-
2
-
-
14144256567
-
Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool
-
Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M (2005) Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci 14:633-643
-
(2005)
Protein Sci
, vol.14
, pp. 633-643
-
-
Alexandrov, V.1
Lehnert, U.2
Echols, N.3
Milburn, D.4
Engelman, D.5
Gerstein, M.6
-
3
-
-
0037236095
-
The role of the protein side chain fluctuations on the strength of pair wise electrostatic interactions. Comparing experimental with computed pKa's
-
Alexov E (2003) The role of the protein side chain fluctuations on the strength of pair wise electrostatic interactions. Comparing experimental with computed pKa's. Proteins 50:94-103
-
(2003)
Proteins
, vol.50
, pp. 94-103
-
-
Alexov, E.1
-
4
-
-
3142708566
-
Calculating proteon uptake/release and the binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association. Application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes
-
Alexov E (2004a) Calculating proteon uptake/release and the binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association. Application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes. Proteins 56:572-584
-
(2004)
Proteins
, vol.56
, pp. 572-584
-
-
Alexov, E.1
-
5
-
-
1642499126
-
Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and 3D structure
-
Alexov E (2004b) Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and 3D structure. Eur J Biochem 271:173-185
-
(2004)
Eur J Biochem
, vol.271
, pp. 173-185
-
-
Alexov, E.1
-
6
-
-
0030945495
-
Incorporating protein conformation flexibility into the calculation of pH-dependent protein properties
-
Alexov E, Gunner M (1997) Incorporating protein conformation flexibility into the calculation of pH-dependent protein properties. Biophys J 74:2075-2093
-
(1997)
Biophys J
, vol.74
, pp. 2075-2093
-
-
Alexov, E.1
Gunner, M.2
-
7
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
8
-
-
10044258573
-
Target selectivity in EF-hand calcium binding proteins. Biochim Biophys Acta (BBA) - Mol
-
Bhattacharya S, Bunick C, Chazin W (2004) Target selectivity in EF-hand calcium binding proteins. Biochim Biophys Acta (BBA) - Mol Cell Res 1742:69-79
-
(2004)
Cell Res
, vol.1742
, pp. 69-79
-
-
Bhattacharya, S.1
Bunick, C.2
Chazin, W.3
-
9
-
-
84986512474
-
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217
-
-
-
-
10
-
-
1942457231
-
Backbone dynamic properties of the central linker region of calcium-calmodulin in 35% trifluroethanol
-
Broxk R, Scheek R, Weljie A, Vogel H (2004) Backbone dynamic properties of the central linker region of calcium-calmodulin in 35% trifluroethanol. J Struct Biol 146:272-280
-
(2004)
J Struct Biol
, vol.146
, pp. 272-280
-
-
Broxk, R.1
Scheek, R.2
Weljie, A.3
Vogel, H.4
-
13
-
-
3042801661
-
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model
-
Felts AK, Harano Y, Gallicchio E, Levy RM (2004) Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins 56:310-321
-
(2004)
Proteins
, vol.56
, pp. 310-321
-
-
Felts, A.K.1
Harano, Y.2
Gallicchio, E.3
Levy, R.M.4
-
14
-
-
26444443482
-
An assessment of the accuracy of methods for predicting hydrogen positions in protein structures
-
Forrest L, Honig B (2005) An assessment of the accuracy of methods for predicting hydrogen positions in protein structures. Proteins 61:296-309
-
(2005)
Proteins
, vol.61
, pp. 296-309
-
-
Forrest, L.1
Honig, B.2
-
15
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating residue pKa's in proteins
-
Georgescu R, Alexov E, Gunner M (2002) Combining conformational flexibility and continuum electrostatics for calculating residue pKa's in proteins. Biophys J 83:1731-1748
-
(2002)
Biophys J
, vol.83
, pp. 1731-1748
-
-
Georgescu, R.1
Alexov, E.2
Gunner, M.3
-
16
-
-
13844272482
-
