Elena_Zubova's Top Recommendations

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	Recent advances in implicit solvent-based methods for biomolecular simulations. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (04 April 2008), pp. 140-148. by Jianhan Chen, Charles L. Brooks, Jana Khandogin posted by 10 people RamuAnandakrishnan mikaellund Structural Biology Group TorVergata oteri nickolay flbarroso choonpeng sobolevnrm baker-group onufriev
	Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation [My Copy] J. Phys. Chem. B, Vol. 111, No. 7. (22 February 2007), pp. 1846-1857. by D. R. Roe, A. Okur, L. Wickstrom, V. Hornak, C. Simmerling posted by 7 people RamuAnandakrishnan flbarroso baaden choonpeng sobolevnrm baker-group onufriev
	Protein-protein binding is often associated with changes in protonation state [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Aaron C. Mason, Jan H. Jensen posted by 10 people flbarroso onufriev csrocha bicko sobolevnrm baker-group RamuAnandakrishnan barry structural_bioinformatics McCammon
	The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Paul Labute posted by 8 people onufriev sobolevnrm baker-group RamuAnandakrishnan middledomain sunhwan dmobley GermanErlenkamp
	Dipolar Poisson-Boltzmann Equation: Ions and Dipoles Close to Charge Interfaces [My Copy] Physical Review Letters, Vol. 99, No. 7. (2007), 077801. by Ariel Abrashkin, David Andelman, Henri Orland posted by 3 people onufriev sobolevnrm baker-group
	Benchmarking pKa Prediction Methods for Residues in Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 6. (1 June 2008), pp. 951-966. by Courtney L. Stanton, Kendall N. Houk posted by 6 people scampos flbarroso franklu310 onufriev sobolevnrm baker-group
	Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models? [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by David S. Cerutti, Nathan A. Baker, Andrew J. Mccammon posted by 4 people flbarroso sobolevnrm baker-group onufriev
	Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups [My Copy] Biophys. J. (4 January 2008), biophysj.107.122473. by Jamie L. Schlessman, Colby Abe, Apostolos Gittis, Daniel A. Karp, Michael A. Dolan, Bertrand Garcia-Moreno posted by 4 people paulschlesinger onufriev sobolevnrm baker-group
	Charge asymmetries in hydration of polar solutes. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 8. (28 February 2008), pp. 2405-2414. by D. L. Mobley, A. E. Barber, C. J. Fennell, K. A. Dill posted by 6 people flbarroso sobolevnrm baker-group onufriev dmobley middledomain
	Calculation of protein-ligand binding free energy by using a polarizable potential [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295. by Dian Jiao, Pavel A. Golubkov, Thomas A. Darden, Pengyu Ren posted by 9 people flbarroso onufriev jmccammon biehl sobolevnrm baker-group barry structural_bioinformatics McCammon
	Linking folding with aggregation in Alzheimer's beta-amyloid peptides [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 16880-16885. by Jana Khandogin, Charles L. Brooks posted by 5 people scampos Diego_Prada onufriev sobolevnrm baker-group
	Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method [My Copy] Journal of Computational Chemistry, Vol. 25, No. 16. (2004), pp. 2049-2064. by Ninad V. Prabhu, Peijuan Zhu, Kim A. Sharp posted by 3 people sobolevnrm baker-group onufriev
	Determination of electrostatic interaction energies and protonation state populations in enzyme active sites [My Copy] Journal of Molecular Biology, Vol. In Press, Accepted Manuscript by Chresten R. Sondergaard, Lawrence P. Mcintosh, Gianluca Pollastri, Jens E. Nielsen posted by 6 people onufriev barry sobolevnrm structural_bioinformatics baker-group skoddet
	Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 488-498. by Asim Okur, Lauren Wickstrom, Carlos Simmerling posted by 4 people onufriev sobolevnrm baker-group dmobley
	Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions [My Copy] J. Phys. Chem. B, Vol. 105, No. 28. (19 July 2001), pp. 6507-6514. by W. Rocchia, E. Alexov, B. Honig posted by 3 people onufriev sobolevnrm baker-group
	Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA. [My Copy] Biopolymers, Vol. 16, No. 7. (July 1977), pp. 1415-1434. by J. A. Schellman posted by 3 people baker-group sobolevnrm onufriev
	On the Dielectric Boundary in Poisson-Boltzmann Calculations [My Copy] J. Chem. Theory Comput., Vol. 4, No. 3. (11 March 2008), pp. 507-514. by H. Tjong, H. X. Zhou posted by 3 people sobolevnrm baker-group onufriev
	Local electrostatics algorithm for classical molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 127, No. 13. (2007), 134104. by Jörg Rottler posted by 7 people sobolevnrm baker-group afenley softsimu mikaellund OndrejMarsalek michaelbussmann
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted by 19 people mijogiffin Chang group flbarroso GermanErlenkamp onufriev arlam Structural Biology Group TorVergata oteri McCammon jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted by 7 people anuragsethi klexa tovrstra Structural Biology Group TorVergata oteri onufriev softsimu
	A hierarchy of timescales in protein dynamics is linked to enzyme catalysis [My Copy] Nature (18 November 2007) by Katherine A. Henzler-Wildman, Ming Lei, Vu Thai, Jordan S. Kerns, Martin Karplus, Dorothee Kern posted by 11 people Diego_Prada ruvido tmmurali allmensch cactus sobolevnrm jlh64 baker-group RamuAnandakrishnan dmobley chenway
	Assessing the performance of implicit solvation models at a nucleic acid surface [My Copy] Phys. Chem. Chem. Phys., Vol. 10, No. 32. (2008), pp. 4889-4902. by Feng Dong, Jason A. Wagoner, Nathan A. Baker posted by 5 people sobolevnrm onufriev simone jmccammon McCammon
	Accelerating molecular modeling applications with graphics processors [My Copy] Journal of Computational Chemistry, Vol. 28, No. 16. (25 September 2007), pp. 2618-2640. by John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten posted by 11 people ihaque naoya charris5 timg BragilMassoud ruvido sobolevnrm baker-group yalexeev mikaellund afenley
	The implementation of a fast and accurate QM/MM potential method in Amber [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1019-1031. by Ross C. Walker, Michael F. Crowley, David A. Case posted by 3 people onufriev RamuAnandakrishnan softsimu
	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 1. (2009), pp. 138-150. by Serena Donnini, Alessandra Villa, Gerrit Groenhof, Alan E. Mark, Rik K. Wierenga, André H. Juffer posted by 8 people flbarroso onufriev McCammon rbaron ibuch baker-group sobolevnrm RamuAnandakrishnan
	On the evaluation and optimization of protein X-ray structures for pKa calculations. [My Copy] Protein science : a publication of the Protein Society, Vol. 12, No. 2. (February 2003), pp. 313-326. by J. E. Nielsen, J. A. McCammon posted by 4 people onufriev charris5 softsimu RamuAnandakrishnan
	Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles [My Copy] Structure, Vol. 14, No. 10. (October 2006), pp. 1527-1534. by Filip Lankas, Richard Lavery, John H. Maddocks posted by 3 people Structural Biology Group TorVergata oteri onufriev
