Stephen C. Harvey - Publications

Affiliations: 
1973-2002 Biochemistry University of Alabama, Birmingham, Birmingham, AL, United States 
 2003- Georgia Institute of Technology, Atlanta, GA 
 2015- University of Pennsylvania, Philadelphia, PA, United States 
Area:
Biochemistry
Website:
http://www.harveylabpenn.net/

150 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
2015 Petrov AS, Gulen B, Norris AM, Kovacs NA, Bernier CR, Lanier KA, Fox GE, Harvey SC, Wartell RM, Hud NV, Williams LD. History of the ribosome and the origin of translation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26621738 DOI: 10.1073/pnas.1509761112  0.96
2015 Garmann RF, Gopal A, Athavale SS, Knobler CM, Gelbart WM, Harvey SC. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. Rna (New York, N.Y.). 21: 877-86. PMID 25752599 DOI: 10.1261/rna.047506.114  1
2015 Harvey SC. The scrunchworm hypothesis: transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages. Journal of Structural Biology. 189: 1-8. PMID 25486612 DOI: 10.1016/j.jsb.2014.11.012  1
2014 Bernier CR, Petrov AS, Waterbury CC, Jett J, Li F, Freil LE, Xiong X, Wang L, Migliozzi BL, Hershkovits E, Xue Y, Hsiao C, Bowman JC, Harvey SC, Grover MA, et al. RiboVision suite for visualization and analysis of ribosomes. Faraday Discussions. 169: 195-207. PMID 25340471 DOI: 10.1039/c3fd00126a  0.96
2014 Petrov AS, Bernier CR, Hsiao C, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM, Hud NV, Williams LD. Evolution of the ribosome at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 111: 10251-6. PMID 24982194 DOI: 10.1073/pnas.1407205111  0.96
2014 Petrov AS, Bernier CR, Gulen B, Waterbury CC, Hershkovits E, Hsiao C, Harvey SC, Hud NV, Fox GE, Wartell RM, Williams LD. Secondary structures of rRNAs from all three domains of life. Plos One. 9: e88222. PMID 24505437 DOI: 10.1371/journal.pone.0088222  0.96
2014 Harvey SC. Comment on the letter by A. Ben-Shaul: "entropy, energy, and bending of DNA in viral capsids". Biophysical Journal. 106: 489-92. PMID 24461024 DOI: 10.1016/j.bpj.2013.12.012  1
2013 Rahman KS, Cui G, Harvey SC, McCarty NA. Modeling the conformational changes underlying channel opening in CFTR. Plos One. 8: e74574. PMID 24086355 DOI: 10.1371/journal.pone.0074574  1
2013 Harvey SC, Zeng Y, Heitsch CE. The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites. Journal of Biological Physics. 39: 163-72. PMID 23860866 DOI: 10.1007/s10867-013-9312-1  1
2013 Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD. Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Research. 41: 7522-35. PMID 23771137 DOI: 10.1093/nar/gkt513  0.96
2013 Hsiao C, Chou IC, Okafor CD, Bowman JC, O'Neill EB, Athavale SS, Petrov AS, Hud NV, Wartell RM, Harvey SC, Williams LD. RNA with iron(II) as a cofactor catalyses electron transfer. Nature Chemistry. 5: 525-8. PMID 23695635 DOI: 10.1038/nchem.1649  1
2013 Petrov AS, Douglas SS, Harvey SC. Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 25: 115101. PMID 23399864 DOI: 10.1088/0953-8984/25/11/115101  1
2013 Hsiao C, Lenz TK, Peters JK, Fang PY, Schneider DM, Anderson EJ, Preeprem T, Bowman JC, O'Neill EB, Lie L, Athavale SS, Gossett JJ, Trippe C, Murray J, Petrov AS, ... ... Harvey SC, et al. Molecular paleontology: a biochemical model of the ancestral ribosome. Nucleic Acids Research. 41: 3373-85. PMID 23355613 DOI: 10.1093/nar/gkt023  1
2013 Athavale SS, Gossett JJ, Bowman JC, Hud NV, Williams LD, Harvey SC. In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus. Plos One. 8: e54384. PMID 23349871 DOI: 10.1371/journal.pone.0054384  1
2013 Horowitz ED, Rahman KS, Bower BD, Dismuke DJ, Falvo MR, Griffith JD, Harvey SC, Asokan A. Biophysical and ultrastructural characterization of adeno-associated virus capsid uncoating and genome release. Journal of Virology. 87: 2994-3002. PMID 23269804 DOI: 10.1128/JVI.03017-12  1
