556 related articles for article (PubMed ID: 15229889)
1. Calculating proton uptake/release and 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
Proteins; 2004 Aug; 56(3):572-84. PubMed ID: 15229889
[TBL] [Abstract][Full Text] [Related]
2. Dissection of the pH dependence of inhibitor binding energetics for an aspartic protease: direct measurement of the protonation states of the catalytic aspartic acid residues.
Xie D; Gulnik S; Collins L; Gustchina E; Suvorov L; Erickson JW
Biochemistry; 1997 Dec; 36(51):16166-72. PubMed ID: 9405050
[TBL] [Abstract][Full Text] [Related]
3. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin.
Gómez J; Freire E
J Mol Biol; 1995 Sep; 252(3):337-50. PubMed ID: 7563055
[TBL] [Abstract][Full Text] [Related]
4. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.
Krystek S; Stouch T; Novotny J
J Mol Biol; 1993 Dec; 234(3):661-79. PubMed ID: 8254666
[TBL] [Abstract][Full Text] [Related]
5. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase.
Archontis G; Simonson T; Karplus M
J Mol Biol; 2001 Feb; 306(2):307-27. PubMed ID: 11237602
[TBL] [Abstract][Full Text] [Related]
6. Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor.
Gutiérrez-de-Terán H; Nervall M; Dunn BM; Clemente JC; Aqvist J
FEBS Lett; 2006 Oct; 580(25):5910-6. PubMed ID: 17045991
[TBL] [Abstract][Full Text] [Related]
7. Molecular dynamics simulations of the three dimensional model of plasmepsin II-peptidic inhibitor complexes.
Pranav Kumar SK; Kulkarni VM
Drug Des Discov; 2001; 17(4):293-313. PubMed ID: 11765133
[TBL] [Abstract][Full Text] [Related]
8. Very fast prediction and rationalization of pKa values for protein-ligand complexes.
Bas DC; Rogers DM; Jensen JH
Proteins; 2008 Nov; 73(3):765-83. PubMed ID: 18498103
[TBL] [Abstract][Full Text] [Related]
9. Continuum electrostatic model for the binding of cytochrome c2 to the photosynthetic reaction center from Rhodobacter sphaeroides.
Miyashita O; Onuchic JN; Okamura MY
Biochemistry; 2003 Oct; 42(40):11651-60. PubMed ID: 14529275
[TBL] [Abstract][Full Text] [Related]
10. Crystal structure of aspartic proteinase from Irpex lacteus in complex with inhibitor pepstatin.
Fujimoto Z; Fujii Y; Kaneko S; Kobayashi H; Mizuno H
J Mol Biol; 2004 Aug; 341(5):1227-35. PubMed ID: 15321718
[TBL] [Abstract][Full Text] [Related]
11. Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level.
Jayaram B; McConnell K; Dixit SB; Das A; Beveridge DL
J Comput Chem; 2002 Jan; 23(1):1-14. PubMed ID: 11913374
[TBL] [Abstract][Full Text] [Related]
12. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations.
Archontis G; Simonson T; Moras D; Karplus M
J Mol Biol; 1998 Feb; 275(5):823-46. PubMed ID: 9480772
[TBL] [Abstract][Full Text] [Related]
13. Catalysis and linear free energy relationships in aspartic proteases.
Bjelic S; Aqvist J
Biochemistry; 2006 Jun; 45(25):7709-23. PubMed ID: 16784222
[TBL] [Abstract][Full Text] [Related]
14. Assessment of solvation effects on calculated binding affinity differences: trypsin inhibition by flavonoids as a model system for congeneric series.
Checa A; Ortiz AR; de Pascual-Teresa B; Gago F
J Med Chem; 1997 Dec; 40(25):4136-45. PubMed ID: 9406602
[TBL] [Abstract][Full Text] [Related]
15. Structure-based thermodynamic design of peptide ligands: application to peptide inhibitors of the aspartic protease endothiapepsin.
Luque I; Gómez J; Semo N; Freire E
Proteins; 1998 Jan; 30(1):74-85. PubMed ID: 9443342
[TBL] [Abstract][Full Text] [Related]
16. Multiple protonation equilibria in electrostatics of protein-protein binding.
Piłat Z; Antosiewicz JM
J Phys Chem B; 2008 Nov; 112(47):15074-85. PubMed ID: 18950218
[TBL] [Abstract][Full Text] [Related]
17. Energetics of target peptide recognition by calmodulin: a calorimetric study.
Wintrode PL; Privalov PL
J Mol Biol; 1997 Mar; 266(5):1050-62. PubMed ID: 9086281
[TBL] [Abstract][Full Text] [Related]
18. Proton release due to manganese binding and oxidation in modified bacterial reaction centers.
Kálmán L; Thielges MC; Williams JC; Allen JP
Biochemistry; 2005 Oct; 44(40):13266-73. PubMed ID: 16201752
[TBL] [Abstract][Full Text] [Related]
19. Quantifying protein microstructure and electrostatic effects on the change in Gibbs free energy of binding in immobilized metal affinity chromatography.
Pathange LP; Bevan DR; Zhang C
Anal Chem; 2008 Mar; 80(5):1628-40. PubMed ID: 18229947
[TBL] [Abstract][Full Text] [Related]
20. The carboxyl side chain of glutamate 681 interacts with a chloride binding modifier site that allosterically modulates the dimeric conformational state of band 3 (AE1). Implications for the mechanism of anion/proton cotransport.
Salhany JM; Sloan RL; Cordes KS
Biochemistry; 2003 Feb; 42(6):1589-602. PubMed ID: 12578372
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
