sobolevnrm's pka [119 articles] Export

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	A fast and accurate method for predicting pKa of residues in proteins [My Copy] Protein Engineering, Design and Selection In Protein Engineering, Design and Selection, Vol. 23, No. 1. (1 January 2010), pp. 35-42. by Ri-Bo Huang, Qi-Shi Du, Cheng-Hua Wang, Si-Ming Liao, Kuo-Chen Chou posted to pka bioinformatics by sobolevnrm on 2009-12-12 20:26:28 as along with 2 people anuragsethi carlosjavierna
	Titration_DB: Storage and analysis of NMR-monitored protein pH titration curves [My Copy] Proteins by Damien Farrell, Emanuel S. Miranda, Helen Webb, et al.Nikolaj Georgi, Peter B. Crowley, Lawrence P. McIntosh, Jens E. Nielsen posted to solvation pka electrostatics database by sobolevnrm on 2009-11-09 23:13:46 as
	Predicting pKa [My Copy] J. Chem. Inf. Model., Vol. 49, No. 9. (Sep 2009), pp. 2013-2033. by Adam C. Lee, Gordon M. Crippen posted to solvation pka electrostatics by sobolevnrm on 2009-11-06 12:56:28 as along with 1 person anuragsethi
	Challenges in pKa predictions for proteins: the case of Asp213 in human proteinase 3 [My Copy] The journal of physical chemistry A, Vol. 113, No. 43. (Oct 2009), pp. 11783-92. by Eric Hajjar, Annick Dejaegere, Nathalie Reuter posted to solvation pka electrostatics by sobolevnrm on 2009-10-31 21:32:14 as
	pKa and Solubility of Drugs in Water, Ethanol, and 1-Octanol† [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8941-8947. by Urszula Domańska, Aneta Pobudkowska, Aleksandra Pelczarska, Paweł Gierycz posted to pka solvation by sobolevnrm on 2009-06-30 12:48:35 as along with 1 person flbarroso
	Molecular determinants of the p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values of Asp and Glu residues in staphylococcal nuclease [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Carlos A. Castañeda, Carolyn A. Fitch, Ananya Majumdar, Victor Khangulov, Jamie L. Schlessman, Bertrand E. García-Moreno posted to electrostatics pka solvation by sobolevnrm on 2009-06-18 13:43:56 as along with 2 people flbarroso RamuAnandakrishnan
	The origin of the electrostatic perturbation in acetoacetate decarboxylase [My Copy] Nature, Vol. 459, No. 7245. (21 May 2009), pp. 393-397. by Meng-Chiao Ho, Jean-Francois Menetret, Hiro Tsuruta, Karen N. Allen posted to electrostatics pka solvation structure by sobolevnrm on 2009-05-21 12:08:06 as along with 2 people and 1 group girayenkavi flbarroso baker-group
	Characterization of Large Conformational Changes and Autoproteolysis in the Maturation of a T=4 Virus Capsid [My Copy] J. Virol., Vol. 83, No. 2. (15 January 2009), pp. 1126-1134. by Tsutomu Matsui, Gabriel Lander, John E. Johnson posted to electrostatics pka structure virus by sobolevnrm on 2009-05-19 11:59:50 as along with 1 group baker-group
	The role of lipid composition for insertion and stabilization of amino acids in membranes [My Copy] The Journal of Chemical Physics, Vol. 130, No. 18. (2009), 185101. by Anna C. V. Johansson, Erik Lindahl posted to biomembranes electrostatics pka solvation by sobolevnrm on 2009-05-13 12:10:44 as along with 2 people and 1 group agrossfield paulschlesinger baker-group
	Reproducing Basic pKa Values for Turkey Ovomucoid Third Domain Using a Polarizable Force Field [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Timothy H. Click, George A. Kaminski posted to electrostatics molecular_simulation pka solvation by sobolevnrm on 2009-05-13 12:10:31 as along with 1 group baker-group
	Protein Ionizable Groups: pK Values and Their Contribution to Protein Stability and Solubility [My Copy] Journal of Biological Chemistry, Vol. 284, No. 20. (15 May 2009), pp. 13285-13289. by C. Nick Pace, Gerald R. Grimsley, J. Martin Scholtz posted to electrostatics pka protein_folding review solvation by sobolevnrm on 2009-05-11 12:27:23 as along with 6 people and 3 groups pjkiley scampos klexa nanonan barry paulschlesinger structural_bioinformatics McCammon baker-group
