-
1
-
-
0033794367
-
High-throughput protein crystallization
-
Stevens RC (2000) High-throughput protein crystallization. Curr Opin Struct Biol 10(5):558-563
-
(2000)
Curr Opin Struct Biol
, vol.10
, Issue.5
, pp. 558-563
-
-
Stevens, R.C.1
-
2
-
-
0026206788
-
Sparse matrix sampling: A screening method for crystallization of proteins
-
Jancarik J, Kim SH (1991) Sparse matrix sampling: A screening method for crystallization of proteins. J Appl Crystallogr 24:409-411
-
(1991)
J Appl Crystallogr
, vol.24
, pp. 409-411
-
-
Jancarik, J.1
Kim, S.H.2
-
3
-
-
0035501932
-
Efficiency analysis of sampling protocols used in protein crystallization screening
-
Segelke BW (2001) Efficiency analysis of sampling protocols used in protein crystallization screening. J Cryst Growth 232(1-4):553-562
-
(2001)
J Cryst Growth
, vol.232
, Issue.1-4
, pp. 553-562
-
-
Segelke, B.W.1
-
4
-
-
36749034218
-
In situ proteolysis for protein crystallization and structure determination
-
Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P Jr, Flodin S, Flores A, Graslund S, Hammerstrom M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H (2007) In situ proteolysis for protein crystallization and structure determination. Nat Methods 4(12): 1019-1021
-
(2007)
Nat Methods
, vol.4
, Issue.12
, pp. 1019-1021
-
-
Dong, A.1
Xu, X.2
Edwards, A.M.3
Chang, C.4
Chruszcz, M.5
Cuff, M.6
Cymborowski, M.7
Di Leo, R.8
Egorova, O.9
Evdokimova, E.10
Filippova, E.11
Gu, J.12
Guthrie, J.13
Ignatchenko, A.14
Joachimiak, A.15
Klostermann, N.16
Kim, Y.17
Korniyenko, Y.18
Minor, W.19
Que, Q.20
Savchenko, A.21
Skarina, T.22
Tan, K.23
Yakunin, A.24
Yee, A.25
Yim, V.26
Zhang, R.27
Zheng, H.28
Akutsu, M.29
Arrowsmith, C.30
Avvakumov, G.V.31
Bochkarev, A.32
Dahlgren, L.G.33
Dhe-Paganon, S.34
Dimov, S.35
Dombrovski, L.36
Finerty Jr., P.37
Flodin, S.38
Flores, A.39
Graslund, S.40
Hammerstrom, M.41
Herman, M.D.42
Hong, B.S.43
Hui, R.44
Johansson, I.45
Liu, Y.46
Nilsson, M.47
Nedyalkova, L.48
Nordlund, P.49
Nyman, T.50
Min, J.51
Ouyang, H.52
Park, H.W.53
Qi, C.54
Rabeh, W.55
Shen, L.56
Shen, Y.57
Sukumard, D.58
Tempel, W.59
Tong, Y.60
Tresagues, L.61
Vedadi, M.62
Walker, J.R.63
Weigelt, J.64
Welin, M.65
Wu, H.66
Xiao, T.67
Zeng, H.68
Zhu, H.69
more..