2012 Smyda MR, Harvey SC. The entropic cost of polymer confinement. The Journal of Physical Chemistry. B. 116: 10928-34. PMID 22905742 DOI: 10.1021/jp302807r  1
2012 Rishishwar L, Varghese N, Tyagi E, Harvey SC, Jordan IK, McCarty NA. Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR). Plos One. 7: e42336. PMID 22879944 DOI: 10.1371/journal.pone.0042336  1
2012 Zeng Y, Larson SB, Heitsch CE, McPherson A, Harvey SC. A model for the structure of satellite tobacco mosaic virus. Journal of Structural Biology. 180: 110-6. PMID 22750417 DOI: 10.1016/j.jsb.2012.06.008  1
2012 Swenson MS, Anderson J, Ash A, Gaurav P, Sükösd Z, Bader DA, Harvey SC, Heitsch CE. GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops. Bmc Research Notes. 5: 341. PMID 22747589 DOI: 10.1186/1756-0500-5-341  1
2012 Petrov AS, Bernier CR, Hsiao C, Okafor CD, Tannenbaum E, Stern J, Gaucher E, Schneider D, Hud NV, Harvey SC, Williams LD. RNA-magnesium-protein interactions in large ribosomal subunit. The Journal of Physical Chemistry. B. 116: 8113-20. PMID 22712611 DOI: 10.1021/jp304723w  1
2012 Athavale SS, Petrov AS, Hsiao C, Watkins D, Prickett CD, Gossett JJ, Lie L, Bowman JC, O'Neill E, Bernier CR, Hud NV, Wartell RM, Harvey SC, Williams LD. RNA folding and catalysis mediated by iron (II). Plos One. 7: e38024. PMID 22701543 DOI: 10.1371/journal.pone.0038024  1
2012 Athavale SS, Gossett JJ, Hsiao C, Bowman JC, O'Neill E, Hershkovitz E, Preeprem T, Hud NV, Wartell RM, Harvey SC, Williams LD. Domain III of the T. thermophilus 23S rRNA folds independently to a near-native state. Rna (New York, N.Y.). 18: 752-8. PMID 22334759 DOI: 10.1261/rna.030692.111  1
2011 Chen W, Lou J, Hsin J, Schulten K, Harvey SC, Zhu C. Molecular dynamics simulations of forced unbending of integrin α(v)β₃. Plos Computational Biology. 7: e1001086. PMID 21379327 DOI: 10.1371/journal.pcbi.1001086  1
2011 Harvey SC, Petrov AS, Devkota B, Boz MB. Computational approaches to modeling viral structure and assembly. Methods in Enzymology. 487: 513-43. PMID 21187237 DOI: 10.1016/B978-0-12-381270-4.00018-4  1
2011 Gossett JJ, Harvey SC. Computational screening and design of DNA-linked molecular nanowires. Nano Letters. 11: 604-8. PMID 21174452 DOI: 10.1021/nl103665z  1
2011 Petrov AS, Bowman JC, Harvey SC, Williams LD. Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding. Rna (New York, N.Y.). 17: 291-7. PMID 21173199 DOI: 10.1261/rna.2390311  1
2011 Petrov AS, Harvey SC. Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4. Journal of Structural Biology. 174: 137-46. PMID 21074621 DOI: 10.1016/j.jsb.2010.11.007  1
2009 Harvey SC, Petrov AS, Devkota B, Boz MB. Viral assembly: a molecular modeling perspective. Physical Chemistry Chemical Physics : Pccp. 11: 10553-64. PMID 20145801 DOI: 10.1039/b912884k  1
2009 Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. Comprehensive molecular structure of the eukaryotic ribosome. Structure (London, England : 1993). 17: 1591-604. PMID 20004163 DOI: 10.1016/j.str.2009.09.015  1
2009 Petrov AS, Locker CR, Harvey SC. Characterization of DNA conformation inside bacterial viruses. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 021914. PMID 19792158 DOI: 10.1103/PhysRevE.80.021914  1
2009 Devkota B, Petrov AS, Lemieux S, Boz MB, Tang L, Schneemann A, Johnson JE, Harvey SC. Structural and electrostatic characterization of pariacoto virus: implications for viral assembly. Biopolymers. 91: 530-8. PMID 19226622 DOI: 10.1002/bip.21168  1
2009 Sarkar T, Petrov AS, Vitko JR, Santai CT, Harvey SC, Mukerji I, Hud NV. Integration host factor (IHF) dictates the structure of polyamine-DNA condensates: implications for the role of IHF in the compaction of bacterial chromatin. Biochemistry. 48: 667-75. PMID 19132923 DOI: 10.1021/bi8019965  1
