onufriev's molecular_dynamics [36 articles] Export

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	On Finite-Size Corrections to the Free Energy of Ionic Hydration [My Copy] The Journal of Physical Chemistry B, Vol. 101, No. 29. (1 July 1997), pp. 5622-5623. by Francisco Figueirido, Gabriela S. Del Buono, Ronald M. Levy posted to molecular_dynamics implicit_solvation by onufriev on 2009-10-30 03:22:38 as
	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 to molecular_dynamics pedagogical by onufriev on 2009-02-18 21:53:43 as along with 8 people saravan yxue adilson_mohr yalexeev baaden aqeel RamuAnandakrishnan LamBras
	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 to molecular_dynamics pedagogical by onufriev on 2009-02-18 21:49:56 as along with 5 people flbarroso apaydin bilab allmensch RamuAnandakrishnan
	MD simulation of crystal growth of NaCl from its supersaturated aqueous solution [My Copy] Journal of Molecular Liquids, Vol. 118, No. 1-3. (15 April 2005), pp. 131-139. by I. Okada, Y. Namiki, H. Uchida, M. Aizawa, K. Itatani posted to molecular_dynamics dna_ions ions by onufriev on 2008-12-20 02:01:40 as
	Toward quantitative simulations of carbon monoxide escape pathways in myoglobin. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 19. (15 May 2008), pp. 6147-6154. by R. Elber, Q. H. Gibson posted to molecular_dynamics myoglobin protein_dynamics by onufriev on 2008-11-18 02:01:48 as
	Similarities between principal components of protein dynamics and random diffusion [My Copy] Physical Review E, Vol. 62, No. 6. (1 December 2000), 8438. by Berk Hess posted to molecular_dynamics protein_dynamics by onufriev on 2008-11-17 01:56:06 as along with 1 person tovrstra
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted to molecular_dynamics protein_dynamics by onufriev on 2008-11-17 01:53:50 as along with 5 people and 1 group anuragsethi klexa tovrstra oteri softsimu Structural Biology Group TorVergata
	Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima. [My Copy] Proteins, Vol. 67, No. 3. (15 May 2007), pp. 569-578. by G. G. Maisuradze, D. M. Leitner posted to molecular_dynamics protein_dynamics by onufriev on 2008-11-17 01:39:36 as along with 2 people scampos Diego_Prada
	Toward the Accurate First-Principles Prediction of Ionization Equilibria in Proteins [My Copy] Biochemistry, Vol. 45, No. 31. (8 August 2006), pp. 9363-9373. by J. Khandogin, C. L. Brooks posted to molecular_dynamics pka by onufriev on 2008-11-08 01:23:26 as
	Computer Simulations of Biomolecular Systems: where do we stand? [My Copy] Proceedings of the NYC Workshop (2008) by van Gunsteren edited by U. H. E. Hansmann posted to molecular_dynamics pedagogical by onufriev on 2008-11-06 18:14:02 as
	Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation [My Copy] J. Phys. Chem. B, Vol. 107, No. 24. (19 June 2003), pp. 5933-5947. by P. Ren, J. W. Ponder posted to molecular_dynamics by onufriev on 2008-11-02 01:58:33 as along with 1 person samjlord
	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 to coarse-grain molecular_dynamics by onufriev on 2008-11-02 01:55:43 as along with 1 person kaz229
	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
	The pH-Dependent Conformational States of Kyotorphin: A Constant-pH Molecular Dynamics Study [My Copy] Biophys. J., Vol. 92, No. 6. (15 March 2007), pp. 1836-1845. by Miguel Machuqueiro, Antonio M. Baptista posted to molecular_dynamics pka by onufriev on 2008-11-01 01:20:18 as
	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 to electrostatics molecular_dynamics by onufriev on 2008-09-14 20:54:08 as along with 8 people Scis0000002 babakap lillekatt ttjoseph dgront RamuAnandakrishnan AndreaColetta r2s2
	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 to implicit_solvation molecular_dynamics pb by onufriev on 2008-09-03 23:04:40 as along with 1 person RamuAnandakrishnan
	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
	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
