308 related articles for article (PubMed ID: 19274707)
1. MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling.
Song Y; Mao J; Gunner MR
J Comput Chem; 2009 Nov; 30(14):2231-47. PubMed ID: 19274707
[TBL] [Abstract][Full Text] [Related]
2. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
Georgescu RE; Alexov EG; Gunner MR
Biophys J; 2002 Oct; 83(4):1731-48. PubMed ID: 12324397
[TBL] [Abstract][Full Text] [Related]
3. 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. PubMed ID: 21910138
[TBL] [Abstract][Full Text] [Related]
4. Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol.
Song Y
Proteins; 2011 Dec; 79(12):3356-63. PubMed ID: 22072519
[TBL] [Abstract][Full Text] [Related]
5. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.
Alexov EG; Gunner MR
Biophys J; 1997 May; 72(5):2075-93. PubMed ID: 9129810
[TBL] [Abstract][Full Text] [Related]
6. Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme.
Warwicker J
Protein Sci; 2004 Oct; 13(10):2793-805. PubMed ID: 15388865
[TBL] [Abstract][Full Text] [Related]
7. 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. PubMed ID: 21748801
[TBL] [Abstract][Full Text] [Related]
8. Electrostatic environment of hemes in proteins: pK(a)s of hydroxyl ligands.
Song Y; Mao J; Gunner MR
Biochemistry; 2006 Jul; 45(26):7949-58. PubMed ID: 16800621
[TBL] [Abstract][Full Text] [Related]
9. Optimizing pKa computation in proteins with pH adapted conformations.
Kieseritzky G; Knapp EW
Proteins; 2008 May; 71(3):1335-48. PubMed ID: 18058906
[TBL] [Abstract][Full Text] [Related]
10. pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.
Spassov VZ; Luecke H; Gerwert K; Bashford D
J Mol Biol; 2001 Sep; 312(1):203-19. PubMed ID: 11545597
[TBL] [Abstract][Full Text] [Related]
11. Rapid calculation of protein pKa values using Rosetta.
Kilambi KP; Gray JJ
Biophys J; 2012 Aug; 103(3):587-595. PubMed ID: 22947875
[TBL] [Abstract][Full Text] [Related]
12. Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions.
Song Y; Gunner MR
Proc Natl Acad Sci U S A; 2014 Nov; 111(46):16377-82. PubMed ID: 25362051
[TBL] [Abstract][Full Text] [Related]
13. 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. PubMed ID: 21744395
[TBL] [Abstract][Full Text] [Related]
14. Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers.
Rabenstein B; Knapp EW
Biophys J; 2001 Mar; 80(3):1141-50. PubMed ID: 11222279
[TBL] [Abstract][Full Text] [Related]
15. Predicting the acid/base behavior of proteins: a constant-pH Monte Carlo approach with generalized born solvent.
Aleksandrov A; Polydorides S; Archontis G; Simonson T
J Phys Chem B; 2010 Aug; 114(32):10634-48. PubMed ID: 20701391
[TBL] [Abstract][Full Text] [Related]
16. Using multiconformation continuum electrostatics to compare chloride binding motifs in alpha-amylase, human serum albumin, and Omp32.
Song Y; Gunner MR
J Mol Biol; 2009 Apr; 387(4):840-56. PubMed ID: 19340943
[TBL] [Abstract][Full Text] [Related]
17. Interhelical ion pairing in coiled coils: solution structure of a heterodimeric leucine zipper and determination of pKa values of Glu side chains.
Marti DN; Jelesarov I; Bosshard HR
Biochemistry; 2000 Oct; 39(42):12804-18. PubMed ID: 11041845
[TBL] [Abstract][Full Text] [Related]
18. Self-consistent field approach to protein structure and stability. I: pH dependence of electrostatic contribution.
Dimitrov RA; Crichton RR
Proteins; 1997 Apr; 27(4):576-96. PubMed ID: 9141137
[TBL] [Abstract][Full Text] [Related]
19. Protein imperfections: separating intrinsic from extrinsic variation of torsion angles.
Butterfoss GL; Richardson JS; Hermans J
Acta Crystallogr D Biol Crystallogr; 2005 Jan; 61(Pt 1):88-98. PubMed ID: 15608380
[TBL] [Abstract][Full Text] [Related]
20. Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function.
Garden DP; Zhorov BS
J Comput Aided Mol Des; 2010 Feb; 24(2):91-105. PubMed ID: 20119653
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