2009 Mathuriya A, Bader DA, Heitsch CE, Harvey SC. GTfold: A scalable multicore code for RNA secondary structure prediction Proceedings of the Acm Symposium On Applied Computing. 981-988. DOI: 10.1145/1529282.1529497  1
2008 Tan RK, Devkota B, Harvey SC. YUP.SCX: coaxing atomic models into medium resolution electron density maps. Journal of Structural Biology. 163: 163-74. PMID 18572416 DOI: 10.1016/j.jsb.2008.05.001  1
2008 Petrov AS, Harvey SC. Packaging double-helical DNA into viral capsids: structures, forces, and energetics. Biophysical Journal. 95: 497-502. PMID 18487310 DOI: 10.1529/biophysj.108.131797  1
2008 Rollins GC, Petrov AS, Harvey SC. The role of DNA twist in the packaging of viral genomes. Biophysical Journal. 94: L38-40. PMID 18192353 DOI: 10.1529/biophysj.107.126698  1
2008 Mears JA, Stagg SM, Harvey SC. Modeling Large RNA Assemblies using a Reduced Representation Handbook of Rna Biochemistry. 546-559. DOI: 10.1002/9783527619504.ch33  0.96
2007 Petrov AS, Boz MB, Harvey SC. The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape. Journal of Structural Biology. 160: 241-8. PMID 17919923 DOI: 10.1016/j.jsb.2007.08.012  1
2007 Petrov AS, Lim-Hing K, Harvey SC. Packaging of DNA by bacteriophage epsilon15: structure, forces, and thermodynamics. Structure (London, England : 1993). 15: 807-12. PMID 17637341 DOI: 10.1016/j.str.2007.05.005  1
2007 Locker CR, Fuller SD, Harvey SC. DNA organization and thermodynamics during viral packing. Biophysical Journal. 93: 2861-9. PMID 17573426 DOI: 10.1529/biophysj.106.094771  1
2007 Petrov AS, Harvey SC. Structural and thermodynamic principles of viral packaging. Structure (London, England : 1993). 15: 21-7. PMID 17223529 DOI: 10.1016/j.str.2006.11.013  1
2006 Tan RK, Petrov AS, Harvey SC. YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models. Journal of Chemical Theory and Computation. 2: 529-540. PMID 22844233 DOI: 10.1021/ct050323r  1
2006 Datta B, Schuster GB, McCook A, Harvey SC, Zakrzewska K. DNA-directed assembly of polyanilines: modified cytosine nucleotides transfer sequence programmability to a conjoined polymer. Journal of the American Chemical Society. 128: 14428-9. PMID 17090004 DOI: 10.1021/ja0648413  1
2006 Catte A, Patterson JC, Jones MK, Jerome WG, Bashtovyy D, Su Z, Gu F, Chen J, Aliste MP, Harvey SC, Li L, Weinstein G, Segrest JP. Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study. Biophysical Journal. 90: 4345-60. PMID 16581834 DOI: 10.1529/biophysj.105.071456  1
2006 Mears JA, Sharma MR, Gutell RR, McCook AS, Richardson PE, Caulfield TR, Agrawal RK, Harvey SC. A structural model for the large subunit of the mammalian mitochondrial ribosome. Journal of Molecular Biology. 358: 193-212. PMID 16510155 DOI: 10.1016/j.jmb.2006.01.094  1
2006 Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, Westhof E. The RNA Ontology Consortium: an open invitation to the RNA community. Rna (New York, N.Y.). 12: 533-41. PMID 16484377 DOI: 10.1261/rna.2343206  1
2006 Locker CR, Harvey SC. A model for viral genome packing Multiscale Modeling and Simulation. 5: 1264-1279. DOI: 10.1137/060650684  1
2005 Stagg SM, Harvey SC. Exploring the flexibility of ribosome recycling factor using molecular dynamics. Biophysical Journal. 89: 2659-66. PMID 16055531 DOI: 10.1529/biophysj.104.052373  1
2005 Richardson PE, Manchekar M, Dashti N, Jones MK, Beigneux A, Young SG, Harvey SC, Segrest JP. Assembly of lipoprotein particles containing apolipoprotein-B: structural model for the nascent lipoprotein particle. Biophysical Journal. 88: 2789-800. PMID 15653747 DOI: 10.1529/biophysj.104.046235  1
2004 Li L, Chen J, Mishra VK, Kurtz JA, Cao D, Klon AE, Harvey SC, Anantharamaiah GM, Segrest JP. Double belt structure of discoidal high density lipoproteins: molecular basis for size heterogeneity. Journal of Molecular Biology. 343: 1293-311. PMID 15491614 DOI: 10.1016/j.jmb.2004.09.017  1