	Unusual Hydrophobic Interactions in Acidic Aqueous Solutions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 20. (21 May 2009), pp. 7291-7297. by Hanning Chen, Jianqing Xu, Gregory A. Voth posted to nonpolar pka solvation by sobolevnrm on 2009-05-01 12:13:47 as along with 1 person and 1 group willard baker-group
	Self-guided Langevin dynamics study of regulatory interactions in NtrC. [My Copy] Proteins (26 March 2009) by Ana Damjanović, Bertrand E E. García-Moreno, Bernard R R. Brooks posted to electrostatics enhanced_sampling pka solvation by sobolevnrm on 2009-04-23 12:30:23 as along with 1 group baker-group
	The Molecular Origin of Like-Charge Arginine−Arginine Pairing in Water [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 27. (9 July 2009), pp. 9041-9045. by Jiří Vondrášek, Philip E. Mason, Jan Heyda, Kim D. Collins, Pavel Jungwirth posted to electrostatics pka solvation by sobolevnrm on 2009-04-15 12:12:24 as along with 2 people and 1 group willard edws baker-group
	The pKa Values of Acidic and Basic Residues Buried at the Same Internal Location in a Protein Are Governed by Different Factors [My Copy] Journal of Molecular Biology, Vol. 389, No. 1. (29 May 2009), pp. 34-47. by Michael J. Harms, Carlos A. Castañeda, Jamie L. Schlessman, et al.Gloria R. Sue, Daniel G. Isom, Brian R. Cannon, García-Moreno posted to electrostatics pka solvation by sobolevnrm on 2009-03-31 12:09:46 as along with 2 people and 1 group girayenkavi paulschlesinger baker-group
	Using Multiconformation Continuum Electrostatics to Compare Chloride Binding Motifs in α-Amylase, Human Serum Albumin, and Omp32 [My Copy] Journal of Molecular Biology, Vol. 387, No. 4. (10 April 2009), pp. 840-856. by Yifan Song, M. R. Gunner posted to electrostatics pka protein-ligand_interactions solvation by sobolevnrm on 2009-03-28 16:17:33 as along with 1 group baker-group
	MCCE2: Improving protein p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> calculations with extensive side chain rotamer sampling [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2231-2247. by Yifan Song, Junjun Mao, M. R. Gunner posted to electrostatics pka software solvation by sobolevnrm on 2009-03-26 11:31:58 as along with 3 people and 1 group girayenkavi flbarroso RamuAnandakrishnan baker-group
	Chapter 9 Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting [My Copy] Methods in enzymology In Computer Methods, Part A, Vol. 454 (2009), pp. 233-258. by Jens E. Nielsen posted to electrostatics pka review solvation by sobolevnrm on 2009-03-25 11:33:14 as along with 4 people and 2 groups scampos anuragsethi jmccammon flbarroso McCammon baker-group
	Microscopic pKa Analysis of Glu286 in Cytochrome c Oxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model† [My Copy] Biochemistry, Vol. 48, No. 11. (24 March 2009), pp. 2468-2485. by Nilanjan Ghosh, Xavier Prat-Resina, M. R. Gunner, Qiang Cui posted to electrostatics pka quantum_mechanics solvation by sobolevnrm on 2009-03-24 12:24:54 as along with 1 person and 1 group xavierprat baker-group
	Differences in lysine pKa values may be used to improve NMR signal dispersion in reductively methylated proteins [My Copy] Journal of Biomolecular NMR by Sherwin Abraham, Tomoyoshi Kobayashi, John, Vadim Gaponenko posted to electrostatics nmr pka solvation by sobolevnrm on 2009-03-23 11:51:41 as along with 1 group baker-group
	pH-Responsive DNA-Binding Activity of Helicobacter pylori NikR† [My Copy] Biochemistry, Vol. 48, No. 11. (24 March 2009), pp. 2486-2496. by Yanjie Li, Deborah B. Zamble posted to metalloregulation nikr pka protein-nucleic_acid_interactions by sobolevnrm on 2009-03-19 12:08:30 as along with 1 group baker-group
	Predicting protein p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> by environment similarity [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Francesca Milletti, Loriano Storchi, Gabriele Cruciani posted to bioinformatics pka structure by sobolevnrm on 2009-03-16 11:57:03 as along with 1 person and 1 group boris_aguilar baker-group
