Group: baker-group - with tag pka [82 articles] Export

Recent papers posted by members of the baker-group group with tag pka

	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 to the group baker-group on 2009-05-21 12:08:07 as along with 2 people girayenkavi flbarroso
	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 to the group baker-group on 2009-05-19 11:59:51 as
	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 to the group baker-group on 2009-05-13 12:10:45 as along with 2 people agrossfield paulschlesinger
	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 to the group baker-group on 2009-05-13 12:10:31 as
	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 to the group baker-group on 2009-05-11 12:27:23 as along with 6 people and 2 groups pjkiley scampos klexa nanonan barry paulschlesinger structural_bioinformatics McCammon
	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 to the group baker-group on 2009-05-01 12:13:47 as along with 1 person willard
	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 to the group baker-group on 2009-04-23 12:30:23 as
	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 to the group baker-group on 2009-04-15 12:12:25 as along with 2 people willard edws
	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 to the group baker-group on 2009-03-31 12:09:46 as along with 2 people girayenkavi paulschlesinger
	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 to the group baker-group on 2009-03-28 16:17:33 as
	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 to the group baker-group on 2009-03-26 11:31:58 as along with 3 people girayenkavi flbarroso RamuAnandakrishnan
	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 to the group baker-group on 2009-03-25 11:33:14 as along with 4 people and 1 group scampos anuragsethi jmccammon flbarroso McCammon
	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 to the group baker-group on 2009-03-24 12:24:54 as along with 1 person xavierprat
	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 to the group baker-group on 2009-03-23 11:51:42 as
	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 to the group baker-group on 2009-03-19 12:08:30 as
	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 to the group baker-group on 2009-03-16 11:57:03 as along with 1 person boris_aguilar
	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 to the group baker-group on 2009-03-16 11:52:57 as
	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 to the group baker-group on 2009-03-05 12:34:37 as
	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 to the group baker-group on 2009-03-05 12:33:56 as along with 2 people nanonan sschurer
	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 to the group baker-group on 2009-03-04 13:11:18 as along with 1 person bmlamb
	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 to the group baker-group on 2009-03-03 15:35:34 as
	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 to the group baker-group on 2009-02-28 21:49:54 as along with 1 person Aginella
	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 to the group baker-group on 2009-02-25 13:04:48 as along with 5 people and 1 group flbarroso onufriev rbaron ibuch RamuAnandakrishnan McCammon
	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 to the group baker-group on 2009-02-24 12:26:09 as along with 1 person paulschlesinger
	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 to the group baker-group on 2009-02-18 12:33:25 as
	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 to the group baker-group on 2009-02-18 12:29:31 as
	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 to the group baker-group on 2009-02-05 12:47:20 as along with 3 people flbarroso dfgreen sim82
	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 to the group baker-group on 2009-02-03 12:41:59 as along with 2 people mikaellund paulschlesinger
	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 to the group baker-group on 2009-01-26 12:49:25 as along with 2 people and 1 group jmccammon paulschlesinger 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 to the group baker-group on 2008-12-28 15:34:46 as
	Very fast prediction and rationalization of p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values for protein-ligand complexes [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Delphine C. Bas, David M. Rogers, Jan H. Jensen posted to bioinformatics electrostatics pka software solvation by sobolevnrm to the group baker-group on 2008-07-22 11:48:46 as along with 2 people onufriev RamuAnandakrishnan
	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. (1 January 2002), pp. 76-92. by Christian Fleck, Roland R. Netz, Hans H. von Grunberg posted to biomembranes electrostatics nucleic_acids pka solvation by sobolevnrm to the group baker-group on 2008-07-16 16:02:21 as along with 2 people softsimu rok
	Membrane Organization and Ionization Behavior of the Minor but Crucial Lipid Ceramide-1-Phosphate [My Copy] Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 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 to the group baker-group on 2008-07-08 12:07:18 as along with 2 people jakeashcraft paulschlesinger
	Calculation of the aqueous solvation free energy of the proton [My Copy] The Journal of Chemical Physics, Vol. 109, No. 12. (1998), pp. 4852-4863. by G. J. Tawa, I. A. Topol, S. K. Burt, R. A. Caldwell, A. A. Rashin posted to electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-06-30 12:27:13 as
	Improved p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> prediction: Combining empirical and semimicroscopic methods [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Gernot Kieseritzky, E. W. Knapp posted to bioinformatics electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-06-27 18:08:01 as along with 1 person RamuAnandakrishnan
	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 electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-06-27 11:54:41 as along with 4 people scampos flbarroso franklu310 onufriev
	A buried lysine that titrates with a normal pKa : Role of conformational flexibility at the protein-water interface as a determinant of pKa values [My Copy] Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 833-845. by Michael J. Harms, Jamie L. Schlessman, Michael S. Chimenti, Gloria R. Sue, Ana Damjanovic, Garcia-Moreno posted to electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-06-05 11:59:31 as along with 3 people and 1 group zfekete skoddet RamuAnandakrishnan Nielsen group
	Electrostatic Effects in a Network of Polar and Ionizable Groups in Staphylococcal Nuclease [My Copy] Journal of Molecular Biology, Vol. 379, No. 5. (20 June 2008), pp. 1045-1062. by Kelli L. Baran, Michael S. Chimenti, Jamie L. Schlessman, Carolyn A. Fitch, Katie J. Herbst, Bertrand E. Garcia-Moreno posted to electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-06-03 17:12:13 as
	Mapping Local Protein Electrostatics by EPR of pH-Sensitive Thiol-Specific Nitroxide [My Copy] Biochemistry, Vol. 47, No. 20. (20 May 2008), pp. 5626-5637. by Maxim A. Voinov, Andres Ruuge, Vladimir A. Reznikov, Igor A. Grigor’ev, Alex I. Smirnov posted to electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-05-27 01:52:16 as along with 1 person and 1 group skoddet Nielsen group
	Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups [My Copy] Biophys. J. (4 January 2008), biophysj.107.122473. by Jamie L. Schlessman, Colby Abe, Apostolos Gittis, Daniel A. Karp, Michael A. Dolan, Bertrand Garcia-Moreno posted to pka solvation by sobolevnrm to the group baker-group on 2008-05-05 11:14:27 as along with 2 people paulschlesinger onufriev
	Acidic range titration of HEWL using a constant-pH molecular dynamics method [My Copy] Proteins (in press) by M. Machuqueiro, A. M. Baptista posted to molecular_dynamics pka solvation by sobolevnrm to the group baker-group on 2008-04-30 11:14:29 as
	Analysing the pH-dependent properties of proteins using pKa calculations [My Copy] Journal of Molecular Graphics and Modelling, Vol. 25, No. 5. (January 2007), pp. 691-699. by Jens E. Nielsen posted to electrostatics pka software solvation by sobolevnrm to the group baker-group on 2008-04-24 15:00:23 as along with 1 person and 1 group skoddet Nielsen group
	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 electrostatics nonpolar pka solvation by sobolevnrm to the group baker-group on 2008-04-15 11:47:07 as along with 8 people and 1 group krapnik RamuAnandakrishnan mikaellund oteri nickolay flbarroso choonpeng onufriev Structural Biology Group TorVergata
	Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors [My Copy] Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 673-685. by Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig posted to electrostatics pka protein-ligand_interactions solvation by sobolevnrm to the group baker-group on 2008-04-03 11:57:02 as along with 4 people mijogiffin dmobley sunhwan boris_aguilar
	Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel [My Copy] PLoS Computational Biology, Vol. 3, No. 2. (2007), e22. by D. L. Bostick, Brooks posted to biomembranes ion_channels pka solvation by sobolevnrm to the group baker-group on 2008-04-01 12:19:18 as
	On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. [My Copy] Biophys J, Vol. 92, No. 12. (15 June 2007) by D. L. Bostick, C. L. Brooks posted to biomembranes ion_channels pka by sobolevnrm to the group baker-group on 2008-04-01 12:16:21 as along with 1 person paulschlesinger
	Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models [My Copy] Journal of the American Chemical Society, Vol. 126, No. 13. (1 April 2004), pp. 4167-4180. by Thomas Simonson, Jens Carlsson, David A. Case posted to electrostatics molecular_dynamics pka solvation by sobolevnrm to the group baker-group on 2008-03-28 10:50:31 as along with 5 people fralium flbarroso 6rheology RamuAnandakrishnan dmobley
	Electrostatic effects in unfolded staphylococcal nuclease [My Copy] Protein Sci, Vol. 17, No. 2. (1 February 2008), pp. 216-227. by Nicholas C. Fitzkee, Garcia-Moreno posted to electrostatics pka protein_folding solvation by sobolevnrm to the group baker-group on 2008-02-26 12:16:44 as
	Does Arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations [My Copy] Biophys. J. (16 January 2008), biophysj.107.122945. by Jejoong Yoo, Qiang Cui posted to biomembranes electrostatics pka solvation by sobolevnrm to the group baker-group on 2008-02-25 12:11:49 as along with 2 people paulschlesinger sunhwan
	Acidic range titration of HEWL using a constant-pH molecular dynamics method [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 72, No. 1. (2008), pp. 289-298. by Miguel Machuqueiro, António M. Baptista posted to molecular_dynamics pka by sobolevnrm to the group baker-group on 2008-02-25 12:09:47 as along with 4 people flbarroso scampos sunhwan skoddet

