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Items: 1 to 20 of 126

1.

Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding.

Fenley AT, Muddana HS, Gilson MK.

Proc Natl Acad Sci U S A. 2012 Dec 4;109(49):20006-11. doi: 10.1073/pnas.1213180109. Epub 2012 Nov 13.

2.

Constraining binding hot spots: NMR and molecular dynamics simulations provide a structural explanation for enthalpy-entropy compensation in SH2-ligand binding.

Ward JM, Gorenstein NM, Tian J, Martin SF, Post CB.

J Am Chem Soc. 2010 Aug 18;132(32):11058-70. doi: 10.1021/ja910535j.

3.

Binding of bovine pancreatic trypsin inhibitor to trypsinogen: spectroscopic and volumetric studies.

Filfil R, Ratavosi A, Chalikian TV.

Biochemistry. 2004 Feb 10;43(5):1315-22.

PMID:
14756568
4.

Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations.

Boned R, van Gunsteren WF, Daura X.

Chemistry. 2008;14(16):5039-46. doi: 10.1002/chem.200701380.

PMID:
18399522
6.

Rigidification of a flexible protease inhibitor variant upon binding to trypsin.

Hanson WM, Domek GJ, Horvath MP, Goldenberg DP.

J Mol Biol. 2007 Feb 9;366(1):230-43. Epub 2006 Nov 7.

8.

Enthalpy-entropy compensations in drug-DNA binding studies.

Breslauer KJ, Remeta DP, Chou WY, Ferrante R, Curry J, Zaunczkowski D, Snyder JG, Marky LA.

Proc Natl Acad Sci U S A. 1987 Dec;84(24):8922-6.

9.

Enthalpy-Entropy Compensation upon Molecular Conformational Changes.

Ahmad M, Helms V, Lengauer T, Kalinina OV.

J Chem Theory Comput. 2015 Apr 14;11(4):1410-8. doi: 10.1021/ct501161t. Epub 2015 Mar 11.

PMID:
26574352
10.

Develop and test a solvent accessible surface area-based model in conformational entropy calculations.

Wang J, Hou T.

J Chem Inf Model. 2012 May 25;52(5):1199-212. doi: 10.1021/ci300064d. Epub 2012 Apr 24.

11.

Thermodynamic characterization of new positive allosteric modulators binding to the glutamate receptor A2 ligand-binding domain: combining experimental and computational methods unravels differences in driving forces.

Nørholm AB, Francotte P, Goffin E, Botez I, Danober L, Lestage P, Pirotte B, Kastrup JS, Olsen L, Oostenbrink C.

J Chem Inf Model. 2014 Dec 22;54(12):3404-16. doi: 10.1021/ci500559b. Epub 2014 Dec 9.

PMID:
25420075
12.

Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability.

Raman EP, MacKerell AD Jr.

J Am Chem Soc. 2015 Feb 25;137(7):2608-21. doi: 10.1021/ja512054f. Epub 2015 Feb 16.

13.

Thermodynamic properties of BPTI variants with highly simplified amino acid sequences.

Kato A, Yamada M, Nakamura S, Kidokoro S, Kuroda Y.

J Mol Biol. 2007 Sep 21;372(3):737-46. Epub 2007 Jun 29.

PMID:
17686492
14.

Thermodynamic and structural analysis of highly stabilized BPTIs by single and double mutations.

Islam MM, Sohya S, Noguchi K, Kidokoro S, Yohda M, Kuroda Y.

Proteins. 2009 Dec;77(4):962-70. doi: 10.1002/prot.22522.

PMID:
19830687
15.

Will molecular dynamics simulations of proteins ever reach equilibrium?

Genheden S, Ryde U.

Phys Chem Chem Phys. 2012 Jun 28;14(24):8662-77. doi: 10.1039/c2cp23961b. Epub 2012 May 22.

PMID:
22614001
16.

Conformational stabilization of an engineered binding protein.

Wahlberg E, Härd T.

J Am Chem Soc. 2006 Jun 14;128(23):7651-60.

PMID:
16756322
17.

Defining the thermodynamics of protein/DNA complexes and their components using micro-calorimetry.

Crane-Robinson C, Dragan AI, Read CM.

Methods Mol Biol. 2009;543:625-51. doi: 10.1007/978-1-60327-015-1_37.

PMID:
19378190
18.

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties.

Brandt T, Holzmann N, Muley L, Khayat M, Wegscheid-Gerlach C, Baum B, Heine A, Hangauer D, Klebe G.

J Mol Biol. 2011 Feb 4;405(5):1170-87. doi: 10.1016/j.jmb.2010.11.038. Epub 2010 Nov 25.

PMID:
21111747
19.

Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.

Chodera JD, Mobley DL.

Annu Rev Biophys. 2013;42:121-42. doi: 10.1146/annurev-biophys-083012-130318. Review.

20.

Water networks contribute to enthalpy/entropy compensation in protein-ligand binding.

Breiten B, Lockett MR, Sherman W, Fujita S, Al-Sayah M, Lange H, Bowers CM, Heroux A, Krilov G, Whitesides GM.

J Am Chem Soc. 2013 Oct 16;135(41):15579-84. doi: 10.1021/ja4075776. Epub 2013 Oct 3.

PMID:
24044696

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