-
5
-
-
0035024436
-
Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of Rho- GDI
-
Longenecker KL, Garrard SM, Sheffield PJ, Derewenda ZS (2001) Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of Rho- GDI. Acta Crystallogr D Biol Crystallogr 57(Pt 5):679-688
-
(2001)
Acta Crystallogr D Biol Crystallogr
, vol.57
, Issue.PART 5
, pp. 679-688
-
-
Longenecker, K.L.1
Garrard, S.M.2
Sheffield, P.J.3
Derewenda, Z.S.4
-
6
-
-
0026059720
-
Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts
-
Lawson DM, Artymiuk PJ, Yewdall SJ, Smith JM, Livingstone JC, Treffry A, Luzzago A, Levi S, Arosio P, Cesareni G et al (1991) Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature 349(6309): 541-544
-
(1991)
Nature
, vol.349
, Issue.6309
, pp. 541-544
-
-
Lawson, D.M.1
Artymiuk, P.J.2
Yewdall, S.J.3
Smith, J.M.4
Livingstone, J.C.5
Treffry, A.6
Luzzago, A.7
Levi, S.8
Arosio, P.9
Cesareni, G.10
-
7
-
-
53249097409
-
Large-scale evaluation of protein reductive methylation for improving protein crystallization
-
Kim Y, Quartey P, Li H, Volkart L, Hatzos C, Chang C, Nocek B, Cuff M, Osipiuk J, Tan K, Fan Y, Bigelow L, Maltseva N, Wu R, Borovilos M, Duggan E, Zhou M, Binkowski TA, Zhang RG, Joachimiak A (2008) Large-scale evaluation of protein reductive methylation for improving protein crystallization. Nat Methods 5(10):853-854
-
(2008)
Nat Methods
, vol.5
, Issue.10
, pp. 853-854
-
-
Kim, Y.1
Quartey, P.2
Li, H.3
Volkart, L.4
Hatzos, C.5
Chang, C.6
Nocek, B.7
Cuff, M.8
Osipiuk, J.9
Tan, K.10
Fan, Y.11
Bigelow, L.12
Maltseva, N.13
Wu, R.14
Borovilos, M.15
Duggan, E.16
Zhou, M.17
Binkowski, T.A.18
Zhang, R.G.19
Joachimiak, A.20
more..
-
8
-
-
0345096595
-
Solvent entropy effects in the formation of protein solid phases
-
Vekilov PG (2003) Solvent entropy effects in the formation of protein solid phases. Methods Enzymol 368:84-105
-
(2003)
Methods Enzymol
, vol.368
, pp. 84-105
-
-
Vekilov, P.G.1
-
9
-
-
0036794760
-
Petsev D solvent entropy contribution to the free energy of protein crystallization
-
Pt 1
-
Vekilov PG, Feeling-Taylor AR, Yau ST (2002) Petsev D solvent entropy contribution to the free energy of protein crystallization. Acta Crystallogr D Biol Crystallogr 58(Pt 10 Pt 1):1611-1616
-
(2002)
Acta Crystallogr D Biol Crystallogr
, vol.58
, Issue.PART 10
, pp. 1611-1616
-
-
Vekilov, P.G.1
Feeling-Taylor, A.R.2
Yau, S.T.3
-
10
-
-
1842555070
-
Rational protein crystallization by mutational surface engineering
-
Derewenda ZS (2004) Rational protein crystallization by mutational surface engineering. Structure 12(4):529-535
-
(2004)
Structure
, vol.12
, Issue.4
, pp. 529-535
-
-
Derewenda, Z.S.1
-
11
-
-
34247465669
-
Protein crystallization by surface entropy reduction: Optimization of the SER strategy
-
Cooper DR, Boczek T, Grelewska K, Pinkowska M, Sikorska M, Zawadzki M, Derewenda Z (2007) Protein crystallization by surface entropy reduction: Optimization of the SER strategy. Acta Crystallogr D Biol Crystallogr 63(Pt 5):636-645
-
(2007)
Acta Crystallogr D Biol Crystallogr
, vol.63
, Issue.PART 5
, pp. 636-645
-
-
Cooper, D.R.1
Boczek, T.2
Grelewska, K.3
Pinkowska, M.4
Sikorska, M.5
Zawadzki, M.6
Derewenda, Z.7
-
12
-
-
33644874674
-
Entropy and surface engineering in protein crystallization
-
Derewenda ZS, Vekilov PG (2006) Entropy and surface engineering in protein crystallization. Acta Crystallogr D Biol Crystallogr 62(Pt 1):116-124
-
(2006)
Acta Crystallogr D Biol Crystallogr
, vol.62
, Issue.PART 1
, pp. 116-124
-
-
Derewenda, Z.S.1
Vekilov, P.G.2
-
13
-
-
33745122241
-
Lysine methylation goes global
-