	A reappraisal of what we have learnt during three decades of computer simulations on water [My Copy] Journal of Molecular Liquids In Molecular Liquids. Water at the New Millenium, Vol. 101, No. 1-3. (November 2002), pp. 219-260. by Bertrand Guillot posted by 6 people pavanghatty flbarroso loison ruvido softsimu onufriev
	AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. [My Copy] Journal of computational chemistry, Vol. 25, No. 4. (March 2004), pp. 479-499. by E. Gallicchio, R. M. Levy posted by 7 people flbarroso melo_mcr aphou dfgreen RamuAnandakrishnan jwagoner onufriev
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted by 19 people bmduggan newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm baker-group boris_aguilar Ema chenway ardalby OPIG
	Application of the level-set method to the implicit solvation of nonpolar molecules [My Copy] The Journal of Chemical Physics, Vol. 127, No. 8. (2007), 084503. by Li T. Cheng, Joachim Dzubiella, J. Andrew Mccammon, Bo Li posted by 5 people afenley structural_bioinformatics csrocha sobolevnrm baker-group
	Improved p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> prediction: Combining empirical and semimicroscopic methods [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Gernot Kieseritzky, E. W. Knapp posted by 3 people sobolevnrm baker-group RamuAnandakrishnan
	Accelerated entropy estimates with accelerated dynamics [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by David D. L. Minh, Donald Hamelberg, Andrew J. Mccammon posted by 5 people pgasper sobolevnrm baker-group afenley dmobley
	Effects of long-range electrostatic forces on simulated protein folding kinetics [My Copy] Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 694-700. by Alex Robertson, Edgar Luttmann, Vijay S. Pande posted by 4 people r2s2 sobolevnrm baker-group RamuAnandakrishnan
	Balancing Solvation and Intramolecular Interactions: Toward a Consistent Generalized Born Force Field [My Copy] Journal of the American Chemical Society, Vol. 128, No. 11. (1 March 2006), pp. 3728-3736. by Jianhan Chen, Wonpil Im, Charles L. Brooks posted by 6 people ckmyo oteri yxue dfgreen onufriev bilab
	Molecular dynamics and protein function. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 19. (10 May 2005), pp. 6679-6685. by M. Karplus, J. Kuriyan posted by 6 people flbarroso onufriev apaydin bilab allmensch RamuAnandakrishnan
	Optimizing pK<SUB><FONT SIZE='-1'>A</FONT></SUB> computation in proteins with pH adapted conformations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Gernot Kieseritzky, Ernst-Walter Knapp posted by 5 people sim82 sobolevnrm baker-group RamuAnandakrishnan boris_aguilar
	The Determinants of pKas in Proteins† [My Copy] Biochemistry, Vol. 35, No. 24. (1 January 1996), pp. 7819-7833. by Jan Antosiewicz, J. Andrew Mccammon, Michael K. Gilson posted by 5 people scampos flbarroso onufriev dfgreen RamuAnandakrishnan
	Statistical mechanics of a Coulomb gas with finite size particles: A lattice field theory approach [My Copy] The Journal of Chemical Physics, Vol. 102, No. 11. (1995), pp. 4584-4594. by Rob D. Coalson, Alan M. Walsh, Anthony Duncan, Nir B. Tal posted by 3 people afenley sobolevnrm baker-group
	Free energy landscape of protein folding in water: Explicit vs. implicit solvent [My Copy] Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161. by Ruhong Zhou posted by 6 people chemrahul82 flbarroso choonpeng RamuAnandakrishnan onufriev msuarezdiez
	Molecular Dynamics Simulations of Proteins: Can the Explicit Water Model Be Varied? [My Copy] J. Chem. Theory Comput., Vol. 3, No. 4. (10 July 2007), pp. 1550-1560. by D. R. Nutt, J. C. Smith posted by 4 people barmak7282 onufriev softsimu LamBras
