Register | Log in | FAQ      [?] 
Recent | Unread | Search | Authors | Tags | Export

onufriev's gb [38 articles]

Recent papers added to onufriev's library classified by the tag gb. You can also see everyone's gb.
  • GBr6: A Parameterization-Free, Accurate, Analytical Generalized Born Method
    J. Phys. Chem. B, Vol. 111, No. 11. (22 March 2007), pp. 3055-3061.
    by H Tjong, HX Zhou
    posted to gb by onufriev on 2008-10-09 19:10:17 as **
  • The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Paul Labute
    posted to gb by onufriev on 2008-10-09 18:45:43 as ** along with 6 people and 1 group sobolevnrm RamuAnandakrishnan middledomain sunhwan dmobley GermanErlenkamp baker-group
  • Generalized born model with a simple smoothing function.
    Journal of computational chemistry, Vol. 24, No. 14. (15 November 2003), pp. 1691-1702.
    by W Im, MS Lee, CL Brooks
    posted to gb by onufriev on 2008-10-09 17:58:03 as **
  • Implicit solvation based on generalized Born theory in different dielectric environments.
    The Journal of chemical physics, Vol. 120, No. 2. (8 January 2004), pp. 903-911.
    by M Feig, W Im, CL Brooks
    posted to gb_membrane gb by onufriev on 2008-10-07 21:51:55 as **
  • An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.
    Biophysical journal, Vol. 85, No. 5. (November 2003), pp. 2900-2918.
    by W Im, M Feig, CL Brooks
    posted to gb_membrane gb by onufriev on 2008-10-07 21:43:25 as ** along with 1 person dimka
  • Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 1. (12 January 2006), pp. 548-556.
    by S Tanizaki, M Feig
    posted to gb_membrane gb by onufriev on 2008-10-07 21:38:07 as ** along with 2 people and 1 group dimka xdeupi LabCompMed
  • A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes.
    The Journal of chemical physics, Vol. 122, No. 12. (22 March 2005)
    by S Tanizaki, M Feig
    posted to gb_membrane gb by onufriev on 2008-10-07 21:29:38 as **
  • Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models
    J. Phys. Chem. B, Vol. 106, No. 34. (29 August 2002), pp. 8726-8738.
    by VZ Spassov, L Yan, S Szalma
    posted to gb_membrane gb by onufriev on 2008-10-07 19:57:27 as **
  • The Gaussian Generalized Born model: application to small molecules
    Phys. Chem. Chem. Phys., Vol. 9, No. 35. (2007), pp. 4913-4922.
    by JA Grant, BT Pickup, MJ Sykes, CA Kitchen, A Nicholls
    posted to gb by onufriev on 2008-10-01 18:35:20 as **
  • 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
  • Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent
    Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1068-1082.
    by Anna Jagielska, Harold A Scheraga
    posted to protein_folding gb by onufriev on 2008-09-12 00:21:32 as ** along with 2 people choonpeng jwagoner
  • Ab Initio Folding of Albumin Binding Domain from All-Atom Molecular Dynamics Simulation
    J. Phys. Chem. B, Vol. 111, No. 19. (17 May 2007), pp. 5458-5463.
    by H Lei, Y Duan
    posted to protein_folding gb by onufriev on 2008-09-12 00:16:28 as **
  • Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.
    J Am Chem Soc, Vol. 128, No. 11. (22 March 2006), pp. 3728-3736.
    by J Chen, W Im, CL Brooks
    posted to protein_folding gb by onufriev on 2008-09-12 00:11:56 as ** along with 1 person bilab
  • A residue-pairwise generalized born scheme suitable for protein design calculations.
    The journal of physical chemistry. B, Vol. 109, No. 47. (1 December 2005), pp. 22667-22673.
    by G Archontis, T Simonson
    posted to protein_folding gb by onufriev on 2008-09-12 00:02:35 as **
  • FACTS: Fast analytical continuum treatment of solvation.
    J Comput Chem (5 October 2007)
    by Urs Haberthür, Amedeo Caflisch
    posted to gb by onufriev on 2008-09-11 21:07:31 as ** along with 1 person apostola
  • Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson-Boltzmann Approach
    J. Phys. Chem. B, Vol. 110, No. 18. (11 May 2006), pp. 9304-9313.
    by HY Liu, X Zou
    posted to protein_ligand protein_electrostatics gb by onufriev on 2008-09-11 20:34:27 as **
  • 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 **
  • Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces
    The Journal of Chemical Physics, Vol. 127, No. 1. (2007)
    by Jaydeep P Bardhan, Michael D Altman, David J Willis, Shaun M Lippow, Bruce Tidor, Jacob K White
    posted to surface pb gb by onufriev on 2008-09-03 00:45:13 as **
  • A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation
    J. Phys. Chem. B (10 May 2008)
    by Scott M Shell, Ryan Ritterson, Ken A Dill
    posted to explicit_solvation gb md by onufriev on 2008-08-22 18:59:21 as read along with 1 person middledomain
  • Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 657-672.
    by Birgit Strodel, David J Wales
    posted to gb molecular_dynamics performance by onufriev on 2008-08-14 21:46:26 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
  • Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity
    J. Chem. Theory Comput., Vol. 3, No. 5. (11 September 2007), pp. 1734-1748.
    by M Feig
    posted to gb md by onufriev on 2008-08-13 02:11:15 as **
  • 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
  • Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling
    J. Chem. Theory Comput., Vol. 4, No. 5. (13 May 2008), pp. 855-868.
    by Anthony K Felts, Emilio Gallicchio, Dmitriy Chekmarev, Kristina A Paris, Richard A Friesner, Ronald M Levy
    posted to gb by onufriev on 2008-08-13 01:58:16 as **
  • Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.
    Journal of computational chemistry, Vol. 23, No. 2. (30 January 2002), pp. 214-221.
    by O Guvench, J Weiser, P Shenkin, I Kolossváry, WC Still
    posted to gb md by onufriev on 2008-08-13 01:52:05 as **
  • A generalized born implicit-membrane representation compared to experimental insertion free energies.
    Biophys J, Vol. 92, No. 7. (1 April 2007), pp. 2338-2349.
    by MB Ulmschneider, JP Ulmschneider, MS Sansom, A Di Nola
    posted to gb gb_membrane by onufriev on 2008-08-10 21:23:19 as ** along with 1 person dimka
  • 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 **
  • 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 **
  • 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
  • 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
  • The Gaussian Generalized Born model: application to small molecules (DOI: 10.1039/b707574j)
    by Grant
    posted to gb molecular_geometry by onufriev on 2007-10-17 18:20:42 as ****
  • Second derivatives in generalized Born theory.
    J Comput Chem, Vol. 27, No. 14. (15 November 2006), pp. 1662-1675.
    by RA Brown, DA Case
    posted to gb by onufriev on 2007-10-12 22:43:50 as ** along with 2 people and 2 groups BragilMassoud jwm Radiation_Damage Stressosome
  • 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
  • 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 **
    • Note: You may cite this page as: http://www.citeulike.org/user/onufriev/tag/gb

    RIS BibTeX
    CiteULike organises scholarly (or academic) papers or literature and provides bibliographic (which means it makes bibliographies) for universities and higher education establishments. It helps undergraduates and postgraduates. People studying for PhDs or in postdoctoral (postdoc) positions. The service is similar in scope to EndNote or RefWorks or any other reference manager like BibTeX, but it is a social bookmarking service for scientists and humanities researchers.