Morgunkova A, Barlev NA (2006) Lysine methylation goes global. Cell Cycle 5(12):1308-1312
-
(2006)
Cell Cycle
, vol.5
, Issue.12
, pp. 1308-1312
-
-
Morgunkova, A.1
Barlev, N.A.2
-
14
-
-
67650461956
-
A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome
-
Nimura K, Ura K, Shiratori H, Ikawa M, Okabe M, Schwartz RJ, Kaneda Y (2009) A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome. Nature 460(7252): 287-291
-
(2009)
Nature
, vol.460
, Issue.7252
, pp. 287-291
-
-
Nimura, K.1
Ura, K.2
Shiratori, H.3
Ikawa, M.4
Okabe, M.5
Schwartz, R.J.6
Kaneda, Y.7
-
15
-
-
84893169025
-
General atomic and molecular electronic structure system
-
Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, John A, Montgomery J (1993) General atomic and molecular electronic structure system. J Comput Chem 14(11):1347-1363
-
(1993)
J Comput Chem
, vol.14
, Issue.11
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
Su, S.10
Windus, T.L.11
Dupuis, M.12
John, A.13
Montgomery, J.14
-
16
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
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(2):187-217
-
(1983)
J Comput Chem
, vol.4
, Issue.2
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
17
-
-
0025728614
-
OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform
-
Pranata J, Wierschke SG, Jorgensen WL (1991) OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform. J Am Chem Soc 113(8):2810-2819
-
(1991)
J Am Chem Soc
, vol.113
, Issue.8
, pp. 2810-2819
-
-
Pranata, J.1
Wierschke, S.G.2
Jorgensen, W.L.3
-
18
-
-
0034250744
-
An improved empirical potential energy function for molecular simulations of phospholipids
-
Feller SE, MacKerell AD (2000) An improved empirical potential energy function for molecular simulations of phospholipids. J Phys Chem B 104(31):7510-7515
-
(2000)
J Phys Chem B
, vol.104
, Issue.31
, pp. 7510-7515
-
-
Feller, S.E.1
MacKerell, A.D.2
-
19
-
-
0000628743
-
Conformational flexibility of ophosphorylcholine and o- phosphorylethanolamine: A molecular dynamics study of solvation effects
-
Woolf TB, Roux B (1994) Conformational flexibility of ophosphorylcholine and o-phosphorylethanolamine: A molecular dynamics study of solvation effects. J Am Chem Soc 116(13): 5916-5926
-
(1994)
J Am Chem Soc
, vol.116
, Issue.13
, pp. 5916-5926
-
-
Woolf, T.B.1
Roux, B.2
-
20
-
-
0027370168
-
Determination of the side chain pKa values of the lysine residues in calmodulin
-
Zhang M, Vogel HJ (1993) Determination of the side chain pKa values of the lysine residues in calmodulin. J Biol Chem 268(30):22420-22428
-
(1993)
J Biol Chem
, vol.268
, Issue.30
, pp. 22420-22428
-
-
Zhang, M.1
Vogel, H.J.2
-
21
-
-
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(2):926-935
-
(1983)
J Chem Phys
, vol.79
, Issue.2
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
22
-
-
33846823909
-
Particle mesh Ewald: An N × log(N) method for Ewald sums in large systems
-
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N × log(N) method for Ewald sums in large systems. J Chem Phys 98(12):10089-10092
-
(1993)
J Chem Phys
, vol.98
, Issue.12
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
23
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert J-P, 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(3):327-341
-
(1977)
J Comput Phys
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J-.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
24
-
-
77955549204
-
-
James CP, Rosemary B, Wei W, James G, Emad T, Elizabeth V, Christophe C, Robert DS, Laxmikant K, Klaus S (2005) Scalable molecular dynamics with NAMD. 26:1781-1802
-
(2005)
Scalable Molecular Dynamics with NAMD.