	Integrated Modeling Program, Applied Chemical Theory (IMPACT). [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1752-1780. by Jay L. Banks, Hege S. Beard, Yixiang Cao, et al.Art E. Cho, Wolfgang Damm, Ramy Farid, Anthony K. Felts, Thomas A. Halgren, Daniel T. Mainz, Jon R. Maple, Robert Murphy, Dean M. Philipp, Matthew P. Repasky, Linda Y. Zhang, Bruce J. Berne, Richard A. Friesner, Emilio Gallicchio, Ronald M. Levy posted by 3 people oteri flbarroso onufriev
	Protein folding and misfolding [My Copy] Nature, Vol. 426, No. 6968. (18 December 2003), pp. 884-890. by Christopher M. Dobson posted by 11 people pfluffernuugen onufriev Diego_Prada chiufanlee penka allmensch choonpeng anyscientist dougjoemartin Nie Ema
	Where the linearized Poisson--Boltzmann cell model fails: Spurious phase separation in charged colloidal suspensions [My Copy] The Journal of Chemical Physics, Vol. 119, No. 3. (2003), pp. 1855-1865. by M. N. Tamashiro, H. Schiessel posted by 2 people onufriev softsimu
	Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions [My Copy] The Journal of Physical Chemistry A, Vol. 101, No. 43. (1 October 1997), pp. 8098-8106. by Marco Scarsi, Joannis Apostolakis, Amedeo Caflisch posted by 4 people flbarroso dmitry_s_yershov onufriev RamuAnandakrishnan
	Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 30. (1 July 2008), pp. 9020-9041. by In S. Joung, Thomas E. Cheatham posted by 2 people softsimu onufriev
	Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models [My Copy] The Journal of Physical Chemistry, Vol. 98, No. 7. (1 February 1994), pp. 1978-1988. by Doree Sitkoff, Kim A. Sharp, Barry Honig posted by 5 people melo_mcr onufriev dmitry_s_yershov flbarroso dfgreen
	Multiscale modeling of lipids and lipid bilayers [My Copy] European Biophysics Journal, Vol. 35, No. 1. (19 December 2005), pp. 53-61. by Alexander Lyubartsev posted by 2 people onufriev softsimu
	Beyond the Poisson-Boltzmann Model: Modeling Biomolecule-Water and Water-Water Interactions [My Copy] Physical Review Letters, Vol. 102, No. 8. (2009), 087801. by Patrice Koehl, Henri Orland, Marc Delarue posted by 4 people sobolevnrm onufriev baker-group paulschlesinger
	Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors [My Copy] Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 673-685. by Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig posted by 6 people mijogiffin sobolevnrm baker-group dmobley sunhwan boris_aguilar
	Implicit Solvent Electrostatics in Biomolecular Simulation [My Copy] New Algorithms for Macromolecular Simulation (2006), pp. 263-295. by Nathan Baker, Donald Bashford, David Case posted by 7 people flbarroso Scis0000002 dmitry_s_yershov stephenbond sunhwan onufriev qwermish
	Structural identification of the pathway of long-range communication in an allosteric enzyme [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 6. (12 February 2008), pp. 1832-1837. by Prafull S. Gandhi, Zhiwei Chen, F. Scott Mathews, Enrico Di Cera posted by 5 people boris_aguilar lna cactus sobolevnrm baker-group
	Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory [My Copy] The Journal of Chemical Physics, Vol. 129, No. 14. (2008) by Jaydeep P. Bardhan posted by 4 people baker-group sobolevnrm onufriev agrossfield
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science (New York, N.Y.), Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted by 11 people bmduggan kgutwin Diego_Prada onufriev apaydin dfgreen jwm hmk heymiki kevinchannon ca3295
	On removal of charge singularity in Poisson--Boltzmann equation [My Copy] The Journal of Chemical Physics, Vol. 130, No. 14. (2009), 145101. by Qin Cai, Jun Wang, Hong K. Zhao, Ray Luo posted by 3 people onufriev baker-group sobolevnrm
