TGQR 2010Q4 Report.pdf - Teragridforum.org

Blocked Amino-Acid Residues, for Coarse-Grained Simulations of Protein Structure and Folding I: The
Method. JOURNAL OF COMPUTATIONAL CHEMISTRY, 31 1143-1153 2010 DOI: 10.1002/jcc.21399
446. Kozlowska, U; Maisuradze, GG; Liwo, A; Scheraga, HA. Determination of Side-Chain-Rotamer and
Side-Chain and Backbone Virtual-Bond-Stretching Potentials of Mean Force from AM1 Energy Surfaces
of Terminally-Blocked Amino-Acid Residues, for Coarse-Grained Simulations of Protein Structure and
Folding II: Results, Comparison with Statistical Potentials, and Implementation in the UNRES Force
Field. JOURNAL OF COMPUTATIONAL CHEMISTRY, 31 1154-1167 2010 DOI: 10.1002/jcc.21402
447. Martin, OA; Villegas, ME; Vila, JA; Scheraga, HA. Analysis of C-13(alpha) and C-13(beta) chemical
shifts of cysteine and cystine residues in proteins: a quantum chemical approach. JOURNAL OF
BIOMOLECULAR NMR, 46 217-225 2010 DOI: 10.1007/s10858-010-9396-x
448. Liwo, A; Oldziej, S; Czaplewski, C; Kleinerman, DS; Blood, P; Scheraga, HA. Implementation of
Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively
Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and
Thermodynamics. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 890-909 2010 DOI:
10.1021/ct9004068
449. Maisuradze, GG; Liwo, A; Scheraga, HA. Relation between Free Energy Landscapes of Proteins and
Dynamics. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6 583-595 2010 DOI:
10.1021/ct9005745
450. Makowski, M; Czaplewski, C; Liwo, A; Scheraga, HA. Potential of Mean Force of Association of Large
Hydrophobic Particles: Toward the Nanoscale Limit. JOURNAL OF PHYSICAL CHEMISTRY B, 114
993-1003 2010 DOI: 10.1021/jp907794h
451. Vila, JA; Scheraga, HA. Assessing the Accuracy of Protein Structures by Quantum Mechanical
Computations of C-13(alpha) Chemical Shifts. ACCOUNTS OF CHEMICAL RESEARCH, 42 1545-1553
2009 DOI: 10.1021/ar900068s
452. Vila, JA; Arnautova, YA; Martin, OA; Scheraga, HA. Quantum-mechanics-derived C-13(alpha) chemical
shift server (CheShift) for protein structure validation. PROCEEDINGS OF THE NATIONAL ACADEMY
OF SCIENCES OF THE UNITED STATES OF AMERICA, 106 16972-16977 2009 DOI:
10.1073/pnas.0908833106
453. Sobolewski, E; Makowski, M; Oldziej, S; Czaplewski, C; Liwo, A; Scheraga, HA. Towards temperaturedependent
coarse-grained potentials of side-chain interactions for protein folding simulations. I:
Molecular dynamics study of a pair of methane molecules in water at various temperatures. PROTEIN
ENGINEERING DESIGN & SELECTION, 22 547-552 2009 DOI: 10.1093/protein/gzp028
454. He, Y; Xiao, Y; Liwo, A; Scheraga, HA. Exploring the Parameter Space of the Coarse-Grained UNRES
Force Field by Random Search: Selecting a Transferable Medium-Resolution Force Field. JOURNAL
OF COMPUTATIONAL CHEMISTRY, 30 2127-2135 2009 DOI: 10.1002/jcc.21215
MCB080011
455. Sodium release triggers galactose exit from the sodium-galactose transporter, vSGLT. Watanabe, A.S.
Choe, V. Chaptal, J.M. Rosenberg, E.M. Wright, M. Grabe, and J. Abramson Nature (in press)
456. Water permeation through the sodium-dependent galactose cotransporter vSGLT. Choe, S., J.M.
Rosenberg, J. Abramson, E.M. Wright, and M. Grabe Biophys. J. 99: L56-L58.
MCB080014
457. G. Reddy, J.E. Straub and D. Thirumalai, “Dry amyloid fibril assembly in a yeast prion peptide is
mediated by long-lived structures containing water wires”, Proc. Natl. Acad. Sci. (in review).
458. M.S. Li, N.T. Co, G. Reddy, C.K. Hu and D. Thirumalai, “Determination of factors governing
fibrillogenesis using lattice models”, Phys. Rev. Lett. (in review).
MCB090005
459. Genchev, G. Z., M. Kallberg, G. Gursoy, A. Mittal, L. Dubey, O. Perisic, G. Feng, R. Langlois, and H.
Lu. 2009. Mechanical signaling on the single protein level studied using steered molecular dynamics.
Cell Biochem Biophys 55:141-152
MCB090110
460. Goetz, A.W., Woelfe, T., Walker, R.C., "Quantum Chemistry on Graphics Processing Units", Ann. Rev.
Comp. Chem., 2010, Accepted.
461. Xu, D., Williamson, M.J., Walker, R.C., "Advancements in Molecular Dynamics Simulations of
Biomolecules on Graphical Processing Units.", Ann. Rev. Comp. Chem., 2010, Accepted
462. Lawrenz, M., Wereszczynski, J., Amaro, R., Walker, R.C., Roitberg, A.E., McCammon, J.A., "Impact of
calcium on N1 influenza neuraminidase dynamics and binding free energy", Proteins, 2010, Accepted.