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Items: 1 to 20 of 95

1.

Progress in the prediction of pKa values in proteins.

Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MH, Shen JK, Warwicker J, Williams S, Word JM.

Proteins. 2011 Dec;79(12):3260-75. doi: 10.1002/prot.23189. Epub 2011 Oct 15. Review.

2.

The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins.

Nielsen JE, Gunner MR, García-Moreno BE.

Proteins. 2011 Dec;79(12):3249-59. doi: 10.1002/prot.23194. Epub 2011 Oct 15. Review.

3.

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
4.

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
5.

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.

6.

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
7.

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.

8.

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
9.

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
10.

Electrostatic pKa computations in proteins: role of internal cavities.

Meyer T, Kieseritzky G, Knapp EW.

Proteins. 2011 Dec;79(12):3320-32. doi: 10.1002/prot.23092. Epub 2011 Jul 8.

PMID:
21744394
11.

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.

12.

On the development of protein pKa calculation algorithms.

Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE.

Proteins. 2011 Dec;79(12):3287-98. doi: 10.1002/prot.23091. Epub 2011 Jul 8.

13.

Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?

Machuqueiro M, Baptista AM.

Proteins. 2011 Dec;79(12):3437-47. doi: 10.1002/prot.23115. Epub 2011 Aug 30.

PMID:
22072522
14.

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
15.
16.

Structure-based pKa calculations using continuum electrostatics methods.

Fitch CA, García-Moreno E B.

Curr Protoc Bioinformatics. 2007 Jan;Chapter 8:Unit 8.11. doi: 10.1002/0471250953.bi0811s16.

PMID:
18428794
17.

Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins.

Foloppe N, Sagemark J, Nordstrand K, Berndt KD, Nilsson L.

J Mol Biol. 2001 Jul 6;310(2):449-70.

PMID:
11428900
18.

Theoretical calculations of acid-dissociation constants of proteins.

Juffer AH.

Biochem Cell Biol. 1998;76(2-3):198-209. Review.

PMID:
9923689
19.

Fast empirical pKa prediction by Ewald summation.

Krieger E, Nielsen JE, Spronk CA, Vriend G.

J Mol Graph Model. 2006 Dec;25(4):481-6. Epub 2006 Apr 27.

PMID:
16644253
20.

Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

Salsbury FR Jr, Poole LB, Fetrow JS.

Proteins. 2012 Nov;80(11):2583-91. doi: 10.1002/prot.24142. Epub 2012 Aug 21.

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