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Results: 1 to 20 of 106

Similar articles for PubMed (Select 21744395)

1.

Developing hybrid approaches to predict pKa values of ionizable groups.

Witham S, Talley K, Wang L, Zhang Z, Sarkar S, Gao D, Yang W, Alexov E.

Proteins. 2011 Dec;79(12):3389-99. doi: 10.1002/prot.23097. Epub 2011 Jul 8.

2.

Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol.

Song Y.

Proteins. 2011 Dec;79(12):3356-63. doi: 10.1002/prot.23146. Epub 2011 Aug 30.

PMID:
22072519
3.

Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values.

Word JM, Nicholls A.

Proteins. 2011 Dec;79(12):3400-9. doi: 10.1002/prot.23079. Epub 2011 Jun 9.

PMID:
21661059
4.

pKa predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.

Warwicker J.

Proteins. 2011 Dec;79(12):3374-80. doi: 10.1002/prot.23078. Epub 2011 Jun 9.

PMID:
21661058
5.

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics.

Arthur EJ, Yesselman JD, Brooks CL 3rd.

Proteins. 2011 Dec;79(12):3276-86. doi: 10.1002/prot.23195. Epub 2011 Oct 15.

6.

Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study.

Williams SL, Blachly PG, McCammon JA.

Proteins. 2011 Dec;79(12):3381-8. doi: 10.1002/prot.23136. Epub 2011 Aug 30.

7.

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

Gunner MR, Zhu X, Klein MC.

Proteins. 2011 Dec;79(12):3306-19. doi: 10.1002/prot.23124. Epub 2011 Sep 9.

PMID:
21910138
8.

Histidine in continuum electrostatics protonation state calculations.

Couch V, Stuchebrukhov A.

Proteins. 2011 Dec;79(12):3410-9. doi: 10.1002/prot.23114. Epub 2011 Aug 30.

9.

Structural origins of high apparent dielectric constants experienced by ionizable groups in the hydrophobic core of a protein.

Chimenti MS, Castañeda CA, Majumdar A, García-Moreno E B.

J Mol Biol. 2011 Jan 14;405(2):361-77. doi: 10.1016/j.jmb.2010.10.001. Epub 2010 Nov 6.

10.
11.

Protein electrostatics and pKa blind predictions; contribution from empirical predictions of internal ionizable residues.

Olsson MH.

Proteins. 2011 Dec;79(12):3333-45. doi: 10.1002/prot.23113. Epub 2011 Aug 30.

PMID:
22072518
12.

Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential.

Shan J, Mehler EL.

Proteins. 2011 Dec;79(12):3346-55. doi: 10.1002/prot.23098. Epub 2011 Jul 11.

13.

Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen BL, Xia K, Shen JK.

Proteins. 2011 Dec;79(12):3364-73. doi: 10.1002/prot.23080. Epub 2011 Jul 11.

PMID:
21748801
14.

Predicting pKa values with continuous constant pH molecular dynamics.

Wallace JA, Shen JK.

Methods Enzymol. 2009;466:455-75. doi: 10.1016/S0076-6879(09)66019-5. Epub 2009 Nov 13.

PMID:
21609872
15.

pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.

Ghosh N, Cui Q.

J Phys Chem B. 2008 Jul 17;112(28):8387-97. doi: 10.1021/jp800168z. Epub 2008 Jun 10.

16.

Electrostatic effects in unfolded staphylococcal nuclease.

Fitzkee NC, García-Moreno E B.

Protein Sci. 2008 Feb;17(2):216-27. doi: 10.1110/ps.073081708.

17.

Blind, one-eyed, or eagle-eyed? pKa calculations during blind predictions with staphylococcal nuclease.

Czodrowski P.

Proteins. 2011 Dec;79(12):3299-305. doi: 10.1002/prot.23110. Epub 2011 Aug 23.

PMID:
22072517
18.

Electrostatic effects in a network of polar and ionizable groups in staphylococcal nuclease.

Baran KL, Chimenti MS, Schlessman JL, Fitch CA, Herbst KJ, Garcia-Moreno BE.

J Mol Biol. 2008 Jun 20;379(5):1045-62. doi: 10.1016/j.jmb.2008.04.021. Epub 2008 Apr 16.

PMID:
18499123
19.

Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease.

Karp DA, Stahley MR, García-Moreno B.

Biochemistry. 2010 May 18;49(19):4138-46. doi: 10.1021/bi902114m.

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