Tom Woolf - Publications

Johns Hopkins University, Baltimore, MD 

90 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 Perilla JR, Woolf TB. Computing ensembles of transitions with molecular dynamics simulations. Methods in Molecular Biology (Clifton, N.J.). 1215: 237-52. PMID 25330966 DOI: 10.1007/978-1-4939-1465-4_11  1
2014 Braiterman LT, Murthy A, Jayakanthan S, Nyasae L, Tzeng E, Gromadzka G, Woolf TB, Lutsenko S, Hubbard AL. Distinct phenotype of a Wilson disease mutation reveals a novel trafficking determinant in the copper transporter ATP7B. Proceedings of the National Academy of Sciences of the United States of America. 111: E1364-73. PMID 24706876 DOI: 10.1073/pnas.1314161111  1
2013 Woolf TB. A tale of two ions and their membrane interactions: clearly the same or clearly different? Biophysical Journal. 104: 746-7. PMID 23442952 DOI: 10.1016/j.bpj.2013.01.010  1
2013 Perilla JR, Leahy DJ, Woolf TB. Molecular dynamics simulations of transitions for ECD epidermal growth factor receptors show key differences between human and drosophila forms of the receptors. Proteins. 81: 1113-26. PMID 23348956 DOI: 10.1002/prot.24257  1
2013 Nutanong S, Carey N, Ahmad Y, Szalay AS, Woolf TB. Adaptive exploration for large-scale protein analysis in the molecular dynamics database Acm International Conference Proceeding Series. DOI: 10.1145/2484838.2484872  1
2012 Nagarajan A, Andersen JP, Woolf TB. Coarse-grained simulations of transitions in the E2-to-E1 conformations for Ca ATPase (SERCA) show entropy-enthalpy compensation. Journal of Molecular Biology. 422: 575-93. PMID 22684148 DOI: 10.1016/j.jmb.2012.06.001  1
2012 Wolfe KC, Hastings WA, Dutta S, Long A, Shapiro BA, Woolf TB, Guthold M, Chirikjian GS. Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups. The Journal of Physical Chemistry. B. 116: 8556-72. PMID 22676719 DOI: 10.1021/jp2126015  1
2012 Perilla JR, Woolf TB. Towards the prediction of order parameters from molecular dynamics simulations in proteins. The Journal of Chemical Physics. 136: 164101. PMID 22559464 DOI: 10.1063/1.3702447  1
2012 Nagarajan A, Andersen JP, Woolf TB. The role of domain: domain interactions versus domain: water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA). Proteins. 80: 1929-47. PMID 22422644 DOI: 10.1002/prot.24070  1
2011 Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry. 32: 2319-27. PMID 21500218 DOI: 10.1002/jcc.21787  1
2011 Bondar AN, Woolf TB, Tobias DJ. Festschrift in the honor of Stephen H. White's 70th Birthday. The Journal of Membrane Biology. 239: 1-3. PMID 21191785 DOI: 10.1007/s00232-010-9337-3  1
2011 Perilla JR, Beckstein O, Denning EJ, Woolf TB. Computing ensembles of transitions from stable states: Dynamic importance sampling. Journal of Computational Chemistry. 32: 196-209. PMID 21132840 DOI: 10.1002/jcc.21564  1
2010 Toptygin D, Woolf TB, Brand L. Picosecond protein dynamics: the origin of the time-dependent spectral shift in the fluorescence of the single Trp in the protein GB1. The Journal of Physical Chemistry. B. 114: 11323-37. PMID 20701310 DOI: 10.1021/jp104425t  1
2010 Mirjanian D, Dickey AN, Hoh JH, Woolf TB, Stevens MJ. Splaying of aliphatic tails plays a central role in barrier crossing during liposome fusion. The Journal of Physical Chemistry. B. 114: 11061-8. PMID 20701307 DOI: 10.1021/jp1055182  1
2010 Gentilcore AN, Michaud-Agrawal N, Crozier PS, Stevens MJ, Woolf TB. Examining the origins of the hydration force between lipid bilayers using all-atom simulations. The Journal of Membrane Biology. 235: 1-15. PMID 20387061 DOI: 10.1007/s00232-010-9249-2  1
2010 Denning EJ, Woolf TB. Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations. Proteins. 78: 1105-19. PMID 19950367 DOI: 10.1002/prot.22632  1
