem B
, vol.112
, pp. 6131-6136
-
-
Oliveira, L.C.1
Schug, A.2
Onuchic, J.N.3
-
23
-
-
34247591513
-
Identification of a novel two component system in Thermotoga maritima. Complex stoichiometry and crystallization
-
Casino P, Fernandez-Alvarez A, Alfonso C, Rivas G, Marina A (2007) Identification of a novel two component system in Thermotoga maritima. Complex stoichiometry and crystallization. Biochim Biophys Acta 1774:603-609.
-
(2007)
Biochim Biophys Acta
, vol.1774
, pp. 603-609
-
-
Casino, P.1
Fernandez-Alvarez, A.2
Alfonso, C.3
Rivas, G.4
Marina, A.5
-
24
-
-
29244433095
-
Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein
-
Marina A, Waldburger CD, Hendrickson WA(2005) Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J 24:4247-4259.
-
(2005)
EMBO J
, vol.24
, pp. 4247-4259
-
-
Marina, A.1
Waldburger, C.D.2
Hendrickson, W.A.3
-
25
-
-
0030813090
-
Molecular recognition in signal transduction: The interaction surfaces of the Spo0F response regulator with its cognate phosphorelay proteins revealed by alanine scanning mutagenesis
-
Tzeng YL, Hoch JA (1997) Molecular recognition in signal transduction: The interaction surfaces of the Spo0F response regulator with its cognate phosphorelay proteins revealed by alanine scanning mutagenesis. J Mol Biol 272:200-212.
-
(1997)
J Mol Biol
, vol.272
, pp. 200-212
-
-
Tzeng, Y.L.1
Hoch, J.A.2
-
26
-
-
0037215598
-
The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface
-
Birck C, Chen Y, Hulett FM, Samama JP (2003) The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface. J Bacteriol 185:254-261.
-
(2003)
J Bacteriol
, vol.185
, pp. 254-261
-
-
Birck, C.1
Chen, Y.2
Hulett, F.M.3
Samama, J.P.4
-
27
-
-
0035369115
-
Histidine kinases and response regulator proteins in twocomponent signaling systems
-
West AH, Stock AM (2001) Histidine kinases and response regulator proteins in twocomponent signaling systems. Trends Biochem Sci 26:369-376.
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 369-376
-
-
West, A.H.1
Stock, A.M.2
-
28
-
-
33947411953
-
Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition
-
McLaughlin PD, et al. (2007) Predominantly buried residues in the response regulator Spo0F influence specific sensor kinase recognition. FEBS Lett 581:1425-1429.
-
(2007)
FEBS Lett
, vol.581
, pp. 1425-1429
-
-
McLaughlin, P.D.1
-
29
-
-
33745471490
-
The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state
-
Varughese KI, Tsigelny I, Zhao H (2006) The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state. J Bacteriol 188:4970-4977.
-
(2006)
J Bacteriol
, vol.188
, pp. 4970-4977
-
-
Varughese, K.I.1
Tsigelny, I.2
Zhao, H.3
-
30
-
-
0034879819
-
Keeping signals straight in phosphorelay signal transduction
-
Hoch JA, Varughese KI (2001) Keeping signals straight in phosphorelay signal transduction. J Bacteriol 183:4941-4949.
-
(2001)
J Bacteriol
, vol.183
, pp. 4941-4949
-
-
Hoch, J.A.1
Varughese, K.I.2
-
31
-
-
0035162594
-
RefSeq and LocusLink: NCBI gene-centered resources
-
Pruitt KD, Maglott DR (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res 29:137-140.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 137-140
-
-
Pruitt, K.D.1
Maglott, D.R.2
-
32
-
-
38549146894
-
The Pfam protein families database
-
Finn RD, et al. (2008) The Pfam protein families database. Nucleic Acids Res 36:281-288.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 281-288
-
-
Finn, R.D.1
-
33
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein-folding - A synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein-folding - A synthesis. Proteins Struct Funct Genet 21:167-195.
-
(1995)
Proteins Struct Funct Genet
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
34
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254:1598-1603.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
35
-
-
70449931860
-
Robustness and generalization of structure-based models for protein folding and function
-
Lammert H, Schug A, Onuchic JN (2009) Robustness and generalization of structure-based models for protein folding and function. Proteins Struct Funct Bioinf 77:881-891.
-
(2009)
Proteins Struct Funct Bioinf
, vol.77
, pp. 881-891
-
-
Lammert, H.1
Schug, A.2
Onuchic, J.N.3
-
36
-
-
4444295047
-
A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory
-
Finke JM, Cheung MS, Onuchic JN (2004) A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophys J 87:1900-1918.
-
(2004)
Biophys J
, vol.87
, pp. 1900-1918
-
-
Finke, J.M.1
Cheung, M.S.2
Onuchic, J.N.3
-
37
-
-
0035917318
-
The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation
-
Shimada J, Kussell EL, Shakhnovich EI (2001) The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. J Mol Biol 308:79-95.
-
(2001)
J Mol Biol
, vol.308
, pp. 79-95
-
-
Shimada, J.1
Kussell, E.L.2
Shakhnovich, E.I.3
-
38
-
-
0037113227
-
The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom G(o)over-bar model of fragment B of staphylococcal protein A
-
Linhananta A, Zhou YQ (2002) The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom G(o)over-bar model of fragment B of staphylococcal protein A. J Chem Phys 117:8983-8995.
-
(2002)
J Chem Phys
, vol.117
, pp. 8983-8995
-
-
Linhananta, A.1
Zhou, Y.Q.2
-
39
-
-
0037612553
-
Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G
-
Zhou Y, Zhang C, Stell G, Wang J (2003) Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G. J Am Chem Soc 125:6300-6305.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 6300-6305
-
-
Zhou, Y.1
Zhang, C.2
Stell, G.3
Wang, J.4
-
40
-
-
34547241687
-
Speeding up parallel GROMACS on high-latency networks
-
Kutzner C, et al. (2007) Speeding up parallel GROMACS on high-latency networks. J Comput Chem 28:2075-2084.
-
(2007)
J Comput Chem
, vol.28
, pp. 2075-2084
-
-
Kutzner, C.1
-
41
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comp Chem 26:1701-1718.
-
(2005)
J Comp Chem
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
-
42
-
-
0001398008
-
Howwell does a restrained electrostatic potential (RESP) perform in calculating conformational energies of organic and biological molecules?
-
Wang J, Cieplak P, Kollman PA (2000) Howwell does a restrained electrostatic potential (RESP) perform in calculating conformational energies of organic and biological molecules? J Chem Phys 21:1049-1074.
-
(2000)
J Chem Phys
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
43
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926 -935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
44
-
-
33645961739
-
A smooth particle Ewald method
-
Essmann U, et al. (1995) A smooth particle Ewald method. J Chem Phys 103:8577-8593.
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
-
45
-
-
70349795241
-
Structural insights into partner specificity and phosphoryl transfer in two-component signal transduction
-
Casino P, Rubio V, Marina A (2009) Structural insights into partner specificity and phosphoryl transfer in two-component signal transduction. Cell 139:325-336.
-
(2009)
Cell
, vol.139
, pp. 325-336
-
-
Casino, P.1
Rubio, V.2
Marina, A.3
|