	Molecular simulation with variable protonation states at constant pH [My Copy] The Journal of Chemical Physics, Vol. 126, No. 16. (2007), 164112. by Harry A. Stern posted to electrostatics molecular_simulation pka solvation by sobolevnrm on 2009-03-16 11:52:57 as along with 1 group baker-group
	Spin-Labeled pH-Sensitive Phospholipids for Interfacial pKa Determination: Synthesis and Characterization in Aqueous and Micellar Solutions [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Maxim A. Voinov, Igor A. Kirilyuk, Alex I. Smirnov posted to biomembranes electrostatics pka solvation by sobolevnrm on 2009-03-05 12:34:36 as along with 1 group baker-group
	A conserved protonation-dependent switch controls drug binding in the Abl kinase [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 1. (6 January 2009), pp. 139-144. by Yibing Shan, Markus A. Seeliger, Michael P. Eastwood, et al.Filipp Frank, Huafeng Xu, Morten Jensen, Ron O. Dror, John Kuriyan, David E. Shaw posted to pka protein-ligand_interactions by sobolevnrm on 2009-03-05 12:33:56 as along with 2 people and 1 group nanonan sschurer baker-group
	Are Carboxyl Groups the Most Acidic Sites in Amino Acids? Gas-Phase Acidities, Photoelectron Spectra, and Computations on Tyrosine, p-Hydroxybenzoic Acid, and Their Conjugate Bases [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Zhixin Tian, Xue-Bin Wang, Lai-Sheng Wang, Steven R. Kass posted to electrostatics pka solvation by sobolevnrm on 2009-03-04 13:11:18 as along with 1 person and 1 group bmlamb baker-group
	Titratable Amino Acid Solvation in Lipid Membranes as a Function of Protonation State [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Anna C. Johansson, Erik Lindahl posted to biomembranes electrostatics ligand-membrane_interactions pka solvation by sobolevnrm on 2009-03-03 15:35:34 as along with 1 group baker-group
	Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 4. (1 July 2007), pp. 1590-1598. by Paul Czodrowski, Christoph A. Sotriffer, Gerhard Klebe posted to electrostatics pka solvation by sobolevnrm on 2009-02-28 21:49:54 as along with 1 person and 1 group Aginella baker-group
	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 electrostatics pka protein-ligand_interactions solvation by sobolevnrm on 2009-02-25 13:04:48 as along with 5 people and 2 groups flbarroso onufriev rbaron ibuch RamuAnandakrishnan McCammon baker-group
	High tolerance for ionizable residues in the hydrophobic interior of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 46. (18 November 2008), pp. 17784-17788. by Daniel G. Isom, Brian R. Cannon, Carlos A. Castañeda, Aaron Robinson, García-Moreno posted to electrostatics pka solvation by sobolevnrm on 2009-02-24 12:26:09 as along with 1 person and 1 group paulschlesinger baker-group
	Chapter 5 Analyzing Protein NMR pH-Titration Curves [My Copy] Annual Reports in Computational Chemistry, Vol. 4 (2008), pp. 89-106. by J. Nielsen posted to electrostatics nmr pka review solvation by sobolevnrm on 2009-02-18 12:33:25 as along with 1 group baker-group
	The natural mutation by deletion of Lys9 in the thrombin A-chain affects the p<i>K</i><sub>a</sub> value of catalytic residues, the overall enzyme's stability and conformational transitions linked to Na<sup>+</sup> binding [My Copy] FEBS Journal, Vol. 273, No. 1. (2006), pp. 159-169. by Raimondo Cristofaro, Andrea Carotti, Sepideh Akhavan, et al.Roberta Palla, Flora Peyvandi, Cosimo Altomare, Pier M. Mannucci posted to allostery pka thrombin by sobolevnrm on 2009-02-18 12:29:31 as along with 1 group baker-group
	Prediction of pK<SUB><FONT SIZE='-1'>a</FONT></SUB> shifts in proteins using a combination of molecular mechanical and continuum solvent calculations [My Copy] Journal of Computational Chemistry, Vol. 25, No. 15. (2004), pp. 1865-1872. by Bernd Kuhn, Peter A. Kollman, Martin Stahl posted to electrostatics molecular_dynamics pka solvation by sobolevnrm on 2009-02-05 12:47:20 as along with 3 people and 1 group flbarroso dfgreen sim82 baker-group
