-
1
-
-
0020490340
-
Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein
-
Aiba H, Fujimoto S, Ozaki N, (1982) Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucleic Acids Res 10: 1345-1361.
-
(1982)
Nucleic Acids Res
, vol.10
, pp. 1345-1361
-
-
Aiba, H.1
Fujimoto, S.2
Ozaki, N.3
-
2
-
-
0035810698
-
Allosteric regulation of the cAMP receptor protein
-
Harman JG, (2001) Allosteric regulation of the cAMP receptor protein. Biochim Biophys Acta 1547: 1-17.
-
(2001)
Biochim Biophys Acta
, vol.1547
, pp. 1-17
-
-
Harman, J.G.1
-
3
-
-
0023661228
-
Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution
-
Weber IT, Steitz TA, (1987) Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution. J Mol Biol 198: 311-326.
-
(1987)
J Mol Biol
, vol.198
, pp. 311-326
-
-
Weber, I.T.1
Steitz, T.A.2
-
4
-
-
0000445736
-
The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer
-
Passner JM, Steitz TA, (1997) The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl Acad Sci U S A 94: 2843-2847.
-
(1997)
Proc Natl Acad Sci U S A
, vol.94
, pp. 2843-2847
-
-
Passner, J.M.1
Steitz, T.A.2
-
5
-
-
46749128556
-
Syn-, anti, and finally both: Cyclic AMP conformation altered CRP dependent transcription initiation mechanism in E. coli lac operon
-
Tutar Y, (2008) Syn-, anti, and finally both: Cyclic AMP conformation altered CRP dependent transcription initiation mechanism in E. coli lac operon. Cell Biochem Funct 26: 399-405.
-
(2008)
Cell Biochem Funct
, vol.26
, pp. 399-405
-
-
Tutar, Y.1
-
6
-
-
0019463941
-
Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA
-
McKay DB, Steitz TA, (1981) Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA. Nature 290: 745-749.
-
(1981)
Nature
, vol.290
, pp. 745-749
-
-
McKay, D.B.1
Steitz, T.A.2
-
7
-
-
20544478449
-
Proposed structural mechanism of Escherichia coli cAMP receptor protein cAMP-dependent proteolytic cleavage protection and selective and nonselective DNA binding
-
Scott SP, Jarjous S, (2005) Proposed structural mechanism of Escherichia coli cAMP receptor protein cAMP-dependent proteolytic cleavage protection and selective and nonselective DNA binding. Biochemistry 44: 8370-8748.
-
(2005)
Biochemistry
, vol.44
, pp. 8370-8748
-
-
Scott, S.P.1
Jarjous, S.2
-
8
-
-
0030659457
-
PDBsum: A web-based database of summaries and analyses of all PDB structures
-
Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, et al. (1997) PDBsum: A web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci 22: 488-490.
-
(1997)
Trends Biochem Sci
, vol.22
, pp. 488-490
-
-
Laskowski, R.A.1
Hutchinson, E.G.2
Michie, A.D.3
Wallace, A.C.4
Jones, M.L.5
-
9
-
-
0029128444
-
Evidence for contact between the cyclic AMP receptor protein and the subunit of Escherichia coli RNA polymerase
-
Jin R, Sharif K, Krakow J, (1995) Evidence for contact between the cyclic AMP receptor protein and the subunit of Escherichia coli RNA polymerase. J Biol Chem 270: 19213-19216.
-
(1995)
J Biol Chem
, vol.270
, pp. 19213-19216
-
-
Jin, R.1
Sharif, K.2
Krakow, J.3
-
10
-
-
0029987740
-
Orientation of functional activating regions in the Escherichia Coli CRP protein during transcription activation at class II promoters
-
Williams RM, Rhodius VA, Bell AI, Kolb A, Busby S, (1996) Orientation of functional activating regions in the Escherichia Coli CRP protein during transcription activation at class II promoters. Nucleic Acids Res 24: 1112-1118.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 1112-1118
-
-
Williams, R.M.1
Rhodius, V.A.2
Bell, A.I.3
Kolb, A.4
Busby, S.5
-
11
-
-
0032698634
-
Transcription activation by catabolite activator protein (CAP)
-
Busby S, Ebright RH, (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293: 199-213.
-
(1999)
J Mol Biol
, vol.293
, pp. 199-213
-
-
Busby, S.1
Ebright, R.H.2
-
12
-
-
0037200079
-
Structural basis of transcription activation: the CAP-αCTD-DNA complex
-
Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, et al. (2002) Structural basis of transcription activation: the CAP-αCTD-DNA complex. Science 297: 1562-1566.
