onufriev's protein_ligand [15 articles] Export

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	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 to protein_ligand pka by onufriev on 2009-11-04 23:52:27 as along with 5 people and 2 groups flbarroso rbaron ibuch sobolevnrm RamuAnandakrishnan McCammon baker-group
	Computational Alanine Scanning of Protein-Protein Interfaces [My Copy] Sci. STKE, Vol. 2004, No. 219. (10 February 2004), pl2. by Tanja Kortemme, David E. Kim, David Baker posted to protein_ligand pka by onufriev on 2009-08-26 02:25:09 as along with 8 people and 6 groups chemrahul82 pablocarb bicko barry sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	A simple physical model for binding energy hot spots in proteinâprotein complexes [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121. by Tanja Kortemme, David Baker posted to protein_ligand by onufriev on 2009-08-26 02:22:57 as along with 8 people and 1 group chemrahul82 oceanwind lna jwm bicko cjeans hmk skoddet Nielsen group
	Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies [My Copy] Journal of the American Chemical Society, Vol. 121, No. 36. (1 September 1999), pp. 8133-8143. by Irina Massova, Peter A. Kollman posted to protein_ligand by onufriev on 2009-07-18 07:58:40 as along with 2 people chemrahul82 boris_aguilar
	Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. [My Copy] J Mol Biol, Vol. 330, No. 4. (18 July 2003), pp. 891-913. by H. Gohlke, C. Kiel, D. A. Case posted to protein_ligand by onufriev on 2009-05-21 08:15:07 as along with 2 people bmduggan lillekatt
	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 to protein_ligand by onufriev on 2009-02-04 20:47:08 as along with 15 people and 3 groups mijogiffin flbarroso GermanErlenkamp arlam oteri jmccammon bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata McCammon
	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 to protein_ligand by onufriev on 2009-01-31 23:12:25 as along with 5 people and 3 groups flbarroso jmccammon biehl sobolevnrm barry baker-group structural_bioinformatics McCammon
	Calculation of absolute protein-ligand binding free energy using distributed replica sampling. [My Copy] The Journal of chemical physics, Vol. 129, No. 15. (21 October 2008) by T. Rodinger, P. L. Howell, R. Pomès posted to protein_ligand by onufriev on 2009-01-31 23:05:38 as along with 2 people flbarroso kentsis
	Charge optimization leads to favorable electrostatic binding free energy [My Copy] Physical Review E, Vol. 59, No. 5. (1 May 1999), 5958. by Erik Kangas, Bruce Tidor posted to electrostatics pka protein_ligand by onufriev on 2009-01-23 23:58:35 as along with 1 person boris_aguilar
	Protein Structural Change Upon Ligand Binding: Linear Response Theory [My Copy] Physical Review Letters, Vol. 94, No. 7. (2005) by Mitsunori Ikeguchi, Jiro Ueno, Miwa Sato, Akinori Kidera posted to electrostatics pka protein_ligand by onufriev on 2009-01-23 23:57:13 as along with 3 people boris_aguilar apaydin aqeel
	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
	DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases [My Copy] Journal of Computer-Aided Molecular Design (May 2001), pp. 411-428. by T. J. A. Ewing, S. Makino, A. G. Skillman, I. D. Kuntz posted to protein_ligand by onufriev on 2008-11-02 02:10:12 as
	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
	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 to pka protein_ligand by onufriev on 2008-10-15 15:00:16 as along with 6 people and 3 groups flbarroso csrocha bicko sobolevnrm RamuAnandakrishnan barry baker-group structural_bioinformatics McCammon
	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

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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 protein_ligand [15 articles] Export

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