Mark AE - Search Results

1

On the characterization of host-guest complexes: surface tension, calorimetry, and molecular dynamics of cyclodextrins with a non-ionic surfactant.

Piñeiro A, Banquy X, Pérez-Casas S, Tovar E, García A, Villa A, Amigo A, Mark AE, Costas M. Piñeiro A, et al. Among authors: mark ae. J Phys Chem B. 2007 May 3;111(17):4383-92. doi: 10.1021/jp0688815. Epub 2007 Apr 12. J Phys Chem B. 2007. PMID: 17428087

2

Calculation of the free energy of solvation for neutral analogs of amino acid side chains.

Villa A, Mark AE. Villa A, et al. Among authors: mark ae. J Comput Chem. 2002 Apr 15;23(5):548-53. doi: 10.1002/jcc.10052. J Comput Chem. 2002. PMID: 11948581

3

Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin.

Talhout R, Villa A, Mark AE, Engberts JB. Talhout R, et al. Among authors: mark ae. J Am Chem Soc. 2003 Sep 3;125(35):10570-9. doi: 10.1021/ja034676g. J Am Chem Soc. 2003. PMID: 12940739

4

Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin.

Villa A, Zangi R, Pieffet G, Mark AE. Villa A, et al. Among authors: mark ae. J Comput Aided Mol Des. 2003 Oct;17(10):673-86. doi: 10.1023/b:jcam.0000017374.53591.32. J Comput Aided Mol Des. 2003. PMID: 15068366

5

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Oostenbrink C, Villa A, Mark AE, van Gunsteren WF. Oostenbrink C, et al. Among authors: mark ae. J Comput Chem. 2004 Oct;25(13):1656-76. doi: 10.1002/jcc.20090. J Comput Chem. 2004. PMID: 15264259

6

Incorporating the effect of ionic strength in free energy calculations using explicit ions.

Donnini S, Mark AE, Juffer AH, Villa A. Donnini S, et al. Among authors: mark ae. J Comput Chem. 2005 Jan 30;26(2):115-22. doi: 10.1002/jcc.20156. J Comput Chem. 2005. PMID: 15584080

7

Advanced approaches for the characterization of a de novo designed antiparallel coiled coil peptide.

Pagel K, Seeger K, Seiwert B, Villa A, Mark AE, Berger S, Koksch B. Pagel K, et al. Among authors: mark ae. Org Biomol Chem. 2005 Apr 7;3(7):1189-94. doi: 10.1039/b418167k. Epub 2005 Feb 24. Org Biomol Chem. 2005. PMID: 15785806

8

A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: possibilities and limitations.

Piñeiro A, Villa A, Vagt T, Koksch B, Mark AE. Piñeiro A, et al. Among authors: mark ae. Biophys J. 2005 Dec;89(6):3701-13. doi: 10.1529/biophysj.104.055590. Epub 2005 Sep 8. Biophys J. 2005. PMID: 16150975 Free PMC article.

9

Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study.

Villa A, Mark AE, Saracino GA, Cosentino U, Pitea D, Moro G, Salmona M. Villa A, et al. Among authors: mark ae. J Phys Chem B. 2006 Jan 26;110(3):1423-8. doi: 10.1021/jp052722o. J Phys Chem B. 2006. PMID: 16471693

10

How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

Villa A, Fan H, Wassenaar T, Mark AE. Villa A, et al. Among authors: mark ae. J Phys Chem B. 2007 May 31;111(21):6015-25. doi: 10.1021/jp068580v. Epub 2007 May 10. J Phys Chem B. 2007. PMID: 17489626

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