Tag pka [at least 200 articles] Export

Recent papers classified by the tag pka.

	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 4 people and 2 groups rbaron ibuch sobolevnrm RamuAnandakrishnan McCammon baker-group
	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 pka by fralium on 2009-10-21 21:51:23 as along with 5 people and 1 group flbarroso 6rheology sobolevnrm RamuAnandakrishnan dmobley baker-group
	Protein kinase C inhibition of cloned inward rectifier (HRK1/KIR2.3) K+ channels expressed in Xenopus oocytes. [My Copy] The Journal of physiology, Vol. 495 ( Pt 3) (15 September 1996), pp. 681-688. by P. Henry, W. L. Pearson, C. G. Nichols posted to pkc pka phosphorylation kir23 kir21 kir11 by dimka on 2009-10-19 03:57:37 as
	Distal recognition sites in substrates are required for efficient phosphorylation by the cAMP-dependent protein kinase. [My Copy] Genetics, Vol. 182, No. 2. (June 2009), pp. 529-539. by Stephen J. Deminoff, Vidhya Ramachandran, Paul K. Herman posted to structure pka kinase by renatomilani on 2009-10-15 14:34:29 as
	Towards a first principles prediction of p<i>K</i><sub>a</sub>: COSMO-RS and the cluster-continuum approach [My Copy] Molecular Physics: An International Journal at the Interface Between Chemistry and Physics (2009) by Frank Eckert, Michael Diedenhofen, Andreas Klamt posted to solvation quantum_chemistry pka by flbarroso on 2009-10-13 20:28:43 as
	pKa Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols [My Copy] The Journal of Physical Chemistry B, Vol. 109, No. 37. (1 September 2005), pp. 17715-17733. by Demian Riccardi, Patricia Schaefer, Qiang Cui posted to pka free_energy by qshao on 2009-10-12 22:48:55 as along with 1 person flbarroso
	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
	The opposing roles of Wnt-5a in cancer [My Copy] British Journal of Cancer, Vol. 101, No. 2. (21 July 2009), pp. 209-214. by S. L. McDonald, A. Silver posted to wnt5a review pka cancer b_catenin by tonamswish on 2009-09-18 18:09:11 as
	Apparent pKa shifts of titratable residues at high denaturant concentration and the impact on protein stability [My Copy] Biophysical Chemistry, Vol. 118, No. 2-3. (01 December 2005), pp. 88-92. by Daniel N. Marti posted to urea titratable stability residues protein pka guanidine denaturant by htn4g on 2009-09-16 14:02:26 as
	Are Acidic and Basic Groups in Buried Proteins Predicted to be Ionized? [My Copy] Journal of Molecular Biology, Vol. 348, No. 5. (20 May 2005), pp. 1283-1298. by Jinrang Kim, Junjun Mao, M. R. Gunner posted to pka electrostatics by flbarroso on 2009-09-13 00:39:32 as along with 1 person nickolay
	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 pka mc electrostatics continnum by flbarroso on 2009-09-12 23:26:15 as along with 3 people and 1 group girayenkavi sobolevnrm RamuAnandakrishnan baker-group
	PKA-induced F-actin rearrangement requires phosphorylation of Hsp27 by the MAPKAP kinase MK5. [My Copy] Cellular signalling, Vol. 21, No. 5. (May 2009), pp. 712-718. by Sergiy Kostenko, Mona Johannessen, Ugo Moens posted to pka phosphorylation mk5 hsp27 cytoskeleton by nns1987 on 2009-09-11 14:07:03 as
	Prediction of pKa Values for Oligo-methacrylic Acids Using Combined Classical and Quantum Approaches [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Haitao Dong, Hongbo Du, Xianghong Qian posted to pka by qshao on 2009-09-10 17:47:07 as
	Computation of Conformational Coupling in Allosteric Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted to protein_mechanics protein_ligand pka by boris_aguilar on 2009-09-09 18:09:27 as along with 6 people and 1 group sobolevnrm klexa oteri bmduggan barry zwang McCammon
	Protein kinase A phosphorylates and regulates dimerization of 14-3-3 epsilon. [My Copy] FEBS letters, Vol. 580, No. 1. (9 January 2006), pp. 305-310. by Young-Mi M. Gu, Yun-Hye H. Jin, Joong-Kook K. Choi, Kwang-Hyun H. Baek, Chang-Yeol Y. Yeo, Kwang-Youl Y. Lee posted to ser58 pka phosphorylation 14-3-3zeta by nns1987 on 2009-09-09 12:23:03 as
