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onufriev's implicit_solvation [41 articles]

Recent papers added to onufriev's library classified by the tag implicit_solvation. You can also see everyone's implicit_solvation.
  • Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
    J. Phys. Chem. A, Vol. 101, No. 43. (23 October 1997), pp. 8098-8106.
    by M Scarsi, J Apostolakis, A Caflisch
    posted to implicit_solvation gb by onufriev on 2008-09-18 00:27:29 as ** along with 1 person RamuAnandakrishnan
  • Implicit Solvent Electrostatics in Biomolecular Simulation
    New Algorithms for Macromolecular Simulation (2006), pp. 263-295.
    by Nathan Baker, Donald Bashford, David Case
    posted to pb implicit_solvation gb by onufriev on 2008-09-14 23:15:03 as read along with 2 people sunhwan qwermish
  • Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models
    Journal of Computational Chemistry, Vol. 25, No. 13. (2004), pp. 1623-1629.
    by Jason Wagoner, Nathan A Baker
    posted to water_models pb implicit_solvation by onufriev on 2008-09-14 20:52:11 as read along with 1 person qwermish
  • Solvation of complex molecules in a polar liquid: An integral equation theory
    The Journal of Chemical Physics, Vol. 104, No. 21. (1996), pp. 8678-8689.
    by Dmitrii Beglov, Benoît Roux
    posted to water_models implicit_solvation electrostatics by onufriev on 2008-09-14 03:57:25 as read
  • Computational sidechain placement and protein mutagenesis with implicit solvent models.
    Proteins, Vol. 67, No. 4. (1 June 2007), pp. 853-867.
    by A Lopes, A Alexandrov, C Bathelt, G Archontis, T Simonson
    posted to protein_folding implicit_solvation by onufriev on 2008-09-11 20:20:25 as ** along with 1 person msuarezdiez
  • Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
    Journal of Computational Chemistry, Vol. 24, No. 12. (2003), pp. 1432-1436.
    by Bojan Zagrovic, Vijay Pande
    posted to protein_folding implicit_solvation gb by onufriev on 2008-09-10 05:33:35 as **
  • Continuum polarizable force field within the Poisson-Boltzmann framework.
    The journal of physical chemistry. B, Vol. 112, No. 25. (26 June 2008), pp. 7675-7688.
    by YH Tan, C Tan, J Wang, R Luo
    posted to pb molecular_dynamics md implicit_solvation by onufriev on 2008-09-03 23:04:40 as **
  • Insight into the role of hydration on protein dynamics.
    The Journal of chemical physics, Vol. 125, No. 9. (7 September 2006)
    by D Hamelberg, T Shen, JA McCammon
    posted to gb implicit_solvation time_scale by onufriev on 2008-08-14 07:53:52 as ** along with 1 person pgasper
  • Potential energy functions for protein design.
    Curr Opin Struct Biol (24 March 2007)
    by F Edward E Boas, Pehr B B Harbury
    posted to implicit_solvation protein_folding by onufriev on 2008-08-13 02:13:24 as ** along with 2 people BragilMassoud aalibes
  • On the Dielectric Boundary in Poisson-Boltzmann Calculations
    J. Chem. Theory Comput., Vol. 4, No. 3. (11 March 2008), pp. 507-514.
    by H Tjong, HX Zhou
    posted to gb implicit_solvation pb by onufriev on 2008-08-13 02:08:57 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Recent advances in implicit solvent-based methods for biomolecular simulations
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Jianhan Chen, Brooks, Jana Khandogin
    posted to implicit_solvation molecular_dynamics by onufriev on 2008-08-13 02:04:41 as ** along with 2 people and 1 group choonpeng sobolevnrm baker-group
  • Protein molecular dynamics with the generalized born/ACE solvent model
    Proteins: Structure, Function, and Genetics, Vol. 45, No. 2. (2001), pp. 144-158.
    by Nicolas Calimet, Michael Schaefer, Thomas Simonson
    posted to molecular_dynamics md implicit_solvation gb by onufriev on 2008-08-02 01:42:44 as **
  • Electrostatics and dynamics of proteins
    Reports of Progress in Physics, Vol. 66 (May 2003), pp. 737-787.