	Multiple Protonation Equilibria in Electrostatics of Protein−Protein Binding [My Copy] J. Phys. Chem. B (25 October 2008) by Zofia Piłat, Jan M. Antosiewicz posted to electrostatics pka protein-protein_interactions solvation by sobolevnrm on 2009-02-03 12:41:59 as along with 2 people and 1 group mikaellund paulschlesinger baker-group
	Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study [My Copy] Biophys. J. (18 July 2008), biophysj.108.130906. by Ana Damjanovic, Xiongwu Wu, Bertrand Garcia-Moreno, Bernard R. Brooks posted to pka protein_folding solvation by sobolevnrm on 2009-01-26 12:49:24 as along with 2 people and 2 groups jmccammon paulschlesinger baker-group McCammon
	Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 10. (27 October 2008), pp. 2021-2029. by Ana Damjanović, Benjamin T. Miller, Torre J. Wenaus, Petar Maksimović, García-Moreno, Bernard R. Brooks posted to molecular_dynamics pka programming software solvation by sobolevnrm on 2008-12-28 15:34:46 as along with 1 group baker-group
	Direct Evidence for Deprotonation of a Lysine Side Chain Buried in the Hydrophobic Core of a Protein [My Copy] Journal of the American Chemical Society, Vol. 130, No. 21. (2008), 6714-6715. by Yuki au Takayama posted to electrostatics pka solvation by sobolevnrm on 2008-12-22 13:40:55 as
	Progress in Ab Initio QM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies‚Ä† [My Copy] The Journal of Physical Chemistry B by Shina C. Kamerlin, Maciej Haranczyk, Arieh Warshel posted to electrostatics pka solvation quantum_mechanics by sobolevnrm on 2008-12-15 12:52:13 as
	Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures [My Copy] Proteins: Structure, Function, and Bioinformatics by Paul Labute posted to pdb2pqr pka software solvation by sobolevnrm on 2008-12-15 12:52:12 as
	Prediction of Protein Solubility from Calculation of Transfer Free Energy [My Copy] Biophysical Journal, Vol. 95, No. 6. (2008), 2601-2609. by Harianto Tjong, Huan-Xiang Zhou posted to electrostatics pka solvation molecular_simulation by sobolevnrm on 2008-12-15 12:52:11 as
	Optimizing pKa computation in proteins with pH adapted conformations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 3. (2008), 1335 - 1348. by Gernot Kieseritzky, Ernst-Walter Knapp posted to electrostatics pka solvation by sobolevnrm on 2008-12-15 12:52:07 as
	Benchmarking pKa Prediction Methods for Residues in Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 6. (2008), 951--966. by Courtney L. Stanton, Kendall N. Houk posted to electrostatics pka solvation by sobolevnrm on 2008-12-15 12:52:06 as
	Improved p$K_a$ prediction: Combining empirical and semimicroscopic methods [My Copy] Journal of Computational Chemistry, Vol. 29, No. 15. (2008), 2575 - 2581. by Gernot Kieseritzky, E. W. Knapp posted to bioinformatics electrostatics pka solvation by sobolevnrm on 2008-12-15 12:52:06 as
	Membrane Organization and Ionization Behavior of the Minor but Crucial Lipid Ceramide-1-Phosphate [My Copy] Biophysical Journal, Vol. 94, No. 11. (2008), 4320--4330. by Edgar E. Kooijman, Jesus Sot, Montes, et al.Alicia Alonso, Arne Gericke, Ben de Kruijff, Satyendra Kumar, Felix M. Goni posted to biomembranes pka by sobolevnrm on 2008-12-15 12:52:06 as
	Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane [My Copy] Biophys. J., Vol. 82, No. 1. (2002), 76--92. by Christian Fleck, Roland R. Netz, Hans H. von Grunberg posted to biomembranes electrostatics pka solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:06 as
	Forces Between Protein Molecules in Solution Arising from Fluctuations in Proton Charge and Configuration [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 38, No. 10. (1952), pp. 863-871. by John G. Kirkwood, John B. Shumaker posted to electrostatics pka solvation beyond_mean_field by sobolevnrm on 2008-10-20 13:10:42 as