	Very fast empirical prediction and rationalization of protein pK<SUB><FONT SIZE='-1'>a</FONT></SUB> values [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 4. (1 December 2005), pp. 704-721. by Hui Li, Andrew D. Robertson, Jan H. Jensen posted to titration pka electrostatics by flbarroso on 2009-09-04 02:44:08 as along with 9 people and 1 group Martin8223 franklu310 RamuAnandakrishnan gisle bicko sim82 barry sunhwan mschofie Bioinformatics
	Predicting pKa [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 9. (28 September 2009), pp. 2013-2033. by Adam C. Lee, Gordon M. Crippen posted to pka by qshao on 2009-08-26 17:54:44 as along with 1 person abhishek_tiwari
	Regulation of the Src homology 2 domain-containing inositol 5'-phosphatase (SHIP1) by the cyclic AMP-dependent protein kinase. [My Copy] The Journal of biological chemistry, Vol. 284, No. 30. (24 July 2009), pp. 20070-20078. by Jun Zhang, Scott F. Walk, Kodi S. Ravichandran, James C. Garrison posted to ship pka by guhjy on 2009-08-26 10:58:14 as
	Computational alanine scanning of protein-protein interfaces. [My Copy] Science's STKE : signal transduction knowledge environment, Vol. 2004, No. 219. (10 February 2004) 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 7 people and 6 groups pablocarb bicko barry sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
	Epik: a software program for pK prediction and protonation state generation for drug-like molecules [My Copy] Journal of Computer-Aided Molecular Design, Vol. 21, No. 12. (1 December 2007), pp. 681-691. by John Shelley, Anuradha Cholleti, Leah Frye, Jeremy Greenwood, Mathew Timlin, Makoto Uchimaya posted to titration pka drug-design by flbarroso on 2009-08-15 00:48:12 as
	H++: a server for estimating pKas and adding missing hydrogens to macromolecules [My Copy] Nucl. Acids Res., Vol. 33, No. suppl_2. (1 July 2005), pp. W368-371. by John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, Alexey Onufriev posted to pka by franklu310 on 2009-08-15 00:40:02 as along with 3 people rodrigofaccioli flbarroso choonpeng
	Prediction and Rationalization of Protein pKa Values Using QM and QM/MM Methods [My Copy] The Journal of Physical Chemistry A, Vol. 109, No. 30. (1 August 2005), pp. 6634-6643. by Jan H. Jensen, Hui Li, Andrew D. Robertson, Pablo A. Molina posted to qmmm pka electrostatics by flbarroso on 2009-08-14 20:15:47 as
	Cyclic-AMP and Pseudosubstrate Effects on Type-I A-Kinase Regulatory and Catalytic Subunit Binding Kinetics† [My Copy] Biochemistry, Vol. 46, No. 32. (1 August 2007), pp. 9283-9291. by Ganesh Anand, Susan S. Taylor, David A. Johnson posted to pka c-amp amp by rok on 2009-08-12 21:52:57 as
	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 pka protein by anuragsethi on 2009-08-04 16:28:25 as along with 4 people and 2 groups sobolevnrm scampos jmccammon flbarroso McCammon baker-group
	Epac and PKA: a tale of two intracellular cAMP receptors. [My Copy] Acta biochimica et biophysica Sinica, Vol. 40, No. 7. (July 2008), pp. 651-662. by Xiaodong Cheng, Zhenyu Ji, Tamara Tsalkova, Fang Mei posted to camp epac pka review by guhjy on 2009-08-02 10:02:38 as
	Regulation of cardiac fibroblast collagen synthesis by adenosine: roles for Epac and PI3K [My Copy] Am J Physiol Cell Physiol, Vol. 296, No. 5. (1 May 2009), pp. C1178-1184. by Francisco Villarreal, Sara A. Epperson, Israel Ramirez-Sanchez, Katrina G. Yamazaki, Laurence L. Brunton posted to adenosine camp collagen epac fbl pi3k pka by guhjy on 2009-08-02 09:56:26 as
	First Principle Theory for pKa Prediction at Molecular Level: pH Effects Based on Explicit Solvent Model [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10509-10514. by Kentaro Kido, Hirofumi Sato, Shigeyoshi Sakaki posted to pka water by qshao on 2009-07-29 21:07:03 as along with 4 people and 2 groups scampos jmccammon franklu310 whitead McCammon Jiang Research Group