-
(2002)
Science
, vol.297
, pp. 1562-1566
-
-
Benoff, B.1
Yang, H.2
Lawson, C.L.3
Parkinson, G.4
Liu, J.5
-
13
-
-
1342345189
-
Catabolite activator protein: DNA binding and transcription activation
-
Lawson CL, Swigon D, Murakami KS, Darst SA, Berman HM, et al. (2004) Catabolite activator protein: DNA binding and transcription activation. Curr Opin Struct Biol 14: 10-20.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 10-20
-
-
Lawson, C.L.1
Swigon, D.2
Murakami, K.S.3
Darst, S.A.4
Berman, H.M.5
-
14
-
-
69249241732
-
Structural overview on the allosteric activation of cyclic AMP receptor protein
-
Won HS, Lee YS, Lee SH, Lee BJ, (2009) Structural overview on the allosteric activation of cyclic AMP receptor protein. Biochim Biophys Acta 1794: 1299-1308.
-
(2009)
Biochim Biophys Acta
, vol.1794
, pp. 1299-1308
-
-
Won, H.S.1
Lee, Y.S.2
Lee, S.H.3
Lee, B.J.4
-
15
-
-
0014779269
-
Mechanism of activation of catabolite-sensitive genes: A positive control system
-
Zubay G, Schwartz D, Beckwith J, (1970) Mechanism of activation of catabolite-sensitive genes: A positive control system. Proc Natl Acad Sci U S A 66: 104-110.
-
(1970)
Proc Natl Acad Sci U S A
, vol.66
, pp. 104-110
-
-
Zubay, G.1
Schwartz, D.2
Beckwith, J.3
-
16
-
-
33750982725
-
CRP subunit association and hinge conformation changes in response to cAMP binding: Analysis of C-helix cysteine-substituted CRP
-
Tomlinson SR, Tutar Y, Harman JG, (2006) CRP subunit association and hinge conformation changes in response to cAMP binding: Analysis of C-helix cysteine-substituted CRP. Biochemistry 45: 13438-13446.
-
(2006)
Biochemistry
, vol.45
, pp. 13438-13446
-
-
Tomlinson, S.R.1
Tutar, Y.2
Harman, J.G.3
-
17
-
-
0030068480
-
Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation
-
Garcia A, Harman JG, (1996) Simulations of CRP:(cAMP)2 in noncrystalline environments show a subunit transition from the open to the closed conformation. Protein Science 5: 62-71.
-
(1996)
Protein Science
, vol.5
, pp. 62-71
-
-
Garcia, A.1
Harman, J.G.2
-
18
-
-
33847385851
-
Catabolite activator protein in aqueous solution: A molecular simulation study
-
Berrera M, Pantano S, Carloni P, (2007) Catabolite activator protein in aqueous solution: A molecular simulation study. J Phys Chem 111: 1496-1501.
-
(2007)
J Phys Chem
, vol.111
, pp. 1496-1501
-
-
Berrera, M.1
Pantano, S.2
Carloni, P.3
-
19
-
-
38049089909
-
A computational investigation of allostery in the catabolite activator protein
-
Li L, Uversky VN, Dunker AK, Meroueh SO, (2007) A computational investigation of allostery in the catabolite activator protein. J Am Chem Soc 129: 15668-15676.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 15668-15676
-
-
Li, L.1
Uversky, V.N.2
Dunker, A.K.3
Meroueh, S.O.4
-
20
-
-
66349083528
-
Structural basis for cAMP-mediated allosteric transition in the catabolite activator protein
-
Popovych N, Tzeng SR, Tonelli M, Ebright RH, Kalodimos CG, (2009) Structural basis for cAMP-mediated allosteric transition in the catabolite activator protein. Proc Natl Acad Sci U S A 106: 6927-6932.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 6927-6932
-
-
Popovych, N.1
Tzeng, S.R.2
Tonelli, M.3
Ebright, R.H.4
Kalodimos, C.G.5
-
21
-
-
0025914242
-
Crystal structure of a CAP-DNA complex: The DNA is bent by 90°
-
Schultz S, Shields G, Steitz TA, (1991) Crystal structure of a CAP-DNA complex: The DNA is bent by 90°. Science 253: 1001-1007.