2004 Tihova M, Dryden KA, Le TV, Harvey SC, Johnson JE, Yeager M, Schneemann A. Nodavirus coat protein imposes dodecahedral RNA structure independent of nucleotide sequence and length. Journal of Virology. 78: 2897-905. PMID 14990708 DOI: 10.1128/JVI.78.6.2897-2905.2004  1
2004 LaMarque JC, Le TV, Harvey SC. Packaging double-helical DNA into viral capsids. Biopolymers. 73: 348-55. PMID 14755571 DOI: 10.1002/bip.10529  1
2003 Valle M, Zavialov A, Li W, Stagg SM, Sengupta J, Nielsen RC, Nissen P, Harvey SC, Ehrenberg M, Frank J. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nature Structural Biology. 10: 899-906. PMID 14566331 DOI: 10.1038/nsb1003  1
2003 Dupuy LC, Kelly NJ, Elgavish TE, Harvey SC, Morrow CD. Probing the importance of tRNA anticodon: human immunodeficiency virus type 1 (HIV-1) RNA genome complementarity with an HIV-1 that selects tRNA(Glu) for replication. Journal of Virology. 77: 8756-64. PMID 12885895 DOI: 10.1128/JVI.77.16.8756-8764.2003  1
2003 Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J. Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Cell. 113: 789-801. PMID 12809609 DOI: 10.1016/S0092-8674(03)00427-6  1
2003 Stagg SM, Mears JA, Harvey SC. A structural model for the assembly of the 30S subunit of the ribosome. Journal of Molecular Biology. 328: 49-61. PMID 12683996 DOI: 10.1016/S0022-2836(03)00174-8  1
2003 Sheldahl C, Xing J, Dong WJ, Harvey SC, Cheung HC. The calcium-saturated cTnI/cTnC complex: structure of the inhibitory region of cTnI. Biophysical Journal. 84: 1057-64. PMID 12547787 DOI: 10.1016/S0006-3495(03)74922-4  1
2003 Harvey SC, Wang C, Teletchea S, Lavery R. Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking. Journal of Computational Chemistry. 24: 1-9. PMID 12483670 DOI: 10.1002/jcc.10173  1
2002 Arsuaga J, Tan RK, Vazquez M, Sumners DW, Harvey SC. Investigation of viral DNA packaging using molecular mechanics models. Biophysical Chemistry. 101: 475-84. PMID 12488021 DOI: 10.1016/S0301-4622(02)00197-7  1
2002 Klon AE, Segrest JP, Harvey SC. Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apo A-I belt model. Journal of Molecular Biology. 324: 703-21. PMID 12460572 DOI: 10.1016/S0022-2836(02)01143-9  1
2002 Stagg SM, Valle M, Agrawal RK, Frank J, Harvey SC. Problems with the transorientation hypothesis. Rna (New York, N.Y.). 8: 1093-4. PMID 12358427 DOI: 10.1017/S1355838202027061  1
2002 Klon AE, Segrest JP, Harvey SC. Comparative models for human apolipoprotein A-I bound to lipid in discoidal high-density lipoprotein particles. Biochemistry. 41: 10895-905. PMID 12206659 DOI: 10.1021/bi020315m  1
2002 Mears JA, Cannone JJ, Stagg SM, Gutell RR, Agrawal RK, Harvey SC. Modeling a minimal ribosome based on comparative sequence analysis. Journal of Molecular Biology. 321: 215-34. PMID 12144780 DOI: 10.1016/S0022-2836(02)00568-5  1
2002 Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. Rna (New York, N.Y.). 8: 707-17. PMID 12088144 DOI: 10.1017/S1355838202028017  1
2002 Flood C, Gustafsson M, Richardson PE, Harvey SC, Segrest JP, Borén J. Identification of the proteoglycan binding site in apolipoprotein B48. The Journal of Biological Chemistry. 277: 32228-33. PMID 12070165 DOI: 10.1074/jbc.M204053200  1
2001 Elgavish T, Cannone JJ, Lee JC, Harvey SC, Gutell RR. AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices. Journal of Molecular Biology. 310: 735-53. PMID 11453684 DOI: 10.1006/jmbi.2001.4807  1
2001 Stagg SM, Frazer-Abel AA, Hagerman PJ, Harvey SC. Structural studies of the tRNA domain of tmRNA. Journal of Molecular Biology. 309: 727-35. PMID 11397092 DOI: 10.1006/jmbi.2001.4632  1