2009 Denning EJ, Crozier PS, Sachs JN, Woolf TB. From the gating charge response to pore domain movement: initial motions of Kv1.2 dynamics under physiological voltage changes. Molecular Membrane Biology. 26: 397-421. PMID 19883299 DOI: 10.3109/09687680903278539  1
2009 Beckstein O, Denning EJ, Perilla JR, Woolf TB. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. Journal of Molecular Biology. 394: 160-76. PMID 19751742 DOI: 10.1016/j.jmb.2009.09.009  1
2008 Jang H, Michaud-Agrawal N, Johnston JM, Woolf TB. How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers. Proteins. 72: 299-312. PMID 18214961 DOI: 10.1002/prot.21925  1
2008 Denning EJ, Woolf TB. Chapter 14 Computational Models for Electrified Interfaces Current Topics in Membranes. 60: 385-403. DOI: 10.1016/S1063-5823(08)00014-8  1
2007 Crozier PS, Stevens MJ, Woolf TB. How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. Proteins. 66: 559-74. PMID 17109408 DOI: 10.1002/prot.21175  1
2007 Weathers EA, Paulaitis ME, Woolf TB, Hoh JH. Insights into protein structure and function from disorder-complexity space. Proteins. 66: 16-28. PMID 17044059 DOI: 10.1002/prot.21055  1
2007 Woolf TB. Introduction to special issue Journal of Membrane Biology. 217: 1. DOI: 10.1007/s00232-007-9070-8  1
2007 Lu N, Woolf TB. Understanding and improving free energy calculations in molecular simulations: Error analysis and reduction methods Springer Series in Chemical Physics. 86: 199-247. DOI: 10.1007/978-3-540-38448-9_6  1
2006 Jang H, Ma B, Woolf TB, Nussinov R. Interaction of protegrin-1 with lipid bilayers: membrane thinning effect. Biophysical Journal. 91: 2848-59. PMID 16861271 DOI: 10.1529/biophysj.106.084046  1
2006 Jang H, Woolf TB. Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling. Journal of Computational Chemistry. 27: 1136-41. PMID 16721720 DOI: 10.1002/jcc.20444  1
2005 Nanda H, Sachs JN, Petrache HI, Woolf TB. Environmental Effects on Glycophorin A Folding and Structure Examined through Molecular Simulations. Journal of Chemical Theory and Computation. 1: 375-88. PMID 26641504 DOI: 10.1021/ct049928y  1
2005 Makrodimitris K, Fernandez EJ, Woolf TB, O'Connell JP. Simulation and experiment of temperature and cosolvent effects in reversed phase chromatography of peptides. Biotechnology Progress. 21: 893-6. PMID 15932270 DOI: 10.1021/bp049547y  1
2005 Nanda H, Lu N, Woolf TB. Using non-Gaussian density functional fits to improve relative free energy calculations. The Journal of Chemical Physics. 122: 134110. PMID 15847458 DOI: 10.1063/1.1877252  1
2005 Nymeyer H, Woolf TB, Garcia AE. Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer. Proteins. 59: 783-90. PMID 15828005 DOI: 10.1002/prot.20460  1
2005 Makrodimitris K, Fernandez EJ, Woolf TB, O'Connell JP. Mesoscopic simulation of adsorption of peptides in a hydrophobic chromatography system. Analytical Chemistry. 77: 1243-52. PMID 15732903 DOI: 10.1021/ac048812r  1
2005 Makrodimitris K, Fernandez EJ, Woolf TB, O'Connell JP. ALLD: An object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes Molecular Simulation. 31: 623-636. DOI: 10.1080/08927020500108262  1
2005 Nanda H, Sachs JN, Petrache HI, Woolf TB. Environmental effects on glycophorin a folding and structure examined through molecular simulations Journal of Chemical Theory and Computation. 1: 375-388. DOI: 10.1021/ct049928y  1
2004 Sachs JN, Crozier PS, Woolf TB. Atomistic simulations of biologically realistic transmembrane potential gradients. The Journal of Chemical Physics. 121: 10847-51. PMID 15634036 DOI: 10.1063/1.1826056  1
2004 Jang H, Grimson MJ, Woolf TB. Stochastic dynamics and the dynamic phase transition in thin ferromagnetic films. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 70: 047101. PMID 15600564 DOI: 10.1103/PhysRevE.70.047101  1