-
(1991)
Science
, vol.253
, pp. 1001-1007
-
-
Schultz, S.1
Shields, G.2
Steitz, T.A.3
-
22
-
-
0034671172
-
Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution
-
Passner JM, Schultz SC, Steitz TA, (2000) Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 Å resolution. J Mol Biol 304: 847-859.
-
(2000)
J Mol Biol
, vol.304
, pp. 847-859
-
-
Passner, J.M.1
Schultz, S.C.2
Steitz, T.A.3
-
23
-
-
70450191983
-
Dynamic activation of an allosteric regulatory protein
-
Tzeng SR, Kalodimos CG, (2009) Dynamic activation of an allosteric regulatory protein. Nature 462: 368-372.
-
(2009)
Nature
, vol.462
, pp. 368-372
-
-
Tzeng, S.R.1
Kalodimos, C.G.2
-
24
-
-
0034649356
-
Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding
-
Won HY, Yamazaki T, Lee TW, Yoon MK, Park SH, et al. (2000) Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding. Biochemistry 39: 13953-13962.
-
(2000)
Biochemistry
, vol.39
, pp. 13953-13962
-
-
Won, H.Y.1
Yamazaki, T.2
Lee, T.W.3
Yoon, M.K.4
Park, S.H.5
-
25
-
-
0035900005
-
Amino acid substitution at position 99 affects the rate of CRP subunit exchange
-
Baker CH, Tomlinson SR, Garcia AE, Harman JG, (2001) Amino acid substitution at position 99 affects the rate of CRP subunit exchange. Biochemistry 40: 12329-12338.
-
(2001)
Biochemistry
, vol.40
, pp. 12329-12338
-
-
Baker, C.H.1
Tomlinson, S.R.2
Garcia, A.E.3
Harman, J.G.4
-
26
-
-
39049090920
-
Interdomain interaction of cyclic AMP receptor protein in the absence of cyclic AMP
-
Won HS, Seo MD, Ko HS, Choi WS, Lee BJ, (2008) Interdomain interaction of cyclic AMP receptor protein in the absence of cyclic AMP. J Biochem 143: 163-167.
-
(2008)
J Biochem
, vol.143
, pp. 163-167
-
-
Won, H.S.1
Seo, M.D.2
Ko, H.S.3
Choi, W.S.4
Lee, B.J.5
-
27
-
-
0026722419
-
Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation
-
Kim J, Adhya S, Garges S, (1992) Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation. Proc Natl Acad Sci U S A 89: 9700-9704.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 9700-9704
-
-
Kim, J.1
Adhya, S.2
Garges, S.3
-
28
-
-
84864065499
-
Protein function and allostery: A dynamic relationship
-
Kalodimos CG, (2012) Protein function and allostery: A dynamic relationship. Ann N Y Acad Sci 1260: 81-86.
-
(2012)
Ann N Y Acad Sci
, vol.1260
, pp. 81-86
-
-
Kalodimos, C.G.1
-
29
-
-
84864651001
-
Protein activity regulation by conformational entropy
-
Tzeng SR, Kalodimos CG, (2012) Protein activity regulation by conformational entropy. Nature 488: 236-240.
-
(2012)
Nature
, vol.488
, pp. 236-240
-
-
Tzeng, S.R.1
Kalodimos, C.G.2
-
30
-
-
20344370764
-
Allosteric mechanisms of signal transduction
-
Changeux JP, Edelstein SJ, (2005) Allosteric mechanisms of signal transduction. Science 308: 1424-1428.
-
(2005)
Science
, vol.308
, pp. 1424-1428
-
-
Changeux, J.P.1
Edelstein, S.J.2
-
31
-
-
84861219631
-
Allostery and the Monod-Wyman-Changeux model after 50 years
-
Changeux JP, (2011) Allostery and the Monod-Wyman-Changeux model after 50 years. Ann Rev Biophys 41: 103-133.
-
(2011)
Ann Rev Biophys
, vol.41
, pp. 103-133
-
-
Changeux, J.P.1
-
32
-
-
0030623823
-
Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B, (1997) Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential. Fold Des 2: 173-181.
-
(1997)
Fold Des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
33
-
-
0345973041
-
Gaussian dynamics of folded proteins
-
Haliloglu T, Bahar I, Erman B, (1997) Gaussian dynamics of folded proteins. Phys Rev Lett 79: 3090-3093.
