BOOK CHAPTERS:

1. J.-E. Shea, M. Friedel and A. Baumketner, 'Simulations of protein folding', Rev. Comp. Chem. 22, 169 , (2006)

PEER-REVIEWED PAPERS:

2009

43. Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs and W. Cai, ‘An image-based reaction field method for electrostatic interactions in molecular dynamics simulations’, J. Chem. Phys., under review (2009)

42. M. M. Murray, M. G. Krone, S. L. Bernstein, A. Baumketner, M. M. Condron, N. D. Lazo, D. B. Teplow, T. Wyttenbach, J. E. Shea and M. T. Bowers, “Amyloid b-Protein: Experiment and Theory on the 21-30 Fragment”, J. Phys.Chem. B, 113, 6041 (2009)

41. Z. Xu, W. Cai and A. Baumketner, ‘Optimal integral expressions for effective radii in the generalized Born model of molecular solvation’, J. Chem. Phys., under review (2009)

40. L. Negureanu and A. Baumketner, ‘Microscopic factors that control b-sheet registry in Amyloid fibrils formed by 11-25 fragment of Amyloid b peptide: Insights from computer simulations’, J. Mol. Biol., 389, 921 (2009)

39. A. Baumketner, ‘Systematic errors in potentials of mean force computed in molecular dynamics simulations for a pair of solvated ions using group-based reaction field correction method ’ J. Chem. Phys., 130,  104106 (2009)

2008

38. W. Cai, Z. Xu and A. Baumketner, ‘A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation’, J. Comp. Phys., 227, 10162 (2008)

37. M. Krone Griffin, A. Baumketner, and J.-E. Shea, ‘Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid beta-protein’, J. Mol. Biol., 381, 221 (2008)

36. A. Baumketner, M. Krone Griffin and J.-E. Shea, ‘Role of the familial Dutch mutation E22Q in the folding and aggregation of the 15-28 fragment of the Alzheimer Amyloid-b protein’, Proc. Nat. Acad. Sci., 105, 6027 (2008)

2007

35. M. Friedel, A. Baumketner and J.-E. Shea, 'Stability of a protein tethered to a surface', J. Chem. Phys., 121, 095101 (2007)

34. A. Baumketner and J.-E. Shea, ' The structure of Alzheimer amyloid b(10-35) peptide probed through replica exchange molecular dynamics simulations in explicit water', J. Mol. Biol., 366, 275 (2007)

2006

33. D. B. Teplow, N. D. Lazo, G. Bitan, S. Bernstein, T. Wyttenbach, M. T. Bowers, A. Baumketner, J.-E. Shea, B. Urbanc, L. Cruz, J. Borreguero, H. E. Stanley ' Elucidating amyloid beta-protein folding and assembly: A multidisciplinary approach ', Acc. Chem. Res., 39, 635 (2006)

32. A. Baumketner and J.-E. Shea, ' Folding landscapes of the Alzheimer amyloid-beta(12-28) peptide', J. Mol. Biol., 362, 567 (2006)

31. M. Friedel, A. Baumketner and J.-E. Shea, ' Effects of surface tethering on protein folding mechanisms ',Proc. Nat. Acad. Sci, 103, 8396 (2006)

30. A. Baumketner, S. L. Bernstein, T. Wyttenbach, N. D. Lazo, D. B. Teplow, M. T. Bowers and J.-E. Shea, ' Structure of the 21-30 fragment of amyloid Beta protein ', Protein Science, 15, 1239 (2006)

29. P. Soto, A. Baumketner and J.-E. Shea, ' Aggregation of polyalanine in a hydrophobic environment ', J. Chem. Phys. 124, 134904 , (2006)

28. A. Baumketner, S. L. Bernstein, T. Wyttenbach, G. Bitan, D. B. Teplow, M. T. Bowers and J.-E. Shea, ' The structure of the wild type Amyloid-Beta monomer: a computational and experimental study ', Protein Science, 15, 420 (2006)

27. A. Baumketner and J.-E. Shea ' The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations ', Theor. Chem. Acc. 116, 262 (2006)

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