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electrostatics	181
solvation	102
drug_design	40
protein_ligand	40
camp	28
protein	26
structure	21
ligand	19
ca1	18
camp-sensor	18
camp-signaling	18
review	18
biomembranes	17
pb	16
pkc	15
docking	14
molecular_dynamics	14
epac	13
ltp	13
nmr	12
camkii	11
bioinformatics	10
compartments	10
protein_folding	10
titration	10
continnum	9
ph	9
akap	8
neurons	8
phosphorylation	8
protein-ligand_interactions	8
q-paper	8
second-messenger	8
software	8
k	7
prediction	7
histidine	6
microdomain	6
protein-protein	6
ras	6
1	5
agc	5
catalysis	5
darpp-32	5
enzyme	5
mc	5
pi3k	5
tautomerism	5
adenosine	4
adenylyl-cyclase	4
apoptosis	4
development	4
diffusion-barrier	4
dna	4
dopamine	4
erk	4
folding	4
free_energy	4
fret-analysis	4
glutamate	4
hippocampus	4
implicit_solvent	4
kinase	4
molecular_simulation	4
mtor	4
nonpolar	4
pkg	4
protein-protein_interactions	4
statistical_mechanics	4
synaptic_plasticity	4
thrombin	4
yak1	4
akt	3
allostery	3
ampar_p	3
calmodulin	3
camp-pka	3
campssenseur	3
collagen	3
design	3
design-drug	3
dhk	3
drug	3
dynamics	3
glast	3
glutamate_transporters	3
gpa2	3
havealook	3
hg	3
hiv	3
kt	3
mapk	3
mcce	3
myoglobin	3
nucleic_acids	3
propka	3
qmmm	3
rsk	3
src	3
tcrmr	3

Group: baker-group - with tag pka [82 articles] Export

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