, vol.26
, pp. 1781-1802
-
-
James, C.P.1
Rosemary, B.2
Wei, W.3
James, G.4
Emad, T.5
Elizabeth, V.6
Christophe, C.7
Robert, D.S.8
Laxmikant, K.9
Klaus, S.10
-
25
-
-
0027166270
-
Empirical scale of side-chain conformational entropy in protein folding
-
Pickett SD, Sternberg MJ (1993) Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 231(3): 825-839
-
(1993)
J Mol Biol
, vol.231
, Issue.3
, pp. 825-839
-
-
Pickett, S.D.1
Sternberg, M.J.2
-
26
-
-
0028174101
-
Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales
-
Sternberg MJ, Chickos JS (1994) Protein side-chain conformational entropy derived from fusion data-comparison with other empirical scales. Protein Eng 7(2):149-155
-
(1994)
Protein Eng
, vol.7
, Issue.2
, pp. 149-155
-
-
Sternberg, M.J.1
Chickos, J.S.2
-
27
-
-
19644385843
-
Prion and water: Tight and dynamical hydration sites have a key role in structural stability
-
De Simone A, Dodson GG, Verma CS, Zagari A, Fraternali F (2005) Prion and water: Tight and dynamical hydration sites have a key role in structural stability. Proc Natl Acad Sci U S A 102(21):7535-7540
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.21
, pp. 7535-7540
-
-
De Simone, A.1
Dodson, G.G.2
Verma, C.S.3
Zagari, A.4
Fraternali, F.5
-
28
-
-
34547700228
-
CNZH ⋯ O contacts assist crystallization of a ParB-like nuclease
-
Shaw N, Cheng C, Tempel W, Chang J, Ng J, Wang XY, Perrett S, Rose J, Rao Z, Wang BC, Liu ZJ (2007) (NZ)CH ⋯ O contacts assist crystallization of a ParB-like nuclease. BMC Struct Biol 7:46
-
(2007)
BMC Struct Biol
, vol.7
, pp. 46
-
-
Shaw, N.1
Cheng, C.2
Tempel, W.3
Chang, J.4
Ng, J.5
Wang, X.Y.6
Perrett, S.7
Rose, J.8
Rao, Z.9
Wang, B.C.10
Liu, Z.J.11
-
29
-
-
33845554708
-
Crystallographic evidence for the existence of CH ⋯ O, CH ⋯ N and CH ⋯ Cl hydrogen bonds
-
Taylor R, Kennard O (1982) Crystallographic evidence for the existence of CH ⋯ O, CH ⋯ N and CH ⋯ Cl hydrogen bonds. J Am Chem Soc 104(19):5063-5070
-
(1982)
J Am Chem Soc
, vol.104
, Issue.19
, pp. 5063-5070
-
-
Taylor, R.1
Kennard, O.2
-
30
-
-
0034679011
-
How strong is the Calpha-H ⋯ O=C hydrogen bond?
-
Vargas R, Garza J, Dixon DA, Hay BP (2000) How strong is the Calpha-H ⋯ O=C hydrogen bond? J Am Chem Soc 122(19): 4750-4755
-
(2000)
J Am Chem Soc
, vol.122
, Issue.19
, pp. 4750-4755
-
-
Vargas, R.1
Garza, J.2
Dixon, D.A.3
Hay, B.P.4
-
31
-
-
0035971221
-
Strength of the Calpha H ⋯ O hydrogen bond of amino acid residues
-
Scheiner S, Kar T, Gu Y (2001) Strength of the Calpha H ⋯ O hydrogen bond of amino acid residues. J Biol Chem 276(13): 9832-9837
-
(2001)
J Biol Chem
, vol.276
, Issue.13
, pp. 9832-9837
-
-
Scheiner, S.1
Kar, T.2
Gu, Y.3
-
32
-
-
0036286851
-
Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
-
Makarov V, Pettitt BM, Feig M (2002) Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment. Acc Chem Res 35(6):376-384
-
(2002)
Acc Chem Res
, vol.35
, Issue.6
, pp. 376-384
-
-
Makarov, V.1
Pettitt, B.M.2
Feig, M.3
-
33
-
-
33645983232
-
Water structure and interactions with protein surfaces
-