	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 to implicit_solvation molecular_dynamics by onufriev on 2008-08-13 02:04:41 as along with 7 people and 2 groups RamuAnandakrishnan mikaellund oteri nickolay flbarroso choonpeng sobolevnrm Structural Biology Group TorVergata baker-group
	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
	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
	Electrostatics and dynamics of proteins [My Copy] 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 3 people Lombardo_7 chiufanlee medic0747
	Coarse-grained force field for the nucleosome from self-consistent multiscaling [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy Smith posted to molecular_dynamics multiscale nucleosome by onufriev on 2008-06-16 23:43:03 as along with 3 people barmak7282 Elena_Zubova RamuAnandakrishnan
	Molecular Dynamics Basics [My Copy] posted to molecular_dynamics pedagogical by onufriev on 2008-05-16 20:55:43 as
	Local electrostatics algorithm for classical molecular dynamics simulations [My Copy] posted to implicit_solvation molecular_dynamics by onufriev on 2008-03-09 03:13:49 as
	Effective energy function for proteins in solution [My Copy] Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 133-152. by Themis Lazaridis, Martin Karplus posted to implicit_solvation molecular_dynamics by onufriev on 2008-03-09 02:26:18 as along with 1 person edws
	Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1113-1130. 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 5 people and 1 group ras Elena_Zubova sobolevnrm RamuAnandakrishnan dimka 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 to implicit_solvation molecular_dynamics pb by onufriev on 2008-03-08 22:00:22 as along with 1 person and 1 group sobolevnrm baker-group
	Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 39. (25 September 2007), pp. 15230-15235. by I. Daidone, M. B. Ulmschneider, A. Di Nola, A. Amadei, J. C. Smith posted to explicit_solvation implicit_solvation molecular_dynamics by onufriev on 2007-12-28 02:03:54 as along with 3 people jjurban barmak7282 choonpeng
	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 to molecular_dynamics water_models by onufriev on 2007-12-28 01:52:49 as along with 3 people barmak7282 softsimu LamBras
	An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution [My Copy] Journal of Molecular Biology, Vol. 256, No. 5. (15 March 1996), pp. 939-948. by F. Fraternali, W. F. van Gunsteren posted to molecular_dynamics implicit_solvation by onufriev on 2007-12-06 19:52:23 as
	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 to molecular_dynamics by onufriev on 2007-11-08 00:05:51 as along with 1 person RamuAnandakrishnan
	Effect of artificial periodicity in simulations of biomolecules u... [My Copy] posted to molecular_dynamics ewald protein_electrostatics by onufriev on 2007-10-22 22:42:37 as
	A smooth permittivity function for Poisson-Boltzmann solvation methods [My Copy] Journal of Computational Chemistry, Vol. 22, No. 6. (2001), pp. 608-640. by J. Andrew Grant, Barry T. Pickup, Anthony Nicholls posted to molecular_dynamics electrostatics implicit_solvation pb by onufriev on 2007-10-18 17:42:24 as along with 4 people nickolay dmitry_s_yershov stephenbond cen4ik
	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 to molecular_dynamics implicit_solvation by onufriev on 2007-10-02 00:14:08 as along with 3 people r2s2 dsmueller RamuAnandakrishnan

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implicit_solvation	60
gb	49
molecular_dynamics	36
nucleosome	36
pb	25
protein_folding	24
pka	22
electrostatics	20
dna_bending	19
histone_acetylation	19
dna	18
dna_electrostatics	15
higher_order_chromatin	15
protein_ligand	15
nucleosome_stability	13
dna_ions	12
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
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
time_scale	1
water_molecules	1

onufriev's molecular_dynamics [36 articles] Export

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