onufriev's gb [51 articles] Export

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	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 to salt_bridge gb by onufriev on 2009-11-19 18:32:30 as along with 2 people and 1 group sobolevnrm dmobley baker-group
	Investigation of Salt Bridge Stability in a Generalized Born Solvent Model [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 1. (1 January 2006), pp. 115-127. by Raphael Geney, Melinda Layten, Roberto Gomperts, Viktor Hornak, Carlos Simmerling posted to salt_bridge gb by onufriev on 2009-11-19 18:22:09 as along with 2 people baaden choonpeng
	Protein folding by zipping and assembly. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992. by S. B. Ozkan, G. A. Wu, J. D. Chodera, K. A. Dill posted to gb protein_folding by onufriev on 2009-06-21 05:39:45 as along with 4 people aqeel wouterboomsma cdeane ARobson
	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 to gb implicit_solvation surface by onufriev on 2009-06-16 01:34:29 as along with 1 person sobolevnrm
	Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Rommie E. Amaro, Xiaolin Cheng, Ivaylo Ivanov, Dong Xu, Andrew J. Mccammon posted to drug_design gb by onufriev on 2009-05-18 08:25:54 as along with 1 person zwang
	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 to electrostatics gb by onufriev on 2009-01-08 21:56:05 as along with 2 people and 1 group sobolevnrm agrossfield baker-group
	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 to gb by onufriev on 2008-12-23 19:48:50 as along with 1 person RamuAnandakrishnan
	Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model [My Copy] Journal of the American Chemical Society, Vol. 121, No. 35. (1 September 1999), pp. 8033-8043. by Xiaoqin Zou, Yaxiong, Irwin D. Kuntz posted to gb protein_ligand by onufriev on 2008-11-04 23:52:20 as along with 1 person nickolay
	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 to gb molecular_dynamics by onufriev on 2008-11-02 01:44:59 as along with 2 people oteri flbarroso
	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 to gb protein_ligand by onufriev on 2008-11-02 00:40:27 as along with 3 people flbarroso bmduggan lillekatt
	A Generalized-Born Solvation Model for Macromolecular Hybrid-Potential Calculations [My Copy] J. Phys. Chem. A, Vol. 106, No. 7. (21 February 2002), pp. 1316-1326. by E. Pellegrini, M. J. Field posted to gb qmmm by onufriev on 2008-11-02 00:02:48 as along with 1 person pavanghatty
	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 to gb qmmm by onufriev on 2008-11-01 23:50:15 as along with 2 people RamuAnandakrishnan softsimu
	A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction [My Copy] Computational Biology and Chemistry, Vol. 28, No. 4. (October 2004), pp. 265-274. by W. Zheng, V. Spassov, L. Yan, P. Flook, S. Szalma posted to gb gb_membrane by onufriev on 2008-10-31 22:51:31 as
	GBr6: A Parameterization-Free, Accurate, Analytical Generalized Born Method [My Copy] J. Phys. Chem. B, Vol. 111, No. 11. (22 March 2007), pp. 3055-3061. by H. Tjong, H. X. Zhou posted to gb by onufriev on 2008-10-09 19:10:17 as along with 1 person aphou
	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 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 [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 to gb by onufriev on 2008-10-09 17:58:03 as along with 3 people ckmyo stephenbond dfgreen
	Implicit solvation based on generalized Born theory in different dielectric environments. [My Copy] The Journal of chemical physics, Vol. 120, No. 2. (8 January 2004), pp. 903-911. by M. Feig, W. Im, C. L. Brooks posted to gb gb_membrane 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. [My Copy] Biophysical journal, Vol. 85, No. 5. (November 2003), pp. 2900-2918. by W. Im, M. Feig, C. L. Brooks posted to gb gb_membrane by onufriev on 2008-10-07 21:43:25 as along with 2 people flbarroso dimka
	Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. [My Copy] 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 gb_membrane 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. [My Copy] The Journal of chemical physics, Vol. 122, No. 12. (22 March 2005) by S. Tanizaki, M. Feig posted to gb gb_membrane by onufriev on 2008-10-07 21:29:38 as
	Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models [My Copy] J. Phys. Chem. B, Vol. 106, No. 34. (29 August 2002), pp. 8726-8738. by V. Z. Spassov, L. Yan, S. Szalma posted to gb gb_membrane by onufriev on 2008-10-07 19:57:27 as
	The Gaussian Generalized Born model: application to small molecules [My Copy] Phys. Chem. Chem. Phys., Vol. 9, No. 35. (2007), pp. 4913-4922. by J. A. Grant, B. T. Pickup, M. J. Sykes, C. A. Kitchen, A. Nicholls posted to gb by onufriev on 2008-10-01 18:35:20 as
	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 to gb implicit_solvation by onufriev on 2008-09-18 00:27:29 as along with 3 people flbarroso dmitry_s_yershov RamuAnandakrishnan
	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 to gb implicit_solvation pb by onufriev on 2008-09-14 23:15:03 as along with 6 people flbarroso Scis0000002 dmitry_s_yershov stephenbond 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 [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1068-1082. by Anna Jagielska, Harold A. Scheraga posted to gb protein_folding 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 [My Copy] J. Phys. Chem. B, Vol. 111, No. 19. (17 May 2007), pp. 5458-5463. by H. Lei, Y. Duan posted to gb protein_folding by onufriev on 2008-09-12 00:16:28 as
	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 to gb protein_folding by onufriev on 2008-09-12 00:11:56 as along with 5 people ckmyo oteri yxue dfgreen bilab
	A residue-pairwise generalized born scheme suitable for protein design calculations. [My Copy] The journal of physical chemistry. B, Vol. 109, No. 47. (1 December 2005), pp. 22667-22673. by G. Archontis, T. Simonson posted to gb protein_folding by onufriev on 2008-09-12 00:02:35 as
	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 to gb by onufriev on 2008-09-11 21:07:31 as along with 2 people flbarroso apostola
	Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 18. (1 May 2006), pp. 9304-9313. by Hao-Yang Liu, Xiaoqin Zou posted to gb protein_electrostatics protein_ligand by onufriev on 2008-09-11 20:34:27 as along with 2 people nickolay flbarroso
	Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study [My Copy] Journal of Computational Chemistry, Vol. 24, No. 12. (2003), pp. 1432-1436. by Bojan Zagrovic, Vijay Pande posted to gb implicit_solvation protein_folding by onufriev on 2008-09-10 05:33:35 as
	Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces [My Copy] The Journal of Chemical Physics, Vol. 127, No. 1. (2007), 014701. by Jaydeep P. Bardhan, Michael D. Altman, David J. Willis, Shaun M. Lippow, Bruce Tidor, Jacob K. White posted to gb pb surface by onufriev on 2008-09-03 00:45:13 as along with 1 person Cbaker
	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 to explicit_solvation gb molecular_dynamics by onufriev on 2008-08-22 18:59:21 as along with 2 people allmensch middledomain
	Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide [My Copy] 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. [My Copy] The Journal of chemical physics, Vol. 125, No. 9. (7 September 2006) by D. Hamelberg, T. Shen, J. A. 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 [My Copy] J. Chem. Theory Comput., Vol. 3, No. 5. (11 September 2007), pp. 1734-1748. by M. Feig posted to gb molecular_dynamics by onufriev on 2008-08-13 02:11:15 as