-
(1997)
Phys Rev Lett
, vol.79
, pp. 3090-3093
-
-
Haliloglu, T.1
Bahar, I.2
Erman, B.3
-
34
-
-
79960189344
-
Dynamic allostery: Linkers are not merely flexible
-
Ma B, Tsai CJ, Haliloglu T, Nussinov R, (2011) Dynamic allostery: Linkers are not merely flexible. Structure 19: 907-917.
-
(2011)
Structure
, vol.19
, pp. 907-917
-
-
Ma, B.1
Tsai, C.J.2
Haliloglu, T.3
Nussinov, R.4
-
35
-
-
0037022662
-
Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds
-
Garcia A, Sanbonmatsu KY, (2002) Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds. Proc Natl Acad Sci U S A 99: 2782-2787.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 2782-2787
-
-
Garcia, A.1
Sanbonmatsu, K.Y.2
-
37
-
-
0024412668
-
Modulation of the stability of a gene-regulatory protein dimer by DNA and cAMP
-
Brown AM, Crothers DM, (1989) Modulation of the stability of a gene-regulatory protein dimer by DNA and cAMP. Proc Natl Acad Sci U S A 86: 7387-7391.
-
(1989)
Proc Natl Acad Sci U S A
, vol.86
, pp. 7387-7391
-
-
Brown, A.M.1
Crothers, D.M.2
-
38
-
-
0025774847
-
Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli
-
Søgaard-Andersen L, Mironov AS, Pedersen H, Sukhodelets VV, Valentin-Hansen P, (1991) Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli. Proc Natl Acad Sci U S A 88: 4921-4925.
-
(1991)
Proc Natl Acad Sci U S A
, vol.88
, pp. 4921-4925
-
-
Søgaard-Andersen, L.1
Mironov, A.S.2
Pedersen, H.3
Sukhodelets, V.V.4
Valentin-Hansen, P.5
-
39
-
-
33947512110
-
A C-helix residue, Arg-123, has important roles in both the active and inactive forms of the cAMP Receptor Protein
-
Youn H, Kerby RL, Koh J, Roberts GP, (2007) A C-helix residue, Arg-123, has important roles in both the active and inactive forms of the cAMP Receptor Protein. J Biol Chem 282: 3632-3639.
-
(2007)
J Biol Chem
, vol.282
, pp. 3632-3639
-
-
Youn, H.1
Kerby, R.L.2
Koh, J.3
Roberts, G.P.4
-
40
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N, (2010) ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38: W529-W533.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
41
-
-
35048866000
-
Characterization of protein conformational states by normal-mode frequencies
-
Hall BA, Kaye SL, Pang A, Perera R, Biggin PC, (2007) Characterization of protein conformational states by normal-mode frequencies. J Am Chem Soc 129: 11394-11401.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 11394-11401
-
-
Hall, B.A.1
Kaye, S.L.2
Pang, A.3
Perera, R.4
Biggin, P.C.5
-
42
-
-
80053142382
-
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
-
Meireles L, Gur M, Bakan A, Bahar I, (2011) Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Sci 20: 1645-1658.
-
(2011)
Protein Sci
, vol.20
, pp. 1645-1658
-
-
Meireles, L.1
Gur, M.2
Bakan, A.3
Bahar, I.4
-
43
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsera MA, Wriggers W, Oono Y, Schulten K, (1996) Principal component analysis and long time protein dynamics. J Phys Chem 100: 2567-2572.
-
(1996)
J Phys Chem
, vol.100
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
44
-
-
84855658193
-
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
-
Liu L, Gronenborn AM, Bahar I, (2011) Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion. Proteins 80: 616-625.
-
(2011)
Proteins
, vol.80
, pp. 616-625
-
-
Liu, L.1
Gronenborn, A.M.2
Bahar, I.3
-
45
-
-
41149104308
-
Allostery: Absence of a change in shape does not imply that allostery is not at play
-
Tsai CJ, del Sol A, Nussinov R, (2008) Allostery: Absence of a change in shape does not imply that allostery is not at play. J Mol Biol 378: 1-11.
-
(2008)
J Mol Biol
, vol.378
, pp. 1-11
-
-
Tsai, C.J.1
del Sol, A.2
Nussinov, R.3
-
47
-
-
79954495992
-
NMR reveals novel mechanisms of protein activity regulation
-
Kalodimos CG, (2011) NMR reveals novel mechanisms of protein activity regulation. Protein Sci 20: 773-782.