	Molecular dynamics simulations of biomolecules. [My Copy] Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652. by M. Karplus, J. A. McCammon posted by 9 people saravan yxue onufriev adilson_mohr yalexeev baaden aqeel RamuAnandakrishnan LamBras
	A generalized reaction field method for molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 102, No. 13. (1995), pp. 5451-5459. by Ilario G. Tironi, René Sperb, Paul E. Smith, Wilfred F. van Gunsteren posted by 4 people r2s2 dsmueller RamuAnandakrishnan onufriev
	Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme [My Copy] Biophys. J., Vol. 91, No. 2. (15 July 2006), pp. 626-638. by Maryna V. Krasovska, Jana Sefcikova, Kamila Reblova, Bohdan Schneider, Nils G. Walter, Jiri Sponer posted by 3 people baker-group sobolevnrm onufriev
	Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids [My Copy] Journal of the American Chemical Society, Vol. 129, No. 48. (1 December 2007), pp. 14981-14988. by Yu Bai, Max Greenfeld, Kevin J. Travers, et al.Vincent B. Chu, Jan Lipfert, Sebastian Doniach, Daniel Herschlag posted by 3 people itolokh sobolevnrm baker-group
	Electric fields at the active site of an enzyme: direct comparison of experiment with theory. [My Copy] Science (New York, N.Y.), Vol. 313, No. 5784. (14 July 2006), pp. 200-204. by Ian T. Suydam, Christopher D. Snow, Vijay S. Pande, Steven G. Boxer posted by 6 people onufriev charris5 flbarroso mikaellund jbchang kjell
	Symmetry breaking and electrostatic attraction between two identical surfaces [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 4. (2009), 041404. by F. Plouraboué, H. C. Chang posted by 4 people onufriev jeevanjyoti baker-group sobolevnrm
	Nitric oxide reactivity with globins as investigated through computer simulation. [My Copy] Methods in enzymology, Vol. 437 (2008), pp. 477-498. by M. A. Marti, L. Capece, A. Bidon-Chanal, et al.A. Crespo, V. Guallar, F. J. Luque, D. A. Estrin posted by 3 people sobolevnrm baker-group onufriev
	Theoretical Study of CO Escaping Pathway in Myoglobin with the 3D-RISM Theory [My Copy] Journal of the American Chemical Society, Vol. 131, No. 11. (25 March 2009), pp. 3852-3853. by Yasuomi Kiyota, Ryusuke Hiraoka, Norio Yoshida, Yutaka Maruyama, Takashi Imai, Fumio Hirata posted by 4 people linkj2 onufriev baker-group sobolevnrm
	Molecular dynamics simulations of biomolecules: long-range electrostatic effects. [My Copy] Annu Rev Biophys Biomol Struct, Vol. 28 (1999), pp. 155-179. by C. Sagui, T. A. Darden posted by 9 people Scis0000002 babakap onufriev lillekatt ttjoseph dgront RamuAnandakrishnan AndreaColetta r2s2
	Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible [My Copy] The Journal of Chemical Physics, Vol. 127, No. 18. (2007) by Nikolai A. Simonov, Michael Mascagni, Marcia O. Fenley posted by 3 people sobolevnrm baker-group boris_aguilar
	A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces [My Copy] Journal of Mathematical Analysis and Applications, Vol. 340, No. 1. (1 April 2008), pp. 135-164. by Y. C. Zhou, Michael Holst, Andrew J. Mccammon posted by 3 people sobolevnrm baker-group boris_aguilar
	Classical electrostatics in biology and chemistry. [My Copy] Science (New York, N.Y.), Vol. 268, No. 5214. (26 May 1995), pp. 1144-1149. by B. Honig, A. Nicholls posted by 5 people onufriev dmitry_s_yershov stephenbond flbarroso apostola
	Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules [My Copy] The Journal of Chemical Physics, Vol. 123, No. 1. (2005) by Patricia Schaefer, Demian Riccardi, Qiang Cui posted by 3 people baker-group sobolevnrm onufriev
