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Harry A. Stern, Ph.D. - Publications

Affiliations: 
University of Rochester, Rochester, NY 
 2001 Columbia University, New York, NY 
Area:
Theory of liquids, molecular dynamics and Monte Carlo simulations of condensed matter
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21 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH. Revised RNA dihedral parameters for the Amber force field improve RNA molecular dynamics. Journal of Chemical Theory and Computation. PMID 28048939 DOI: 10.1021/Acs.Jctc.6B00870  0.377
2013 Lee AJ, Asher WB, Stern HA, Bren KL, Krauss TD. Single-Molecule Analysis of Cytochrome c Folding by Monitoring the Lifetime of an Attached Fluorescent Probe. The Journal of Physical Chemistry Letters. 4: 2727-2733. PMID 24116268 DOI: 10.1021/Jz401259Y  0.315
2012 Yildirim I, Kennedy SD, Stern HA, Hart JM, Kierzek R, Turner DH. Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs. Journal of Chemical Theory and Computation. 8: 172-181. PMID 22249447 DOI: 10.1021/Ct200557R  0.402
2011 Yildirim I, Stern HA, Tubbs JD, Kennedy SD, Turner DH. Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions. The Journal of Physical Chemistry. B. 115: 9261-70. PMID 21721539 DOI: 10.1021/Jp2016006  0.388
2011 Park MS, Smrcka AV, Stern HA. Conformational flexibility and binding interactions of the G protein βγ heterodimer. Proteins. 79: 518-27. PMID 21064128 DOI: 10.1002/Prot.22899  0.391
2010 Yildirim I, Stern HA, Kennedy SD, Tubbs JD, Turner DH. Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine. Journal of Chemical Theory and Computation. 6: 1520-1531. PMID 20463845 DOI: 10.1021/Ct900604A  0.364
2010 Gao C, Park MS, Stern HA. Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities. Biophysical Journal. 98: 901-10. PMID 20197044 DOI: 10.1016/J.Bpj.2009.11.018  0.313
2010 Smrcka AV, Kichik N, Tarragó T, Burroughs M, Park MS, Itoga NK, Stern HA, Willardson BM, Giralt E. NMR analysis of G-protein betagamma subunit complexes reveals a dynamic G(alpha)-Gbetagamma subunit interface and multiple protein recognition modes. Proceedings of the National Academy of Sciences of the United States of America. 107: 639-44. PMID 20018744 DOI: 10.1073/Pnas.0909503107  0.322
2009 Yildirim I, Stern HA, Sponer J, Spackova N, Turner DH. Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs. Journal of Chemical Theory and Computation. 5: 2088-2100. PMID 20090924 DOI: 10.1021/Ct800540C  0.412
2007 Stern HA. Molecular simulation with variable protonation states at constant pH. The Journal of Chemical Physics. 126: 164112. PMID 17477594 DOI: 10.1063/1.2731781  0.395
2007 Gao C, Stern HA. Scoring function accuracy for membrane protein structure prediction. Proteins. 68: 67-75. PMID 17407162 DOI: 10.1002/Prot.21421  0.312
2004 Kaminski GA, Stern HA, Berne BJ, Friesner RA. Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry Journal of Physical Chemistry A. 108: 621-627. DOI: 10.1021/Jp0301103  0.564
2003 Stern HA, Feller SE. Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation Journal of Chemical Physics. 118: 3401-3412. DOI: 10.1063/1.1537244  0.342
2002 Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YX, Murphy RB, Zhou R, Halgren TA. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. Journal of Computational Chemistry. 23: 1515-31. PMID 12395421 DOI: 10.1002/Jcc.10125  0.636
2002 Margulis CJ, Stern HA, Berne BJ. Computer simulation of a "green chemistry" room-temperature ionic solvent Journal of Physical Chemistry B. 106: 12017-12021. DOI: 10.1021/Jp021392U  0.631
2002 Margulis CJ, Stern HA, Berne BJ. Helix unfolding and intramolecular hydrogen bond dynamics in small α-helices in explicit solvent Journal of Physical Chemistry B. 106: 10748-10752. DOI: 10.1021/Jp0205158  0.646
2002 Xu H, Stern HA, Berne BJ. Can water polarizability be ignored in hydrogen bond kinetics? Journal of Physical Chemistry B. 106: 2054-2060. DOI: 10.1021/Jp013426O  0.633
2001 Stern HA, Berne BJ. Quantum effects in liquid water: Path-integral simulations of a flexible and polarizable ab initio model Journal of Chemical Physics. 115: 7622-7628. DOI: 10.1063/1.1407287  0.563
2001 Stern HA, Rittner F, Berne BJ, Friesner RA. Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function Journal of Chemical Physics. 115: 2237-2251. DOI: 10.1063/1.1376165  0.568
2001 Vargas R, Garza J, Friesner RA, Stern H, Hay BP, Dixon DA. Strength of the N-H⋯O=C and C-H⋯O=C bonds in formamide and N-methylacetamide dimers Journal of Physical Chemistry A. 105: 4963-4968. DOI: 10.1021/Jp003888M  0.36
1999 Stern HA, Kaminski GA, Banks JL, Zhou R, Berne BJ, Friesner RA. Fluctuating charge, polarizable dipole, and combined models: Parameterization from ab initio quantum chemistry Journal of Physical Chemistry B. 103: 4730-4737. DOI: 10.1021/Jp984498R  0.617
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