	The Influence of Dipole Moment Fluctuations on the Dielectric Increment of Proteins in Solution [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 38, No. 10. (1952), pp. 855-862. by John G. Kirkwood, John B. Shumaker posted to electrostatics pka solvation by sobolevnrm on 2008-10-20 13:10:42 as
	An abnormal pKa value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis [My Copy] Biochemical and Biophysical Research Communications, Vol. 376, No. 1. (2008), pp. 32-35. by Takuya Ishikawa, Toshiyuki Chatake, Yukio Morimoto, et al.Mitsuru Maeda, Kazuo Kurihara, Ichiro Tanaka, Nobuo Niimura posted to pka structure by sobolevnrm on 2008-10-03 12:32:35 as
	FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins [My Copy] Journal of Physical Chemistry B, Vol. 112, No. 35. (2008), pp. 11122-11136. by Yury N. Vorobjev, Jorge A. Vila, Harold A. Scheraga posted to electrostatics pka solvation by sobolevnrm on 2008-09-17 12:42:50 as
	Very fast prediction and rationalization of p$K_a$ values for protein-ligand complexes [My Copy] Proteins: Structure, Function, and Bioinformatics (in press) by Delphine C. Bas, David M. Rogers, Jan H. Jensen posted to bioinformatics electrostatics pka software solvation by sobolevnrm on 2008-09-03 13:35:31 as

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electrostatics	2020
solvation	1604
biomembranes	1512
statistical_mechanics	674
mathematics	623
bioinformatics	614
diffusion	528
molecular_dynamics	514
molecular_simulation	512
nucleic_acids	479
multiscale	409
quasiharmonic_models	338
structure	327
nanotech	286
allostery	269
review	210
beyond_mean_field	210
protein_folding	203
protein-protein_interactions	187
systems_biology	186
software	178
kinetics	170
protein-ligand_interactions	167
acetylcholinesterase	167
misc	151
biological_systems	150
experimental_methodology	147
thrombin	143
correlated_mutations	126
neuromuscular_junctions	121
pka	119
protein-nucleic_acid_interactions	116
sterols	113
drug_design	111
outer_hair_cells	104
database	97
metalloregulation	96
structure_prediction	91
cellular_mechanics	91
ontology	87
imaging	86
ccne	84
protein-membrane_interactions	83
quantum_mechanics	83
nonpolar	80
nerve_agents	78
nitric_oxide	74
career	71
visualization	69
emulsions	67
interfaces	57
ligand-membrane_interactions	57
nmr	52
cancer	51
protein_engineering	48
mechanics	44
free_energy	44
integral_equation	41
clustering	41
teaching	39
ion_channels	38
enhanced_sampling	37
ultrasound	33
perfluorocarbons	31
statistics	27
graph_theory	24
sccne	24
programming	23
informatics	22
helicase	22
pgdh	21
flexoelectric	20
ribosome	17
fluid_mechanics	17
molecular-simulation	15
quasiharmonic-models	15
drug_delivery	15
geometry	14
gating	13
toxicity	13
nanotechnology	13
statistical-mechanics	12
apbs	11
energy_landscapes	10
funding	10
pdb2pqr	9
molecular-dynamics	8
cytoskeleton	8
nikr	8
cholesterol	6
electrochemistry	6
protein-protein-interactions	5
protein-ligand-interactions	5
finite_element	5
protein-folding	4
single_molecule	4
nitric-oxide	4
docking	4
finite_differences	3
scattering	3
nucleic-acids	3
optimization	3
ligand-membrane-interactions	3
hydrodynamics	3
thermodynamics	3
integral-equation	3
quantum-mechanics	2
ethics	2
neuroscience	2
conformation	2
boundary_element	2
generalized_born	2
oxysterols	2
biodistribution	2
virus	2
salicylate	2
systems-biology	2
nanoparticles	2
computational_geometry	2
magnetism	2
protein-membrane-interactions	2
web	1
redox_potentials	1
protein-engineering	1
lipids	1
data_mining	1
protein-design	1
integral_equations	1
colloid-complex	1
red_blood_cell	1
hydrogen_bonds	1
mice	1
protein	1
systems	1
phosphatidylcholines	1
protein-allostery	1
text-mining	1
mutual-information	1
protein-nucleic-acid-interactions	1
text_mining	1
cheminformatics	1
melittin	1
fluorescence_quenching	1

sobolevnrm's pka [119 articles] Export

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