2004 Weathers EA, Paulaitis ME, Woolf TB, Hoh JH. Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein. Febs Letters. 576: 348-52. PMID 15498561 DOI: 10.1016/j.febslet.2004.09.036  1
2004 Lu N, Wu D, Woolf TB, Kofke DA. Using overlap and funnel sampling to obtain accurate free energies from nonequilibrium work measurements. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 057702. PMID 15244984  1
2004 Jang H, Crozier PS, Stevens MJ, Woolf TB. How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation. Biophysical Journal. 87: 129-45. PMID 15240452 DOI: 10.1529/biophysj.104.039602  1
2004 Sachs JN, Nanda H, Petrache HI, Woolf TB. Changes in phosphatidylcholine headgroup tilt and water order induced by monovalent salts: molecular dynamics simulations. Biophysical Journal. 86: 3772-82. PMID 15189873 DOI: 10.1529/biophysj.103.035816  1
2004 Woolf TB, Zuckerman DM, Lu N, Jang H. Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics. Journal of Molecular Graphics & Modelling. 22: 359-68. PMID 15099832 DOI: 10.1016/j.jmgm.2003.12.003  1
2004 Lu N, Kofke DA, Woolf TB. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. Journal of Computational Chemistry. 25: 28-39. PMID 14634991 DOI: 10.1002/jcc.10369  1
2004 Lu D, Yan H, Othman T, Turner CP, Woolf T, Rivkees SA. Cytoskeletal protein 4.1G binds to the third intracellular loop of the A1 adenosine receptor and inhibits receptor action. The Biochemical Journal. 377: 51-9. PMID 12974671 DOI: 10.1042/BJ20030952  1
2004 Lu N, Woolf TB. Overlap perturbation methods for computing alchemical free energy changes: Variants, generalizations and evaluations Molecular Physics. 102: 173-181. DOI: 10.1080/00268970310001644603  1
2004 Zuckerman DM, Woolf TB. Systematic finite-sampling inaccuracy in free energy differences and other nonlinear quantities Journal of Statistical Physics. 114: 1303-1323.  1
2003 Sachs JN, Petrache HI, Woolf TB. Interpretation of small angle X-ray measurements guided by molecular dynamics simulations of lipid bilayers. Chemistry and Physics of Lipids. 126: 211-23. PMID 14623455 DOI: 10.1016/j.chemphyslip.2003.08.001  1
2003 Stevens MJ, Hoh JH, Woolf TB. Insights into the molecular mechanism of membrane fusion from simulation: evidence for the association of splayed tails. Physical Review Letters. 91: 188102. PMID 14611319  1
2003 Crozier PS, Stevens MJ, Forrest LR, Woolf TB. Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change. Journal of Molecular Biology. 333: 493-514. PMID 14556740 DOI: 10.1016/j.jmb.2003.08.045  1
2003 Forrest LR, Woolf TB. Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions. Proteins. 52: 492-509. PMID 12910450 DOI: 10.1002/prot.10404  1
2003 Sachs JN, Woolf TB. Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations. Journal of the American Chemical Society. 125: 8742-3. PMID 12862466 DOI: 10.1021/ja0355729  1
2003 Feller SE, Gawrisch K, Woolf TB. Rhodopsin exhibits a preference for solvation by polyunsaturated docosohexaenoic acid. Journal of the American Chemical Society. 125: 4434-5. PMID 12683809 DOI: 10.1021/ja0345874  1
2003 Sachs JN, Petrache HI, Zuckerman DM, Woolf TB. Molecular dynamics simulations of ionic concentration gradients across model bilayers Journal of Chemical Physics. 118: 1957-1969. DOI: 10.1063/1.1531589  1
2003 Lu N, Kofke DA, Woolf TB. Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems Journal of Physical Chemistry B. 107: 5598-5611.  1
2002 Zuckerman DM, Woolf TB. Theory of a systematic computational error in free energy differences. Physical Review Letters. 89: 180602. PMID 12398588  1
2002 Zuckerman DM, Woolf TB. Transition events in butane simulations: Similarities across models Journal of Chemical Physics. 116: 2586-2591. DOI: 10.1063/1.1433501  1
