TGQR 2010Q4 Report.pdf - Teragridforum.org

MCA05S010
401. “Exchange often and properly in replica exchange molecular dynamics.” Daniel J. Sindhikara,
Daniel J. Emerson§, Adrian E. Roitberg. Journal of Chemical Theory and Computation. Submitted and under
review (2010)
402. “Electronic Spectra of the Nanostar Dendrimer: Theory and Experiment.” Julio L. Palma, Evrim
Atas, Lindsay Hardison, Todd B. Marder, Jonathan C. Collings, Andrew Beeby, Joseph S. Melinger, Jeffrey
L. Krause, Valeria D. Kleiman, and Adrian E. Roitberg. Journal of Physical Chemistry. Submitted and under
review (2010)
403. “Comparative validation of computational methods for conformationalanalysis. The Non aromatic
cases of alanine3 and glycine3”. L. Fusti-Molnar, G. Seabra, Robert Abel, A. E. Roitberg and Kenneth M.
Merz, Jr. Journal of Chemical Theory and Computation. Submitted and under review (2010)
404. “p38γ activation triggers dynamical changes in allosteric docking sites”. Ramiro G. Rodriguez
Limardo, Dardo N. Ferreiro, Adrian E. Roitberg, Marcelo A. Marti and Adrian G. Turjanski. Biochemistry.
Submitted and under review (2010)
405. “Unidirectional energy transfer in conjugated molecules: the crucial role of high frequency C(triple)C
bonds.” S. Fernandez-Alberti, Valeria D. Kleiman, S. Tretiak, and Adrian E. Roitberg. Journal of Physical
Chemistry Letters. Submitted and under review (2010) “Substrate Stereo-specificity in tryptophan
dioxygenase and indoleamine 2,3-dioxygenase” L. Capece, M. Arrar, A. E. Roitberg, Syun-Ru Yeh, M. A.
Marti, D. A. Estrin. Proteins: Structure, Function, and Bioinformatics. doi:10.1002/prot.22819 (2010)
406. “Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.” Morgan
Lawrenz, Jeff Wereszczynski, Rommie Amaro, Ross Walker, Adrian Roitberg, J. Andrew McCammon.
Proteins: Structure, Function, and Bioinformatics 78:2523–2532 (2010)
407. "Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation
Model". Meng Y, Roitberg AE, Journal of Chemical Theory and Computation, 6:1401–1412 (2010).
408. “Computational Studies of Ammonia Channel Function in Glutamine 5'-
Phosphoribosylpyrophosphate Amidotransferase”, Wang, XS, Roitberg, AE, Richards, NGJ, Biochemistry,
48:12272-12282 (2009).
409. “Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory
Protein: NikR Characterized by Molecular Dynamics Simulations”, Sindhikara, DJ, Roitberg, AE, Merz, KM,
Biochemistry, 48:12024-12033 (2009).
410. “AM1 Parameters for the Prediction of H-1 and C-13 NMR Chemical Shifts in Proteins”, Williams,
DE, Peters, MB, Wang, B, Roitberg, AE, Merz, KM, Journal of Physical Chemistry A, 113:11550-11559
(2009).
411. “Are Current Semiempirical Methods Better Than Force Fields A Study from the Thermodynamics
Perspective”, Seabra, GD, Walker, RC, Roitberg, AE, Journal of Physical Chemistry A, 113:11938-11948
(2009).
MCA05S027
412. Bellesia, G.; Shea, J.-E. What determines the structure and stability of KFFE monomers, dimers,
and protofibrils Biophys. J. 2009, 96, 875-886.
413. Wu, C.; Murray, M. M.; Bernstein, S. L.; Condron, M. M.; Bitan, G.; Shea, J.-E.; Bowers, M. T. The
structure of A42 C-terminal fragments probed by a combined experimental and theoretical study. J. Mol.
Biol. 2009, 387, 492-501.
414. Murray, M. M.; Krone, M. G.; Bernstein, S. L.; Baumketner, A.; Condron, M. M.; Lazo, N. D.;
Teplow, D. B.; Wyttenbach, T.; Shea, J.-E.; Bowers, M. T. Amyloid -protein: Experiment and theory on the
21-30 fragment. J. Phys. Chem. B 2009, 113, 6041-6046.
415. Bernstein, S. L.; Dupuis, N. F.; Lazo, N. D.; Wyttenbach, T.; Condron, M. M.; Bitan, G.; Teplow, D.
B.; Shea, J.-E.; Ruotolo, B. T.; Robinson, C. V.; Bowers, M. T. Amyloid- protein oligomerization and the
importance of tetramers and dodecamers in the aetiology of Alzheimer's disease. Nat. Chem. 2009, 1, 326-
331.