onufriev's pka [22 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
	Measurement of Nucleobase pKa Values in Model Mononucleotides Shows RNA−RNA Duplexes To Be More Stable than DNA−DNA Duplexes [My Copy] Journal of the American Chemical Society, Vol. 126, No. 9. (1 March 2004), pp. 2862-2869. by P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, J. Chattopadhyaya posted to pka dna by onufriev on 2009-10-11 03:09:39 as
	On the pH dependence of protein stability. [My Copy] Journal of molecular biology, Vol. 231, No. 2. (20 May 1993), pp. 459-474. by A. S. Yang, B. Honig posted to protein_stability pka ph by onufriev on 2009-09-24 14:31:24 as along with 3 people and 1 group scampos flbarroso cat_worth structural_bioinformatics
	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
	On the evaluation and optimization of protein X-ray structures for pKa calculations. [My Copy] Protein science : a publication of the Protein Society, Vol. 12, No. 2. (February 2003), pp. 313-326. by J. E. Nielsen, J. A. McCammon posted to pka by onufriev on 2009-05-12 18:50:22 as along with 3 people charris5 softsimu RamuAnandakrishnan
	Electrostatic calculations of side-chain pKa values in myoglobin and comparison with NMR data for histidines [My Copy] Biochemistry, Vol. 32, No. 31. (1 August 1993), pp. 8045-8056. by Donald Bashford, David A. Case, Claudio Dalvit, Linda Tennant, Peter E. Wright posted to myoglobin pka by onufriev on 2009-04-20 19:57:33 as
	Improving the accuracy of protein pK<SUB><FONT SIZE='-1'>a</FONT></SUB> calculations: Conformational averaging versus the average structure [My Copy] Proteins: Structure, Function, and Genetics, Vol. 33, No. 2. (1998), pp. 145-158. by Herman W. T. van Vlijmen, Michael Schaefer, Martin Karplus posted to pka by onufriev on 2009-02-13 01:51:14 as
	The Determinants of pKas in Proteins† [My Copy] Biochemistry, Vol. 35, No. 24. (1 January 1996), pp. 7819-7833. by Jan Antosiewicz, J. Andrew Mccammon, Michael K. Gilson posted to pka by onufriev on 2009-02-12 01:52:13 as along with 4 people scampos flbarroso dfgreen RamuAnandakrishnan
	Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin [My Copy] Journal of Molecular Biology, Vol. 224, No. 2. (20 March 1992), pp. 473-486. by Donald Bashford, Klaus Gerwert posted to br pka by onufriev on 2009-02-12 01:40:35 as along with 1 person RamuAnandakrishnan
	A novel view of pH titration in biomolecules. [My Copy] Biochemistry, Vol. 40, No. 12. (27 March 2001), pp. 3413-3419. by A. Onufriev, D. A. Case, G. M. Ullmann posted to pka by onufriev on 2009-02-11 23:37:58 as
	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
	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
	Linking folding with aggregation in Alzheimer's beta-amyloid peptides [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 16880-16885. by Jana Khandogin, Charles L. Brooks posted to pka protein_dynamics protein_folding by onufriev on 2008-11-01 02:33:42 as along with 3 people and 1 group scampos Diego_Prada sobolevnrm baker-group
	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
	Benchmarking pKa Prediction Methods for Residues in Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 6. (1 June 2008), pp. 951-966. by Courtney L. Stanton, Kendall N. Houk posted to pka by onufriev on 2008-11-01 01:17:11 as along with 4 people and 1 group scampos flbarroso franklu310 sobolevnrm baker-group
	Determination of electrostatic interaction energies and protonation state populations in enzyme active sites [My Copy] Journal of Molecular Biology, Vol. In Press, Accepted Manuscript by Chresten R. Sondergaard, Lawrence P. Mcintosh, Gianluca Pollastri, Jens E. Nielsen posted to electrostatics pka by onufriev on 2008-10-15 15:28:07 as along with 3 people and 2 groups barry sobolevnrm skoddet structural_bioinformatics baker-group
	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
	Calculations of Electrostatic Interactions and pKas in the Active Site of Escherichia coli Thioredoxin [My Copy] Biochemistry, Vol. 37, No. 28. (14 July 1998), pp. 10298-10306. by V. Dillet, H. J. Dyson, D. Bashford posted to pka by onufriev on 2008-02-13 00:40:41 as
	Variability in the pKa of histidine side-chains correlates with burial within proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 49, No. 1. (2002), pp. 1-6. by Stephen P. Edgcomb, Kenneth P. Murphy posted to pka by onufriev on 2008-02-12 22:31:33 as
	DNA structure at low pH values, in the presence of Mn2+ ions: a Raman study [My Copy] Journal of Raman Spectroscopy, Vol. 36, No. 11. (2005), pp. 1047-1051. by Cristina M. Muntean, Lubomir Dostál, Rolf Misselwitz, Heinz Welfle posted to dna_electrostatics nucleosome_stability pka by onufriev on 2007-11-29 19:24:47 as
	Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin. [My Copy] Journal of molecular biology, Vol. 237, No. 5. (15 April 1994), pp. 602-614. by A. S. Yang, B. Honig posted to free_energy pka protein_electrostatics by onufriev on 2007-11-12 16:16:23 as along with 2 people and 1 group flbarroso cat_worth structural_bioinformatics

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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 pka [22 articles] Export

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