	Analysis of integral expressions for effective Born radii [My Copy] The Journal of Chemical Physics, Vol. 127, No. 18. (2007) by John Mongan, Andreas, Alexey Onufriev posted by 3 people sobolevnrm baker-group sigalov
	A perspective of polyamine metabolism. [My Copy] The Biochemical journal, Vol. 376, No. Pt 1. (15 November 2003), pp. 1-14. by H. M. Wallace, A. V. Fraser, A. Hughes posted by 3 people baker-group sobolevnrm onufriev
	From the Cover: Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 4. (19 February 2002), pp. 1960-1965. by Brent D. Brower-Toland, Corey L. Smith, Richard C. Yeh, John T. Lis, Craig L. Peterson, Michelle D. Wang posted by 2 people onufriev afenley
	Tanford-Kirkwood electrostatics for protein modeling. [My Copy] Proc Natl Acad Sci U S A, Vol. 96, No. 20. (28 September 1999), pp. 11145-11150. by J. J. Havranek, P. B. Harbury posted by 3 people dfgreen onufriev dimka
	Biomolecular Electrostatics with the Linearized Poisson-Boltzmann Equation [My Copy] Biophysical Journal, Vol. 76, No. 1. (January 1999), pp. 1-16. by F. Fogolari posted by 4 people onufriev csrocha dfgreen lillekatt
	A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation [My Copy] Journal of Computational Physics, Vol. 227, No. 24. (20 December 2008), pp. 10162-10177. by W. Cai, Z. Xu, A. Baumketner posted by 2 people onufriev RamuAnandakrishnan
	Generalized coarse-grained model based on point multipole and Gay-Berne potentials [My Copy] The Journal of Chemical Physics, Vol. 125, No. 6. (2006), 064103. by Pavel A. Golubkov, Pengyu Ren posted by 2 people onufriev kaz229
	Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin [My Copy] Journal of Molecular Biology, Vol. 224, No. 2. (20 March 1992), pp. 473-486. by Donald Bashford, Klaus Gerwert posted by 2 people onufriev RamuAnandakrishnan
	Continuum polarizable force field within the Poisson-Boltzmann framework. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 25. (26 June 2008), pp. 7675-7688. by Y. H. Tan, C. Tan, J. Wang, R. Luo posted by 2 people RamuAnandakrishnan onufriev
	Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 1100-1105. by Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, Michele Parrinello posted by 2 people RamuAnandakrishnan onufriev
	Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. [My Copy] Proc Natl Acad Sci U S A, Vol. 92, No. 4. (14 February 1995), pp. 1082-1086. by T. Simonson, D. Perahia posted by 3 people dfgreen chiufanlee onufriev
	Steric Effects in Electrolytes: A Modified Poisson-Boltzmann Equation [My Copy] Physical Review Letters, Vol. 79, No. 3. (21 Jul 1997), pp. 435-438. by Itamar Borukhov, David Andelman, Henri Orland posted by 1 person onufriev
	Histone structure and nucleosome stability. [My Copy] Expert Rev Proteomics, Vol. 2, No. 5. (October 2005), pp. 719-729. by L. Mariño-Ramírez, M. G. Kann, B. A. Shoemaker, D. Landsman posted by 3 people afenley aalibes onufriev
	Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions [My Copy] The European Physical Journal E: Soft Matter and Biological Physics, Vol. 1, No. 2. (19 February 2000), pp. 203-214. by R. R. Netz, H. Orland posted by 2 people sobolevnrm onufriev
	Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. [My Copy] Journal of computational chemistry, Vol. 25, No. 2. (30 January 2004), pp. 238-250. by H. Gohlke, D. A. Case posted by 4 people flbarroso bmduggan onufriev lillekatt
	Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models [My Copy] Journal of Computational Chemistry, Vol. 25, No. 13. (2004), pp. 1623-1629. by Jason Wagoner, Nathan A. Baker posted by 3 people flbarroso onufriev qwermish