2000 Sardesai NY, Stagg SM, Vanloock MS, Harvey SC, Schimmel P. RNA scaffolds for minihelix-based aminoacyl transfer: design of "transpeptizymes". Journal of Biomolecular Structure & Dynamics. 17: 29-37. PMID 22607404 DOI: 10.1080/07391102.2000.10506601  1
2000 Segrest JP, Harvey SC, Zannis V. Detailed molecular model of apolipoprotein A-I on the surface of high-density lipoproteins and its functional implications. Trends in Cardiovascular Medicine. 10: 246-52. PMID 11282302 DOI: 10.1016/S1050-1738(00)00078-5  1
2000 VanLoock MS, Agrawal RK, Gabashvili IS, Qi L, Frank J, Harvey SC. Movement of the decoding region of the 16 S ribosomal RNA accompanies tRNA translocation. Journal of Molecular Biology. 304: 507-15. PMID 11099376 DOI: 10.1006/jmbi.2000.4213  1
2000 Klon AE, Jones MK, Segrest JP, Harvey SC. Molecular belt models for the apolipoprotein A-I Paris and Milano mutations. Biophysical Journal. 79: 1679-85. PMID 10969027 DOI: 10.1016/S0006-3495(00)76417-4  1
1999 Segrest JP, Jones MK, Klon AE, Sheldahl CJ, Hellinger M, De Loof H, Harvey SC. A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein. The Journal of Biological Chemistry. 274: 31755-8. PMID 10542194 DOI: 10.1074/jbc.274.45.31755  1
1999 Sheldahl C, Harvey SC. Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges. Biophysical Journal. 76: 1190-8. PMID 10049304 DOI: 10.1016/S0006-3495(99)77283-8  1
1999 VanLoock MS, Easterwood TR, Harvey SC. Major groove binding of the tRNA/mRNA complex to the 16 S ribosomal RNA decoding site. Journal of Molecular Biology. 285: 2069-78. PMID 9925785 DOI: 10.1006/jmbi.1998.2442  1
1999 Elgavish T, VanLoock MS, Harvey SC. Exploring three-dimensional structures of the HIV-1 RNA/tRNALys3 initiation complex. Journal of Molecular Biology. 285: 449-53. PMID 9878419 DOI: 10.1006/jmbi.1998.2310  1
1999 Harris BA, Harvey SC. Program for analyzing knots represented by polygonal paths Journal of Computational Chemistry. 20: 813-818.  1
1998 VanLoock MS, Harris BA, Harvey SC. To knot or not to knot? Examination of 16S ribosomal RNA models. Journal of Biomolecular Structure & Dynamics. 16: 709-13. PMID 10052626 DOI: 10.1080/07391102.1998.10508282  1
1998 Harvey SC, VanLoock MS, Rasterwood TR, Tan RKZ. Molecular Modeling Studies on the Ribosome Acs Symposium Series. 682: 369-378. DOI: 10.1007/BF00999589  1
1997 VanLoock MS, Easterwood TR, Harvey SC. tRNA/mRNA/rRNA interactions in the Escherichia coli ribosomal decoding site with and without bound aminoglycoside. Nucleic Acids Symposium Series. 68. PMID 9478209  1
1997 Easterwood TR, Harvey SC. Ribonuclease P RNA: models of the 15/16 bulge from Escherichia coli and the P15 stem loop of Bacillus subtilis. Rna (New York, N.Y.). 3: 577-85. PMID 9174093  1
1997 Harvey SC. Slipped structures in DNA triplet repeat sequences: entropic contributions to genetic instabilities. Biochemistry. 36: 3047-9. PMID 9115978 DOI: 10.1021/bi962771e  1
1996 Sprous D, Harvey SC. Action at a distance in supercoiled DNA: effects of sequence on slither, branching, and intramolecular concentration. Biophysical Journal. 70: 1893-908. PMID 8785349 DOI: 10.1016/S0006-3495(96)79754-0  1
1996 Tan RK, Sprous D, Harvey SC. Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions. Biopolymers. 39: 259-78. PMID 8679953 DOI: 10.1002/(SICI)1097-0282(199608)39:2<259::AID-BIP12>3.0.CO;2-9  1
1996 Sprous D, Tan RK, Harvey SC. Molecular modeling of closed circular DNA thermodynamic ensembles. Biopolymers. 39: 243-58. PMID 8679952 DOI: 10.1002/(SICI)1097-0282(199608)39:2<243::AID-BIP11>3.0.CO;2-F  1
1996 Sanghani SR, Zakrzewska K, Harvey SC, Lavery R. Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature. Nucleic Acids Research. 24: 1632-7. PMID 8649979  1
1995 Easterwood TR, Harvey SC. Modeling the structure of the ribosome. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 73: 751-6. PMID 8721991  1