Structure of a trapped intermediate of calmodulin: Calcium regulation of EF-hand proteins from a new perspective
-
Grabarek Z (2005) Structure of a trapped intermediate of calmodulin: calcium regulation of EF-hand proteins from a new perspective. J Mol Biol 346:1351-1366
-
(2005)
J Mol Biol
, vol.346
, pp. 1351-1366
-
-
Grabarek, Z.1
-
17
-
-
0037155689
-
Calmodulinin action: Diversity in target recognition and activation mechanisms
-
Hoeflich K, Ikura M (2002) Calmodulinin action: diversity in target recognition and activation mechanisms. Cell 108:739-742
-
(2002)
Cell
, vol.108
, pp. 739-742
-
-
Hoeflich, K.1
Ikura, M.2
-
18
-
-
4744372036
-
Systematic delineation of a calmodulin peptide interaction
-
Hultschiga C, Hecht H, Frank R (2004) Systematic delineation of a calmodulin peptide interaction. J Mol Biol 343:559-568
-
(2004)
J Mol Biol
, vol.343
, pp. 559-568
-
-
Hultschiga, C.1
Hecht, H.2
Frank, R.3
-
19
-
-
0030032040
-
Calcium binding and conformational response in EF-hand proteins
-
Ikura M (1996) Calcium binding and conformational response in EF-hand proteins. TIBS 21:14-17
-
(1996)
TIBS
, vol.21
, pp. 14-17
-
-
Ikura, M.1
-
20
-
-
0035501713
-
Focusing of the electrostatic potential at EF-hands of calbindin D(9k): Titration of acidic residues
-
Kesvatera T, Jonsson B, Thulin E, Linse S (2001) Focusing of the electrostatic potential at EF-hands of calbindin D(9k): titration of acidic residues. Proteins 45:129-135
-
(2001)
Proteins
, vol.45
, pp. 129-135
-
-
Kesvatera, T.1
Jonsson, B.2
Thulin, E.3
Linse, S.4
-
21
-
-
0034655949
-
The morph server: A standartized system for analyzing and visualizing macromolecular motionsin a database framework
-
Krebs W, Gerstein M (2000) The morph server: a standartized system for analyzing and visualizing macromolecular motionsin a database framework. Nucleic Acids Res 28:1665-1675
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1665-1675
-
-
Krebs, W.1
Gerstein, M.2
-
22
-
-
0029159794
-
Solution structure of calcium-free calmodulin
-
Kuboniwa H, Tjandra N, Grzesiek S, Ren H, Klee CB, Bax A (1995) Solution structure of calcium-free calmodulin. Nat Struct Biol 2:768-779
-
(1995)
Nat Struct Biol
, vol.2
, pp. 768-779
-
-
Kuboniwa, H.1
Tjandra, N.2
Grzesiek, S.3
Ren, H.4
Klee, C.B.5
Bax, A.6
-
23
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD Jr, Bashford D, Bellot M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem 102:3586-3616
-
(1998)
J Phys Chem
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr, A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack Jr, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
24
-
-
0026794065
-
Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex
-
Meador WE, Means AR, Quiocho FA (1992) Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex. Science 257:1251-1254
-
(1992)
Science
, vol.257
, pp. 1251-1254
-
-
Meador, W.E.1
Means, A.R.2
Quiocho, F.A.3
-
25
-
-
0026319199
-
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
-
Nicholls A, Sharp KA, Honig H (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11:281-296
-
(1991)
Proteins
, vol.11
, pp. 281-296
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, H.3
-
27
-
-
0024279165
-
The central helix of calmodulin functions as a flexible tether
-
Persechini A, Kretsinger R (1988) The central helix of calmodulin functions as a flexible tether. J Biol Chem B 101:12175-12178
-
(1988)
J Biol Chem B
, vol.101
, pp. 12175-12178
-
-
Persechini, A.1
Kretsinger, R.2
-
28
-
-
0346122798
-
GRASP2: Visualization, surface properties and electrostatic of macromolecular structures
-
Petrey D, Honig B (2003) "GRASP2: visualization, surface properties and electrostatic of macromolecular structures. Methods Enzymol 374:492-509
-
(2003)
Methods Enzymol
, vol.374
, pp. 492-509
-
-
Petrey, D.1
Honig, B.2
-
30
-
-
0035913537