	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 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 [My Copy] 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. [My Copy] Journal of computational chemistry, Vol. 23, No. 2. (30 January 2002), pp. 214-221. by O. Guvench, J. Weiser, P. Shenkin, I. Kolossváry, W. C. Still posted to molecular_dynamics gb by onufriev on 2008-08-13 01:52:05 as along with 1 person flbarroso
	A generalized born implicit-membrane representation compared to experimental insertion free energies. [My Copy] Biophys J, Vol. 92, No. 7. (1 April 2007), pp. 2338-2349. by M. B. Ulmschneider, J. P. Ulmschneider, M. S. 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 [My Copy] Proteins: Structure, Function, and Genetics, Vol. 45, No. 2. (2001), pp. 144-158. by Nicolas Calimet, Michael Schaefer, Thomas Simonson posted to gb implicit_solvation molecular_dynamics by onufriev on 2008-08-02 01:42:44 as along with 1 person yxue
	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 to explicit_solvation gb implicit_solvation by onufriev on 2008-03-06 01:54:57 as along with 5 people and 1 group RamuAnandakrishnan flbarroso baaden choonpeng 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 to gb implicit_solvation protein_folding by onufriev on 2008-03-06 01:49:56 as along with 5 people chemrahul82 flbarroso choonpeng RamuAnandakrishnan msuarezdiez
	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 to gb implicit_solvation by onufriev on 2008-03-06 01:20:26 as along with 1 person flbarroso
	Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation [My Copy] 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 along with 1 person baaden
	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 to gb implicit_solvation by onufriev on 2007-12-09 23:05:10 as along with 6 people flbarroso melo_mcr aphou dfgreen RamuAnandakrishnan jwagoner
	Comparative Study of Generalized Born Models: Born Radii and Peptide Folding [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 7. (1 February 2005), pp. 3008-3022. by Jiang Zhu, Emil Alexov, Barry Honig posted to gb implicit_solvation protein_electrostatics by onufriev on 2007-10-21 17:00:24 as along with 3 people jjurban flbarroso Vadikus
	The Gaussian Generalized Born model: application to small molecules (DOI: 10.1039/b707574j) [My Copy] by Grant posted to gb molecular_geometry by onufriev on 2007-10-17 18:20:42 as
	Second derivatives in generalized Born theory. [My Copy] J Comput Chem, Vol. 27, No. 14. (15 November 2006), pp. 1662-1675. by R. A. Brown, D. A. 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. [My Copy] J Comput Chem, Vol. 27, No. 1. (January 2006), pp. 72-89. by Z. Yu, M. P. Jacobson, R. A. Friesner posted to electrostatics gb implicit_solvation by onufriev on 2007-10-12 22:42:43 as along with 3 people and 1 group BragilMassoud qzhang choonpeng TSRI_MGL

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implicit_solvation	60
gb	51
molecular_dynamics	36
nucleosome	36
pb	27
protein_folding	24
pka	22
electrostatics	21
dna	20
dna_bending	19
histone_acetylation	19
dna_electrostatics	15
dna_ions	15
higher_order_chromatin	15
protein_ligand	15
nucleosome_stability	13
nucleosome_assembly	11
beyond_pb	8
ions	8
water_models	8
explicit_solvation	7
gb_membrane	7
myoglobin	7
protein_dynamics	7
protein_electrostatics	7
coarse-grain	6
dielectric_in_biopolymers	6
dna_ab	6
dna_nano	5
md_dna	5
pedagogical	5
polyamines	5
surface	5
dna_stacking	4
drug_design	4
multiscale	4
ph	4
phosphorylation	4
rnai	4
image_charge	3
molecular_geometry	3
qmmm	3
rna_sec_structure	3
water_in_biopolymers	3
dna_bend	2
dna_stretching	2
ewald	2
free_energy	2
physics_philosophy	2
salt_bridge	2
analytical	1
br	1
charge_asymmetry	1
classical_mechanics	1
coarse_grain	1
dna_md	1
extremophile	1
hnox	1
monte_carlo	1
non_equilibrium_statmech	1
nucleosome_positioning	1
nucleus	1
performance	1
physics_fundamentals	1
protein_stability	1
spermine	1
time_scale	1
water_molecules	1

onufriev's gb [51 articles] Export

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