1995 Hao MH, Harvey SC. Active transport of ions across membranes: energetic role of electrostatics and binding site asymmetry. Biochimica Et Biophysica Acta. 1234: 5-14. PMID 7880859 DOI: 10.1016/0005-2736(94)00265-Q  1
1995 Schellman JA, Harvey SC. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophysical Chemistry. 55: 95-114. PMID 7632879 DOI: 10.1016/0301-4622(94)00144-9  1
1994 Rudnicki WR, Lesyng B, Harvey SC. Lagrangian molecular dynamics using selected conformational degrees of freedom, with application to the pseudorotation dynamics of furanose rings. Biopolymers. 34: 383-92. PMID 8161710 DOI: 10.1002/bip.360340310  1
1994 Konstant PH, Pearce LL, Harvey SC. Langevin dynamics of the choline head group in a membrane environment. Biophysical Journal. 67: 713-9. PMID 7948684 DOI: 10.1016/S0006-3495(94)80532-6  1
1994 Easterwood TR, Major F, Malhotra A, Harvey SC. Orientations of transfer RNA in the ribosomal A and P sites. Nucleic Acids Research. 22: 3779-86. PMID 7937092 DOI: 10.1093/nar/22.18.3779  1
1994 Malhotra A, Tan RK, Harvey SC. Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques. Biophysical Journal. 66: 1777-95. PMID 7521223 DOI: 10.1016/S0006-3495(94)80972-5  1
1994 Malhotra A, Harvey SC. A quantitative model of the Escherichia coli 16 S RNA in the 30 S ribosomal subunit. Journal of Molecular Biology. 240: 308-40. PMID 7518524 DOI: 10.1006/jmbi.1994.1448  1
1993 Harvey SC. Zippier zaps: faster electrostatics calculations. Biophysical Journal. 65: 19-20. PMID 8369427  1
1993 Harvey SC, Gabb HA. Conformational transitions using molecular dynamics with minimum biasing. Biopolymers. 33: 1167-72. PMID 8364152 DOI: 10.1002/bip.360330803  1
1993 Pearce LL, Harvey SC. Langevin dynamics studies of unsaturated phospholipids in a membrane environment. Biophysical Journal. 65: 1084-92. PMID 8241389 DOI: 10.1016/S0006-3495(93)81143-3  1
1993 Malhotra A, Gabb HA, Harvey SC. Modeling large nucleic acids Current Opinion in Structural Biology. 3: 241-246. DOI: 10.1016/S0959-440X(05)80159-9  1
1993 You TJ, Harvey SC. Finite element approach to the electrostatics of macromolecules with arbitrary geometries Journal of Computational Chemistry. 14: 484-501. DOI: 10.1002/jcc.540140413  1
1993 Tan RKZ, Harvey SC. Yammp: Development of a molecular mechanics program using the modular programming method Journal of Computational Chemistry. 14: 455-470. DOI: 10.1002/jcc.540140410  1
1993 Harvey SC. Hidden message [5] Nature. 362: 300.  1
1993 Gabb HA, Harvey SC. Conformational transitions in potential and free energy space for furanoses and 2′-deoxynucleosides Journal of the American Chemical Society. 115: 4218-4227.  1
1992 Sprous D, Harvey SC. A three-dimensional model for nodule DNA. The Journal of Biological Chemistry. 267: 5502. PMID 1544924  1
1992 Harvey SC, Tan RK. Teaching macromolecular modeling. Biophysical Journal. 63: 1683-8. PMID 1489919 DOI: 10.1016/S0006-3495(92)81758-7  1
1992 Hao MH, Harvey SC. Analyzing the normal mode dynamics of macromolecules by the component synthesis method. Biopolymers. 32: 1393-405. PMID 1420966 DOI: 10.1002/bip.360321012  1
1992 Lavery R, Zakrzewska K, Sun JS, Harvey SC. A comprehensive classification of nucleic acid structural families based on strand direction and base pairing. Nucleic Acids Research. 20: 5011-6. PMID 1383936 DOI: 10.1093/nar/20.19.5011  1
1991 Harvey SC. Need for forums Scientist. 5.  1
1990 Malhotra A, Tan RK, Harvey SC. Prediction of the three-dimensional structure of Escherichia coli 30S ribosomal subunit: a molecular mechanics approach. Proceedings of the National Academy of Sciences of the United States of America. 87: 1950-4. PMID 2408047  1
1990 Sharp KA, Honig B, Harvey SC. Electrical potential of transfer RNAs: codon-anticodon recognition. Biochemistry. 29: 340-6. PMID 2405900 DOI: 10.1021/bi00454a006  1