Raschke TM (2006) Water structure and interactions with protein surfaces. Curr Opin Struct Biol 16(2):152-159
-
(2006)
Curr Opin Struct Biol
, vol.16
, Issue.2
, pp. 152-159
-
-
Raschke, T.M.1
-
34
-
-
0024292355
-
Effect of hydrostatic pressure on the solvent in crystals of hen egg-white lysozyme
-
Kundrot CE, Richards FM (1988) Effect of hydrostatic pressure on the solvent in crystals of hen egg-white lysozyme. J Mol Biol 200(2):401-410
-
(1988)
J Mol Biol
, vol.200
, Issue.2
, pp. 401-410
-
-
Kundrot, C.E.1
Richards, F.M.2
-
35
-
-
33646083683
-
Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5
-
Han Z, Guo L, Wang H, Shen Y, Deng XW, Chai J (2006) Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 22(1):137-144
-
(2006)
Mol Cell
, vol.22
, Issue.1
, pp. 137-144
-
-
Han, Z.1
Guo, L.2
Wang, H.3
Shen, Y.4
Deng, X.W.5
Chai, J.6
-
36
-
-
0000207211
-
Thermodynamic constants of complexes of crown ethers and uncharged molecules and x-ray structure of the 18-crown-6. (MeNO2)2 complex
-
De Boer JAA, Reinhoudt DN, Harkema S, Van Hummel GJ, De Jong F (2002) Thermodynamic constants of complexes of crown ethers and uncharged molecules and x-ray structure of the 18-crown-6. (MeNO2)2 complex. J Am Chem Soc 104(15):4073-4076
-
(2002)
J Am Chem Soc
, vol.104
, Issue.15
, pp. 4073-4076
-
-
De Boer, J.A.A.1
Reinhoudt, D.N.2
Harkema, S.3
Van Hummel, G.J.4
De Jong, F.5
-
37
-
-
33748415525
-
Theoretical calculation of hydrogen-bonding strength for drug molecules
-
Hao M-H (2006) Theoretical calculation of hydrogen-bonding strength for drug molecules. J Chem Theory Comput 2(3):863-872
-
(2006)
J Chem Theory Comput
, vol.2
, Issue.3
, pp. 863-872
-
-
Hao, M.-H.1
-
38
-
-
34547566008
-
Toward rational protein crystallization: A web server for the design of crystallizable protein variants
-
Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D (2007) Toward rational protein crystallization: A web server for the design of crystallizable protein variants. Protein Sci 16(8):1569-1576
-
(2007)
Protein Sci
, vol.16
, Issue.8
, pp. 1569-1576
-
-
Goldschmidt, L.1
Cooper, D.R.2
Derewenda, Z.S.3
Eisenberg, D.4
-
40
-
-
0028228418
-
The entropic cost of bound water in crystals and biomolecules
-
Dunitz JD (1994) The entropic cost of bound water in crystals and biomolecules. Science 264(5159):670
-
(1994)
Science
, vol.264
, Issue.5159
, pp. 670
-
-
Dunitz, J.D.1
-
42
-
-
35748955512
-
Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein sex comb on midleg
-
Grimm C, de Ayala Alonso AG, Rybin V, Steuerwald U, Ly- Hartig N, Fischle W, Muller J, Muller CW (2007) Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein sex comb on midleg. EMBO Rep 8(11):1031-1037
-
(2007)
EMBO Rep
, vol.8
, Issue.11
, pp. 1031-1037
-
-
Grimm, C.1
De Ayala Alonso, A.G.2
Rybin, V.3
Steuerwald, U.4
Ly- Hartig, N.5
Fischle, W.6
Muller, J.7
Muller, C.W.8
-
43
-
-
0032479179
-
Anatomy of hot spots in protein interfaces
-
Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280(1):1-9
-
(1998)
J Mol Biol
, vol.280
, Issue.1
, pp. 1-9
-
-
Bogan, A.A.1
Thorn, K.S.2
|