2002 Petrache HI, Zuckerman DM, Sachs JN, Antoinette Killian J, Koeppe RE, Woolf TB. Hydrophobic matching mechanism investigated by molecular dynamics simulations Langmuir. 18: 1340-1351. DOI: 10.1021/la011338p  1
2002 Grossfield A, Woolf TB. Interaction of tryptophan analogs with POPC lipid bilayers investigated by molecular dynamics calculations Langmuir. 18: 198-210. DOI: 10.1021/la0106485  1
2002 Zuckerman DM, Woolf TB. Overcoming finite-sampling errors in fast-switching free-energy estimates: Extrapolative analysis of a molecular system Chemical Physics Letters. 351: 445-453. DOI: 10.1016/S0009-2614(01)01397-5  1
2002 Sachs JN, Woolf TB. Molecular dynamics simulations of charged plates and electrolyte in a bilayer-like geometry: Molecular ordering and electrostatic potential Annual International Conference of the Ieee Engineering in Medicine and Biology - Proceedings. 1: 356-357.  1
2001 Bright JN, Woolf TB, Hoh JH. Predicting properties of intrinsically unstructured proteins. Progress in Biophysics and Molecular Biology. 76: 131-73. PMID 11709204 DOI: 10.1016/S0079-6107(01)00012-8  1
2001 Zuckerman DM, Woolf TB. Efficient dynamic importance sampling of rare events in one dimension. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 63: 016702. PMID 11304388 DOI: 10.1103/PhysRevE.63.016702  1
2001 Bright JN, Stevens MJ, Hoh J, Woolf TB. Characterizing the function of unstructured proteins: Simulations of charged polymers under confinement Journal of Chemical Physics. 115: 4909-4918. DOI: 10.1063/1.1392361  1
2000 Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB. Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. Journal of Molecular Biology. 302: 727-46. PMID 10986130 DOI: 10.1006/jmbi.2000.4072  1
2000 Grossfield A, Sachs J, Woolf TB. Dipole lattice membrane model for protein calculations. Proteins. 41: 211-23. PMID 10966574 DOI: 10.1002/1097-0134(20001101)41:2<211::AID-PROT60>3.0.CO;2-9  1
2000 Mandal D, Woolf TB, Rao R. Manganese selectivity of pmr1, the yeast secretory pathway ion pump, is defined by residue gln783 in transmembrane segment 6. Residue Asp778 is essential for cation transport. The Journal of Biological Chemistry. 275: 23933-8. PMID 10801856 DOI: 10.1074/jbc.M002619200  1
2000 Wrabl JO, Shortle D, Woolf TB. Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: molecular dynamics simulations of native and denatured staphylococcal nuclease. Proteins. 38: 123-33. PMID 10656260 DOI: 10.1002/(SICI)1097-0134(20000201)38:2<123::AID-PROT2>3.0.CO;2-H  1
2000 Woolf TB, Grossfield A, Tychko M. Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations. Biophysical Journal. 78: 608-25. PMID 10653776 DOI: 10.1016/S0006-3495(00)76621-5  1
1999 Roux B, Woolf TB. The binding site of sodium in the gramicidin A channel. Novartis Foundation Symposium. 225: 113-24; discussion 1. PMID 10472051  1
1999 Woolf TB, Tychko M. The third leg: molecular dynamics simulations of lipid binding proteins. Molecular and Cellular Biochemistry. 192: 143-56. PMID 10331669  1
1999 Zuckerman DM, Woolf TB. Dynamic reaction paths and rates through importance-sampled stochastic dynamics Journal of Chemical Physics. 111: 9475-9484.  1
1999 Woolf TB, Grossfield A, Pearson JG. Indoles at Interfaces: Calculations of Electrostatic Effects with Density Functional and Molecular Dynamics Methods International Journal of Quantum Chemistry. 75: 197-206.  1
1999 Separovic F, Ashida J, Woolf T, Smith R, Terao T. Determination of chemical shielding tensor of an indole carbon and application to tryptophan orientation of a membrane peptide Chemical Physics Letters. 303: 493-498.  1