1989 Tan RK, Harvey SC. Molecular mechanics model of supercoiled DNA. Journal of Molecular Biology. 205: 573-91. PMID 2926819 DOI: 10.1016/0022-2836(89)90227-1  1
1989 Prabahakaran M, Harvey SC. Models for two tRNAs bound to successive codons on mRNA on the ribosome. Journal of Biomolecular Structure & Dynamics. 7: 167-79. PMID 2818867 DOI: 10.1080/07391102.1989.10507758  1
1989 Lopez-Lacomba JL, Guzman M, Cortijo M, Mateo PL, Aguirre R, Harvey SC, Cheung HC. Differential scanning calorimetric study of the thermal unfolding of myosin rod, light meromyosin, and subfragment 2. Biopolymers. 28: 2143-59. PMID 2690963 DOI: 10.1002/bip.360281208  1
1989 Harvey SC. Treatment of electrostatic effects in macromolecular modeling. Proteins. 5: 78-92. PMID 2664766 DOI: 10.1002/prot.340050109  1
1988 Tan RK, Prabhakaran M, Tung CS, Harvey SC. AUGUR: a program to predict, display and analyze the tertiary structure of B-DNA. Computer Applications in the Biosciences : Cabios. 4: 147-51. PMID 3382989 DOI: 10.1093/bioinformatics/4.1.147  1
1988 Prabhakaran M, Harvey SC. Molecular dynamics of structural transitions and intercalation in DNA. Biopolymers. 27: 1239-48. PMID 3219395 DOI: 10.1002/bip.360270805  1
1988 Harvey SC, Luo J, Lavery R. DNA stem-loop structures in oligopurine-oligopyrimidine triplexes. Nucleic Acids Research. 16: 11795-809. PMID 3211749 DOI: 10.1093/nar/16.24.11795  1
1987 Prabhakaran M, Harvey SC. Asymmetric oscillations in cyclodextrin--a molecular dynamics study. Biopolymers. 26: 1087-96. PMID 3620575 DOI: 10.1002/bip.360260708  1
1987 Tung CS, Harvey SC. A common structural feature in promoter sequences of E. coli. Nucleic Acids Research. 15: 4973-85. PMID 3299261 DOI: 10.1093/nar/15.12.4973  1
1987 Tan RK, Harvey SC. A comparison of six DNA bending models. Journal of Biomolecular Structure & Dynamics. 5: 497-512. PMID 3271483 DOI: 10.1080/07391102.1987.10506410  1
1987 Harvey SC, Prabhakaran M. Umbrella sampling: Avoiding possible artifacts and statistical biases Journal of Physical Chemistry. 91: 4799-4801.  1
1986 Tung CS, Harvey SC. Base sequence, local helix structure, and macroscopic curvature of A-DNA and B-DNA. The Journal of Biological Chemistry. 261: 3700-9. PMID 3949785  1
1986 Tung CS, Harvey SC. Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure. Nucleic Acids Research. 14: 381-7. PMID 3753773 DOI: 10.1093/nar/14.1.381  1
1986 Bell CD, Harvey SC. Comparison of free energy surfaces for extended-atom and all-atom models of n-butane Journal of Physical Chemistry. 90: 6595-6597.  1
1986 Harvey SC, Prabhakaran M. Ribose puckering: Structure, dynamics, energetics, and the pseudorotation cycle Journal of the American Chemical Society. 108: 6128-6136.  1
1985 Harvey SC, Prabhakaran M, McCammon JA. Molecular-dynamics simulation of phenylalanine transfer RNA. I. Methods and general results. Biopolymers. 24: 1169-88. PMID 3896333 DOI: 10.1002/bip.360240706  1
1985 Prabhakaran M, McCammon JA, Harvey SC. Atomic motions in phenylalanine transfer RNA probed by molecular dynamics simulations. Progress in Clinical and Biological Research. 172: 123-9. PMID 3846288  1
1985 Kang DS, Harvey SC, Wells RD. Diepoxybutane forms a monoadduct with B-form (dG-dC)n.(dG-dC)n and a crosslinked diadduct with the left-handed Z-form. Nucleic Acids Research. 13: 5645-56. PMID 2994006 DOI: 10.1093/nar/13.15.5645  1
1985 Prabhakaran M, Harvey SC, McCammon JA. Molecular-dynamics simulation of phenylalanine transfer RNA. II. Amplitudes, anisotropies, and anharmonicities of atomic motions. Biopolymers. 24: 1189-204. PMID 2992621 DOI: 10.1002/bip.360240707  1
1985 Prabhakaran M, Harvey SC. Molecular dynamics anneals large-scale deformations of model macromolecules: Stretching the DNA double helix to form an intercalation site Journal of Physical Chemistry. 89: 5767-5769.  1