    by T Simonson
    posted to electrostatics implicit_solvation molecular_dynamics by onufriev on 2008-08-02 01:38:42 as ** along with 1 person medic0747
  • Local electrostatics algorithm for classical molecular dynamics simulations
    posted to implicit_solvation md molecular_dynamics by onufriev on 2008-03-09 03:13:49 as **
  • Effective energy function for proteins in solution
    Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 133-152.
    by Themis Lazaridis, Martin Karplus
    posted to implicit_solvation md molecular_dynamics by onufriev on 2008-03-09 02:26:18 as **
  • Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ninad V Prabhu, Manoranjan Panda, Qingyi Yang, Kim A Sharp
    posted to implicit_solvation md_dna molecular_dynamics by onufriev on 2008-03-09 01:52:28 as ** along with 3 people and 1 group sobolevnrm RamuAnandakrishnan dimka baker-group
  • How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
    J Phys Chem B., Vol. 110, 18680.
    by Tan
    posted to explicit_solvation implicit_solvation pb by onufriev on 2008-03-08 22:26:41 as **
  • Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method
    Journal of Computational Chemistry, Vol. 25, No. 16. (2004), pp. 2049-2064.
    by Ninad V Prabhu, Peijuan Zhu, Kim A Sharp
    posted to implicit_solvation md pb by onufriev on 2008-03-08 22:00:22 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by David S Cerutti, Nathan A Baker, Andrew J Mccammon
    posted to explicit_solvation implicit_solvation by onufriev on 2008-03-08 20:55:40 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Critical Importance of Length-Scale Dependence in Implicit Modeling of Hydrophobic Interactions
    J. Am. Chem. Soc., Vol. 129, No. 9. (7 March 2007), pp. 2444-2445.
    by J Chen, CL Brooks
    posted to implicit_solvation by onufriev on 2008-03-08 20:49:55 as **
  • Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation
    J. Phys. Chem. B, Vol. 111, No. 7. (22 February 2007), pp. 1846-1857.
    by DR Roe, A Okur, L Wickstrom, V Hornak, C Simmerling
    posted to explicit_solvation gb implicit_solvation by onufriev on 2008-03-06 01:54:57 as ** along with 3 people and 1 group baaden choonpeng sobolevnrm baker-group
  • Free energy landscape of protein folding in water: Explicit vs. implicit solvent
    Proteins: Structure, Function, and Genetics, Vol. 53, No. 2. (2003), pp. 148-161.
    by Ruhong Zhou
    posted to gb implicit_solvation protein_folding by onufriev on 2008-03-06 01:49:56 as ** along with 3 people choonpeng RamuAnandakrishnan msuarezdiez
  • Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?
    Proceedings of the National Academy of Sciences, Vol. 99, No. 20. (1 October 2002), pp. 12777-12782.
    by Ruhong Zhou, Bruce J Berne
    posted to gb implicit_solvation by onufriev on 2008-03-06 01:20:26 as **
  • Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations
    J. Am. Chem. Soc., Vol. 125, No. 48. (3 December 2003), pp. 14841-14846.
    by S Jang, E Kim, S Shin, Y Pak
    posted to implicit_solvation protein_folding by onufriev on 2008-03-06 00:28:00 as **
  • Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing
    Journal of Molecular Biology, Vol. 323, No. 5. (8 November 2002), pp. 927-937.
    by Bojan Zagrovic, Christopher D Snow, Michael R Shirts, Vijay S Pande
    posted to implicit_solvation protein_folding by onufriev on 2008-03-05 23:50:04 as **
  • Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 13. (24 June 2003), pp. 7587-7592.
    by JW Pitera, W Swope
    posted to implicit_solvation protein_folding by onufriev on 2008-03-05 23:45:29 as **
  • Tanford-Kirkwood electrostatics for protein modeling.