1998 Woolf TB, Tychko M. Simulations of fatty acid-binding proteins. II. Sites for discrimination of monounsaturated ligands. Biophysical Journal. 74: 694-707. PMID 9533683 DOI: 10.1016/S0006-3495(98)73995-5  1
1998 Woolf TB. Simulations of fatty acid-binding proteins suggest sites important for function. I. Stearic acid. Biophysical Journal. 74: 681-93. PMID 9533682 DOI: 10.1016/S0006-3495(98)73994-3  1
1998 Woolf TB. Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. Interaction energy analysis. Biophysical Journal. 74: 115-31. PMID 9449316 DOI: 10.1016/S0006-3495(98)77773-2  1
1998 Woolf TB. Bacteriorhodopsin α-helices in lipid settings: Insights for structure prediction International Journal of Quantum Chemistry. 69: 105-116.  1
1998 Woolf TB. Path corrected functionals of stochastic trajectories: Towards relative free energy and reaction coordinate calculations Chemical Physics Letters. 289: 433-441.  1
1997 Belohorcová K, Davis JH, Woolf TB, Roux B. Structure and dynamics of an amphiphilic peptide in a lipid bilayer: a molecular dynamics study. Biophysical Journal. 73: 3039-55. PMID 9414218 DOI: 10.1016/S0006-3495(97)78332-2  1
1997 Woolf TB. Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics. Biophysical Journal. 73: 2376-92. PMID 9370432 DOI: 10.1016/S0006-3495(97)78267-5  1
1997 Woolf TB, Roux B. The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data. Biophysical Journal. 72: 1930-45. PMID 9129798 DOI: 10.1016/S0006-3495(97)78839-8  1
1996 Woolf TB, Roux B. Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer. Proteins. 24: 92-114. PMID 8628736 DOI: 10.1002/(SICI)1097-0134(199601)24:1<92::AID-PROT7>3.0.CO;2-Q  1
1995 Woolf TB, Malkin VG, Malkina OL, Salahub DR, Roux B. The backbone 15N chemical shift tensor of the gramicidin channel. A molecular dynamics and density functional study Chemical Physics Letters. 239: 186-194. DOI: 10.1016/0009-2614(95)00424-3  1
1994 Woolf TB, Greer CA. Local communication within dendritic spines: models of second messenger diffusion in granule cell spines of the mammalian olfactory bulb. Synapse (New York, N.Y.). 17: 247-67. PMID 7992200 DOI: 10.1002/syn.890170406  1
1994 Crouzy S, Woolf TB, Roux B. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophysical Journal. 67: 1370-86. PMID 7529578 DOI: 10.1016/S0006-3495(94)80618-6  1
1994 Woolf TB, Roux B. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proceedings of the National Academy of Sciences of the United States of America. 91: 11631-5. PMID 7526400 DOI: 10.1073/pnas.91.24.11631  1
1994 Woolf TB, Roux B. Conformational flexibility of o-phosphorylcholine and o-phosphorylethanolamine: A molecular dynamics study of solvation effects Journal of the American Chemical Society. 116: 5916-5926.  1
1991 Woolf TB, Shepherd GM, Greer CA. Local information processing in dendritic trees: subsets of spines in granule cells of the mammalian olfactory bulb. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 11: 1837-54. PMID 2045889  1
1991 Woolf TB, Shepherd GM, Greer CA. Serial reconstructions of granule cell spines in the mammalian olfactory bulb. Synapse (New York, N.Y.). 7: 181-92. PMID 1882328 DOI: 10.1002/syn.890070303  1
1990 Carnevale NT, Woolf TB, Shepherd GM. Neuron simulations with SABER. Journal of Neuroscience Methods. 33: 135-48. PMID 2232865 DOI: 10.1016/0165-0270(90)90017-A  1
1989 Shepherd GM, Woolf TB, Carnevale NT. Comparisons between Active Properties of Distal Dendritic Branches and Spines: Implications for Neuronal Computations. Journal of Cognitive Neuroscience. 1: 273-86. PMID 23968510 DOI: 10.1162/jocn.1989.1.3.273  1
1988 Carnevale NT, Woolf TB, Shepherd GM. Simulating neurons with SABER Ieee/Engineering in Medicine and Biology Society Annual Conference. 10: 1508.  1
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