-
(2011)
Protein Sci
, vol.20
, pp. 773-782
-
-
Kalodimos, C.G.1
-
48
-
-
33748363077
-
Dynamically driven protein allostery
-
Popovych N, Sun S, Ebright RH, Kalodimos CG, (2006) Dynamically driven protein allostery. Nat Struct Mol Biol 13: 831-838.
-
(2006)
Nat Struct Mol Biol
, vol.13
, pp. 831-838
-
-
Popovych, N.1
Sun, S.2
Ebright, R.H.3
Kalodimos, C.G.4
-
49
-
-
84865525384
-
Sequence evolution correlates with structural dynamics
-
Liu Y, Bahar I, (2012) Sequence evolution correlates with structural dynamics. Mol Biol Evol 29: 2253-2263.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 2253-2263
-
-
Liu, Y.1
Bahar, I.2
-
50
-
-
49049096095
-
Evolutionary conservation of protein vibrational dynamics
-
Maguid S, Fernandez-Alberti S, Parisi G, Echave J, (2008) Evolutionary conservation of protein vibrational dynamics. Gene 422: 7-13.
-
(2008)
Gene
, vol.422
, pp. 7-13
-
-
Maguid, S.1
Fernandez-Alberti, S.2
Parisi, G.3
Echave, J.4
-
51
-
-
79952762072
-
On the role of frustration in the energy landscapes of allosteric proteins
-
Ferreiro DU, Hegler JA, Komives EA, Wolynes PG, (2011) On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci U S A 108: 3499-3503.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 3499-3503
-
-
Ferreiro, D.U.1
Hegler, J.A.2
Komives, E.A.3
Wolynes, P.G.4
-
52
-
-
33646742004
-
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
-
Zheng W, Brooks BR, Thirumalai D, (2006) Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proc Natl Acad Sci U S A 103: 7664-7669.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 7664-7669
-
-
Zheng, W.1
Brooks, B.R.2
Thirumalai, D.3
-
53
-
-
50949099429
-
Allosteric communication in myosin V: From small conformational changes to large directed movements
-
Cecchini M, Houdusse A, Karplus M, (2008) Allosteric communication in myosin V: From small conformational changes to large directed movements. Plos Comput Biol 4: e1000129.
-
(2008)
Plos Comput Biol
, vol.4
-
-
Cecchini, M.1
Houdusse, A.2
Karplus, M.3
-
54
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
-
(2005)
J Comput Chem
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
-
55
-
-
9244260409
-
-
University of California, San Francisco
-
Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, et al. (2004) AMBER 8, University of California, San Francisco.
-
(2004)
AMBER 8
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
-
56
-
-
78049265751
-
-
University of California, San Francisco
-
Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, et al. (2010) AMBER 11, University of California, San Francisco.
-
(2010)
AMBER 11
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, T.E.3
Simmerling, C.L.4
Wang, J.5
-
57
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24: 1999-2012.
-
(2003)
J Comput Chem
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
-
58
-
-
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
-
60
-
-
23144457576
-
H++: A server for estimating pKas and adding missing hydrogens to macromolecules
-
Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, et al. (2005) H++: A server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33: W368-W371.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
-
61
-
-
0025197061
-
pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model
-
Bashford D, Karplus M, (1990) pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 29: 10219-10225.
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
62
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR, (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
63
-
-
33646940952
-
Numerical integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes. J Comput Phys 23: 327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
64
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essman U, Perera L, Berkowitz ML, Darden TA, Lee H, et al. (1995) A smooth particle mesh Ewald method. J Chem Phys 103: 8577-8593.
-
(1995)
J Chem Phys
, vol.103
, pp. 8577-8593
-
-
Essman, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.A.4
Lee, H.5
-
65
-
-
1942423619
-
MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
-
Feig M, Karanicolas J, Brooks CL, (2004) MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 22: 377-395.
-
(2004)
J Mol Graph Model
, vol.22
, pp. 377-395
-
-
Feig, M.1
Karanicolas, J.2
Brooks, C.L.3
-
67
-
-
39749202824
-
HingeProt: Automated prediction of hinges in protein structures
-
Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T, (2008) HingeProt: Automated prediction of hinges in protein structures. Proteins 70: 1219-1227.
-
(2008)
Proteins
, vol.70
, pp. 1219-1227
-
-
Emekli, U.1
Schneidman-Duhovny, D.2
Wolfson, H.J.3
Nussinov, R.4
Haliloglu, T.5
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