Villa A - Search Results

1

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: villa a. Org Biomol Chem. 2005 Apr 7;3(7):1189-94. doi: 10.1039/b418167k. Epub 2005 Feb 24. Org Biomol Chem. 2005. PMID: 15785806

2

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

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

3

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: villa a. 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.

4

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. 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

5

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: villa a. J Am Chem Soc. 2003 Sep 3;125(35):10570-9. doi: 10.1021/ja034676g. J Am Chem Soc. 2003. PMID: 12940739

6

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: villa a. J Comput Chem. 2004 Oct;25(13):1656-76. doi: 10.1002/jcc.20090. J Comput Chem. 2004. PMID: 15264259

7

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. 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

8

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: villa a. J Comput Chem. 2005 Jan 30;26(2):115-22. doi: 10.1002/jcc.20156. J Comput Chem. 2005. PMID: 15584080

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. J Phys Chem B. 2006 Jan 26;110(3):1423-8. doi: 10.1021/jp052722o. J Phys Chem B. 2006. PMID: 16471693

10

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: villa a. 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

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