1985 Prabhakaran M, Harvey SC. Helical oscillations in tRNA and DNA Federation Proceedings. 44.  1
1984 Tung CS, Harvey SC, McCammon JA. Large-amplitude bending motions in phenylalanine transfer RNA. Biopolymers. 23: 2173-93. PMID 6568122 DOI: 10.1002/bip.360231106  1
1984 Harvey SC, Prabhakaran M, Mao B, McCammon JA. Phenylalanine transfer RNA: molecular dynamics simulation. Science (New York, N.Y.). 223: 1189-91. PMID 6560785 DOI: 10.1126/science.6560785  1
1984 Tung CS, Harvey SC. A molecular mechanical model to predict the helix twist angles of B-DNA. Nucleic Acids Research. 12: 3343-56. PMID 6326059 DOI: 10.1093/nar/12.7.3343  1
1983 Harvey SC. DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition. Nucleic Acids Research. 11: 4867-78. PMID 6878036 DOI: 10.1093/nar/11.14.4867  1
1983 Prabhakaran M, Harvey SC, Mao B, McCammon JA. Molecular dynamics of phenylalanine transfer RNA. Journal of Biomolecular Structure & Dynamics. 1: 357-69. PMID 6401115 DOI: 10.1080/07391102.1983.10507447  1
1983 Harvey SC. BeliketheGerman [3] Nature. 306: 530. DOI: 10.1038/306530c0  1
1982 Harvey SC, McCammon JA. Macromolecular conformational energy minimization: An algorithm varying pseudodihedral angles Computers and Chemistry. 6: 173-179. DOI: 10.1016/0097-8485(82)85012-2  1
1981 Harvey SC, McCammon JA. Intramolecular flexibility in phenylalanine transfer RNA. Nature. 294: 286-7. PMID 7029310 DOI: 10.1038/294286a0  1
1980 Harvey SC, De La Torre JG. Coordinate systems for modeling the hydrodynamic resistance and diffusion coefficients of irregularly shaped rigid macromolecules Macromolecules. 13: 960-964.  1
1979 Harvey SC. Experimental detection of macromolecular flexibility by observation of time-dependent diffusion coefficients The Journal of Chemical Physics. 71: 4221-4226.  1
1979 Harvey SC. East is east... [5] Science. 204: 1158.  1
1978 Harvey SC. Diffusion of hinged particles: An exception to the Einstein relation The Journal of Chemical Physics. 69: 3426-3427.  1
1977 Harvey SC, Cheung HC. Fluorescence depolarization studies on the flexibility of myosin rod. Biochemistry. 16: 5181-7. PMID 921927  1
1977 Harvey SC, Cheung HC, Thames KE. Cooperativity in F-actin filaments on binding of myosin subfragments, demonstrated by fluorescence of 1, N6- ethenoadenosine diphosphate. Archives of Biochemistry and Biophysics. 179: 391-6. PMID 322615 DOI: 10.1016/0003-9861(77)90126-6  1
1976 Harvey SC, Cheung HC. Fluorescence studies of 1,N6-ethenoadenosine triphosphate bound to G-actin: the nucleotide base is inaccessible to water. Biochemical and Biophysical Research Communications. 73: 865-8. PMID 15625854  1
1976 Harvey SC, Cheung HC. Fluorescence studies of 1,N6-ethenoadenosine triphosphate bound to G-actin: The nucleotide base is inaccessible to water Biochemical and Biophysical Research Communications. 73: 865-868. DOI: 10.1016/0006-291X(76)90201-1  1
1975 Harvey SC, Cheung HC, Thames KE. Fluorescence studies of the interaction of 1,N6 ethenoadenosine phosphates with actin Biophysical Journal. 15.  1
1974 Thames KE, Cheung HC, Harvey SC. Binding of 1,N6-ethanoadenosine triphosphate to actin. Biochemical and Biophysical Research Communications. 60: 1252-61. PMID 4214008 DOI: 10.1016/0006-291X(74)90333-7  1
1973 Cheung HC, Harvey SC. Fluorescence polarization studies of tropomyosin and troponin Federation Proceedings. 32: 1990.  1
1972 Harvey SC, Cheung HC. Computer simulation of fluorescence depolarization due to brownian motion. Proceedings of the National Academy of Sciences of the United States of America. 69: 3670-2. PMID 16592039  1
1972 Harvey SC, Hoekstra P. Dielectric relaxation spectra of water adsorbed on lysozyme. The Journal of Physical Chemistry. 76: 2987-94. PMID 5073361  1
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