-
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
-
Rocchia W, Alexov E, Honig B (2001) Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem 105:6507-6514
-
(2001)
J Phys Chem
, vol.105
, pp. 6507-6514
-
-
Rocchia, W.1
Alexov, E.2
Honig, B.3
-
31
-
-
0037080244
-
Rapid grid-based construction of the molecular surface and the use of induced surface charges to calculate reaction field energies: Applications to the molecular systems and geometrical objects
-
Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charges to calculate reaction field energies: applications to the molecular systems and geometrical objects. J Comput Chem 23:128-137
-
(2002)
J Comput Chem
, vol.23
, pp. 128-137
-
-
Rocchia, W.1
Sridharan, S.2
Nicholls, A.3
Alexov, E.4
Chiabrera, A.5
Honig, B.6
-
32
-
-
23144465464
-
Solubility enhancement of Cox-2 inhibitors using various solvent systems
-
Seedher N, Bhatia S (2003) Solubility enhancement of Cox-2 inhibitors using various solvent systems. AAPS PharmSciTech 4:1-9
-
(2003)
AAPS PharmSciTech
, vol.4
, pp. 1-9
-
-
Seedher, N.1
Bhatia, S.2
-
33
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978-1988
-
(1994)
J Phys Chem
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
34
-
-
22344451979
-
Single-molecule tracking of sub-millisecond domain motion in calmodulin
-
Slaughter B, Bieber-Urbauer R, Johnson C (2005a) Single-molecule tracking of sub-millisecond domain motion in calmodulin. J Phys Chem B 109(26):12658-12662
-
(2005)
J Phys Chem B
, vol.109
, Issue.26
, pp. 12658-12662
-
-
Slaughter, B.1
Bieber-Urbauer, R.2
Johnson, C.3
-
35
-
-
14844352643
-
Conformational substates of calmodulin revealed by single-pair fluorescence resonance energy transfer: Influence of solution conditions and oxidative modification
-
Slaughter B, Unruh J, Allen M, Bieber R, Johnson C (2005b) Conformational substates of calmodulin revealed by single-pair fluorescence resonance energy transfer: influence of solution conditions and oxidative modification. Biochemistry 44:3694-3707
-
(2005)
Biochemistry
, vol.44
, pp. 3694-3707
-
-
Slaughter, B.1
Unruh, J.2
Allen, M.3
Bieber, R.4
Johnson, C.5
-
36
-
-
0024396312
-
Crystal structures of the helix-loop-helix calcium-binding proteins
-
Strynadka N, James M (1989) Crystal structures of the helix-loop-helix calcium-binding proteins. Annu Rev Biochem 58:951-998
-
(1989)
Annu Rev Biochem
, vol.58
, pp. 951-998
-
-
Strynadka, N.1
James, M.2
-
37
-
-
11144236975
-
Electric charge balance mechanism of extended soluble proteins
-
Uchikoga N, Takahashi SY, Ke R, Sonoyama M, Mitaku S (2005) Electric charge balance mechanism of extended soluble proteins. Protein Sci 14:74-80
-
(2005)
Protein Sci
, vol.14
, pp. 74-80
-
-
Uchikoga, N.1
Takahashi, S.Y.2
Ke, R.3
Sonoyama, M.4
Mitaku, S.5
-
38
-
-
1542358827
-
Structure, dynamics and interaction with kinase targets: Computer simulations of calmodulin
-
Yang C, Jas GS, Kuczera K (2004) Structure, dynamics and interaction with kinase targets: computer simulations of calmodulin. Biochim Biophys Acta 1697:289-300
-
(2004)
Biochim Biophys Acta
, vol.1697
, pp. 289-300
-
-
Yang, C.1
Jas, G.S.2
Kuczera, K.3
-
39
-
-
0029160568
-
Calcium-induced conformational transition revealed by the solution structure of apo calmodulin
-
Zhang M, Tanaka T, Ikura M (1995) Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nat Struct Biol 2:758-767
-
(1995)
Nat Struct Biol
, vol.2
, pp. 758-767
-
-
Zhang, M.1
Tanaka, T.2
Ikura, M.3
-
40
-
-
14544285906
-
Comparative study of generalized born models: Born radii and peptide folding
-
Zhu J, Alexov E, Honig B (2005) Comparative study of generalized born models: born radii and peptide folding. J Phys Chem B 109:3008-3022
-
(2005)
J Phys Chem B
, vol.109
, pp. 3008-3022
-
-
Zhu, J.1
Alexov, E.2
Honig, B.3
|