TGQR 2010Q4 Report.pdf - Teragridforum.org

397. Evaluating the Performance of the FF99SB Force Field Based on NMR Scalar Coupling Data
Wickstrom, L., Okur, A. and Simmerling, C., “”, Biophys. J., 97, 853 (2009)
398. Dynamic Behavior of DNA Duplexes Suggests a Mechanism for Selective Destabilization of Lesions by
a DNA Glycosylase, Bergonzo, C., Song, K., de los Santos, C., Grollman, A., Simmerling, C. (in
revision: Nucleic Acids Research, 2010)
399. Slow onset inhibition of bacterial & β-ketoacyl-ACP synthases by thiolactomycin, Machutta, C., Gopal,
B., Luckner, S., Kapilashrami, K., Ruzsicska, B., Simmerling, C., Kisker, C., and Tonge, P., J. Biol.
Chem. 285, 6161 (2010)
400. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber Luchko, T.,
Gusarov, S., Roe, D., Simmerling, C., Case, D., Tuszynski, J. and Kovalenko, A., J. Chem. Theory &
Comput, 6, 607 (2010).
401. Synthesis and Molecular Modeling of a Nitrogen Mustard DNA Interstrand Crosslink Guainazzi, A.,
Campbell, A., Angelov, T., Simmerling, C. and Schärer, O., “”, Chemistry: A European Journal, in press.
402. Mechanism of Glycosylase Discrimination of Oxidatively Damaged DNA, Arthur J. Campbell, Christina
Bergonzo, Lin Fu, Haoquan Li, Dmitry O. Zharkov, Carlos de los Santos, Arthur Grollman and Carlos
Simmerling, submitted
403. Improving the Description of Salt Bridge Strength and Geometry in a Generalized Born Model, Y.
Shang, H. Nguyen, L. Wickstrom, A. Okur and C. Simmerling, J. Mol. Graphics & Modelling, submitted
404. Role of the Glycosylase Wedge in Base Excision Repair of Oxidative DNA Damage, Campbell, A.,
Bergonzo, C., Fu, L., de los Santos, C., Grollman, A., Zharkov, D. and Simmerling, C., submitted
405. ff10SB: Optimization of protein backbone and sidechain dihedrail parameters from the ff99SB force
field. Martinez, C., Maier, J., Wickstrom, L. and Simmerling, C., in preparation
406. Enhanced Sampling In Multidimensional Replica Exchange Umbrella Sampling, Lin, F., Bergonzo, C.,
C., Grollman, A. and Simmerling, C., in preparation
407. Translocation of Repair Proteins along DNA during Lesion Search, Carvalho, A., Bergonzo, C. and
Simmerling, C., in preparation
408. Mapping Conformational Changes During Base Excision Repair, Bergonzo, C., Campbell, A.J., Fu, L.,
Song, K., de los Santos, C., Grollman, A., Simmerling, C. in preparation
409. Role of the Glycosylase Active Site Loop in Early Recognition of Oxidative DNA Damage. Lin, F.,
Campbell, A., Bergonzo, C., de los Santos, C., Grollman, A. and Simmerling, C., in preparation
410. Changes in Dimer Interface Dynamics Result in Modulation of Drug Sensitivity between HIV-1 Protease
Subtypes, Shang, M., Roitberg, A., Fanucci, G. and Simmerling, C., in preparation
411. Structural Basis of Slow Onset Inhibition Mechanism in Mycobacterium tuberculosis InhA. Lai, C., Li, H.,
Liu, N., Garcia-Diaz, M., Tonge, P. and Simmerling, C., in preparation
412. The Transition between the Closed and Semi-open Form of HIV-1 Protease through Swapping of the
Flap Tip Hydrophobic Cluster, F. Ding and C. Simmerling, in preparation.
413. Flap opening mechanism of HIV-PR explored by microsecond-scale MD simulations: Role of the Dimer
Interface, F. Ding and C. Simmerling, in preparation.
414. Improved Parameters for the Generalized Born Neck Model, Nguyen, H., Roe, D., Shang, Y. and
Simmerling, C. in preparation
MCA05S028
415. B. Luan, R. Carr, M. Caffrey and A. Aksimentiev. The effect of calcium on the conformation of
cobalamin transporter BtuB. Proteins: Structure, Function, and Bioinformatics 78:1153–1162 (2010).
416. B. Luan and A. Aksimentiev. Electric and electrophoretic inversion of the DNA charge in multivalent
electrolytes. Soft Matter 6, 243-246 (2010).
417. A. Aksimentiev. Deciphering ionic current signatures of DNA transport through a nanopore. Nanoscale
2, 468–483 (2010). Cover.
418. W. Timp, U. M. Mirsaidov, D. Wang, J. Comer, A. Aksimentiev, and G. Timp. Nanopore sequencing:
Electrical measurements of the code of life. IEEE Transactions on Nanotechnology 9:281-294 (2010).
Cover.
419. D. Wells, A. Aksimentiev. Mechanical properties of a complete microtubule revealed through molecular
dynamics simulation. Biophysical Journal 99:629-637 (2010).
420. B. Luan and A. Aksimentiev. Control and reversal of the electrophoretic force on DNA in a charged
nanopore. Journal of Physics: Condensed Matter, in press (2010).
421. R. Carr, J. Comer, M. Ginsberg and A. Aksimentiev. Modeling pressure-driven transport of proteins
through a nanochannel. IEEE Transactions on Nanotechnology 99, doi:10.1109/TNANO.2010.2062530
(2010).
422. U. Mirsaidov, J. Comer, V. Dimitrov, A. Aksimentiev and G. Timp. Slowing the translocation of doublestranded
DNA using a nanopore smaller than the double helix. Nanotechnology 21:395501-10 (2010).