	A Gaussian Description of Molecular Shape [My Copy] The Journal of Physical Chemistry, Vol. 99, No. 11. (1 March 1995), pp. 3503-3510. by J. A. Grant, B. T. Pickup posted by 2 people sobolevnrm onufriev
	Generalized born model with a simple smoothing function [My Copy] Journal of Computational Chemistry, Vol. 24, No. 14. (15 November 2003), pp. 1691-1702. by Wonpil Im, Michael S. Lee, Charles L. Brooks posted by 4 people ckmyo stephenbond dfgreen onufriev
	Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 39. (25 September 2007), pp. 15230-15235. by Isabella Daidone, Martin B. Ulmschneider, Alfredo Di Nola, Andrea Amadei, Jeremy C. Smith posted by 5 people qshao jjurban barmak7282 choonpeng onufriev
	A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation [My Copy] J. Phys. Chem. B (10 May 2008) by Scott M. Shell, Ryan Ritterson, Ken A. Dill posted by 3 people allmensch onufriev middledomain
	An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. [My Copy] Biophysical journal, Vol. 85, No. 5. (November 2003), pp. 2900-2918. by W. Im, M. Feig, C. L. Brooks posted by 3 people flbarroso onufriev dimka
	Electrostatics and dynamics of proteins [My Copy] Reports of Progress in Physics, Vol. 66 (May 2003), pp. 737-787. by T. Simonson posted by 4 people Lombardo_7 chiufanlee medic0747 onufriev
	Parameter Dependence in Continuum Electrostatic Calculations: A Study Using Protein Salt Bridges [My Copy] The Journal of Physical Chemistry B, Vol. 102, No. 22. (1 May 1998), pp. 4404-4410. by Zachary S. Hendsch, Charles V. Sindelar, Bruce Tidor posted by 2 people onufriev dfgreen
	Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1068-1082. by Anna Jagielska, Harold A. Scheraga posted by 3 people onufriev choonpeng jwagoner
	The protein folding problem: when will it be solved? [My Copy] Curr Opin Struct Biol (13 June 2007) by Ken A A. Dill, S Banu B. Ozkan, Thomas R R. Weikl, John D D. Chodera, Vincent A A. Voelz posted by 9 people flbarroso onufriev wouterboomsma cat_worth cactus Jporci cdeane kalicuta sebk
	FACTS: Fast analytical continuum treatment of solvation. [My Copy] Journal of computational chemistry, Vol. 29, No. 5. (15 April 2008), pp. 701-715. by U. Haberthür, A. Caflisch posted by 3 people flbarroso onufriev apostola
	Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. [My Copy] Journal of the American Chemical Society, Vol. 129, No. 9. (7 March 2007), pp. 2444-2445. by J. Chen, C. L. Brooks posted by 2 people flbarroso onufriev
	Salt bridge stability in monomeric proteins, [My Copy] Journal of Molecular Biology, Vol. 293, No. 5. (12 November 1999), pp. 1241-1255. by Sandeep Kumar, Ruth Nussinov posted by 4 people merj bicko choonpeng onufriev
	Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions [My Copy] Nature, Vol. 458, No. 7238. (2 April 2009), pp. 591-596. by Peter J. Cook, Bong G. Ju, Francesca Telese, Xiangting Wang, Christopher K. Glass, Michael G. Rosenfeld posted by 5 people wmatsui onufriev fenghezi DevilInPgh paulschlesinger
	What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. [My Copy] J Comput Chem, Vol. 27, No. 1. (January 2006), pp. 72-89. by Z. Yu, M. P. Jacobson, R. A. Friesner posted by 5 people BragilMassoud qzhang choonpeng TSRI_MGL onufriev
	Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water? [My Copy] Proceedings of the National Academy of Sciences, Vol. 99, No. 20. (1 October 2002), pp. 12777-12782. by Ruhong Zhou, Bruce J. Berne posted by 2 people flbarroso onufriev
	On the pH dependence of protein stability. [My Copy] Journal of molecular biology, Vol. 231, No. 2. (20 May 1993), pp. 459-474. by A. S. Yang, B. Honig posted by 5 people onufriev scampos flbarroso cat_worth structural_bioinformatics