    Proc Natl Acad Sci U S A, Vol. 96, No. 20. (28 September 1999), pp. 11145-11150.
    by JJ Havranek, PB Harbury
    posted to image_charge implicit_solvation by onufriev on 2008-02-13 01:24:38 as read along with 1 person dimka
  • Charge Asymmetries in Hydration of Polar Solutes
    J. Phys. Chem. B (6 February 2008)
    by DL Mobley, AE Barber, CJ Fennell, KA Dill
    posted to implicit_solvation water_models by onufriev on 2008-02-08 19:36:13 as **** along with 3 people and 1 group sobolevnrm dmobley middledomain baker-group
  • An Assessment of Potential of Mean Force Calculations with Implicit Solvent Models
    J. Phys. Chem. B, Vol. 108, No. 42. (21 October 2004), pp. 16525-16532.
    by CM Stultz
    posted to implicit_solvation by onufriev on 2008-01-13 04:44:55 as ***
  • Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding.
    Proc Natl Acad Sci U S A, Vol. 104, No. 39. (25 September 2007), pp. 15230-15235.
    by I Daidone, MB Ulmschneider, A Di Nola, A Amadei, JC Smith
    posted to explicit_solvation implicit_solvation md molecular_dynamics by onufriev on 2007-12-28 02:03:54 as ** along with 1 person choonpeng
  • Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation
    The Journal of Chemical Physics, Vol. 119, No. 9. (2003), pp. 4817-4826.
    by Tomasz Grycuk
    posted to electrostatics gb implicit_solvation by onufriev on 2007-12-09 23:21:35 as read along with 1 person baaden
  • AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
    Journal of Computational Chemistry, Vol. 25, No. 4. (2004), pp. 479-499.
    by Emilio Gallicchio, Ronald M Levy
    posted to gb implicit_solvation by onufriev on 2007-12-09 23:05:10 as read along with 2 people RamuAnandakrishnan jwagoner
  • An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution
    Journal of Molecular Biology, Vol. 256, No. 5. (15 March 1996), pp. 939-948.
    by F Fraternali, WF van Gunsteren
    posted to implicit_solvation md by onufriev on 2007-12-06 19:52:23 as ***
  • Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm
    Journal of Computational Chemistry, Vol. 24, No. 16. (2003), pp. 2063-2074.
    by Qing Zhang, Daniel A Beard, Tamar Schlick
    posted to dna_electrostatics electrostatics implicit_solvation by onufriev on 2007-10-31 22:02:58 as ***
  • Comparative study of generalized born models: Born radii and peptide folding.
    J Phys Chem B, Vol. 109, No. 7. (24 February 2005), pp. 3008-3022.
    by J Zhu, E Alexov, B Honig
    posted to gb implicit_solvation protein_electrostatics by onufriev on 2007-10-21 17:00:24 as read
  • Coupling nonpolar and polar solvation free energies in implicit solvent models.
    J Chem Phys, Vol. 124, No. 8. (28 February 2006)
    by J Dzubiella, JM Swanson, JA McCammon
    posted to implicit_solvation water_models by onufriev on 2007-10-21 16:56:19 as read
  • Competition of hydrophobic and Coulombic interactions between nanosized solutes
    posted to electrostatics implicit_solvation water_models by onufriev on 2007-10-21 16:54:51 as read
  • A smooth permittivity function for Poisson-Boltzmann solvation methods
    Journal of Computational Chemistry, Vol. 22, No. 6. (2001), pp. 608-640.
    by Andrew J Grant, Barry T Pickup, Anthony Nicholls
    posted to electrostatics implicit_solvation md pb by onufriev on 2007-10-18 17:42:24 as read
  • What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules.
    J Comput Chem, Vol. 27, No. 1. (January 2006), pp. 72-89.
    by Z Yu, MP Jacobson, RA Friesner
    posted to electrostatics gb implicit_solvation by onufriev on 2007-10-12 22:42:43 as read along with 3 people and 1 group BragilMassoud qzhang choonpeng TSRI_MGL
  • A generalized reaction field method for molecular dynamics simulations
    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 to implicit_solvation md by onufriev on 2007-10-02 00:14:08 as *** along with 1 person RamuAnandakrishnan
  • Extending the fast multipole method to charges inside or outside a dielectric sphere
    Journal of Computational Physics, Vol. 223, No. 2. (1 May 2007), pp. 846-864.
    by Wei Cai, Shaozhong Deng, Donald Jacobs
    posted to gb image_charge implicit_solvation by onufriev on 2007-10-02 00:04:14 as **
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