	Carboxyl pK(a) values, ion pairs, hydrogen bonding, and the pH-dependence of folding the hyperthermophile proteins Sac7d and Sso7d. [My Copy] Journal of molecular biology, Vol. 372, No. 4. (28 September 2007), pp. 992-1008. by A. T. Clark, K. Smith, R. Muhandiram, S. P. Edmondson, J. W. Shriver posted to folding nmr pka protein titration by flbarroso on 2009-07-29 15:25:06 as
	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 nmr pka by flbarroso on 2009-07-21 19:21:00 as along with 2 people RamuAnandakrishnan sobolevnrm
	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 solubility by flbarroso on 2009-07-21 19:18:52 as along with 1 person sobolevnrm
	Measurement and Modelling of Sequence-specific pKaValues of Lysine Residues in Calbindin D9k [My Copy] Journal of Molecular Biology, Vol. 259, No. 4. (21 June 1996), pp. 828-839. by T. Kesvatera posted to calbindin calcium-binding mc nmr pka titration by flbarroso on 2009-07-21 15:41:16 as
	Glycine betaine may have opposite effects on protein stability at high and low pH values [My Copy] Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1794, No. 6. (June 2009), pp. 929-935. by Laishram R. Singh, Tanveer A. Dar, Safikur Rahman, Shazia Jamal, Faizan Ahmad posted to betaine glycine osmolyte ph pka by qshao on 2009-07-20 23:57:50 as
	Counteracting Osmolyte Trimethylamine N-Oxide Destabilizes Proteins at pH below Its pKa: MEASUREMENTS OF THERMODYNAMIC PARAMETERS OF PROTEINS IN THE PRESENCE AND ABSENCE OF TRIMETHYLAMINE N-OXIDE [My Copy] J. Biol. Chem., Vol. 280, No. 12. (25 March 2005), pp. 11035-11042. by Rajendrakumar Singh, Inamul Haque, Faizan Ahmad posted to osmolyte ph pka tmao by qshao on 2009-07-20 23:56:47 as
	Some Theoretical and Computational Aspects of the Inclusion of Proton Isomerism in the Protonation Equilibrium of Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 1. (1 January 2001), pp. 293-309. by Antonio M. Baptista, Claudio M. Soares posted to electrostatics pb pka titration by flbarroso on 2009-07-19 03:32:26 as
	pH-Dependent Processes in Protein [My Copy] Critical Reviews in Biochemistry and Molecular Biology, Vol. 18, No. 2. (January 1985), pp. 91-197. by James B. Matthew, Frank R. N. Gurd, Bertrand E. Garcia-Moreno, Margaret A. Flanagan, Keith L. March, Steven J. Shire posted to electrostatics ph pka titration by flbarroso on 2009-07-15 05:41:34 as along with 1 person scampos
	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 electrostatics folding myoglobin pka stability titration by flbarroso on 2009-07-15 04:13:31 as along with 2 people and 1 group cat_worth onufriev structural_bioinformatics
	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 by flbarroso on 2009-07-15 04:02:23 as along with 4 people and 1 group scampos franklu310 onufriev sobolevnrm baker-group
	Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches [My Copy] The Journal of Physical Chemistry B, Vol. 101, No. 22. (1 May 1997), pp. 4458-4472. by Yuk Y. Sham, Zhen T. Chu, Arieh Warshel posted to electrostatics pka protein by flbarroso on 2009-07-15 04:01:37 as
	Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres [My Copy] Journal of the American Chemical Society, Vol. 79, No. 20. (1 October 1957), pp. 5333-5339. by Charles Tanford, John G. Kirkwood posted to binding continnum dielectric electrostatics pka protein titration by flbarroso on 2009-07-15 03:44:28 as along with 3 people zenofchem mikaellund dfgreen
	pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model [My Copy] Biochemistry, Vol. 29, No. 44. (1 November 1990), pp. 10219-10225. by Donald Bashford, Martin Karplus posted to continnum electrostatics pb pka by flbarroso on 2009-07-15 03:42:00 as along with 3 people girayenkavi scampos dsmueller
	Electrostatic Interactions in Membranes and Proteins [My Copy] Annual Review of Biophysics and Biophysical Chemistry, Vol. 15, No. 1. (1986), pp. 163-193. by B. H. Honig, W. L. Hubbell, R. F. Flewelling posted to electrostatics membrane pka protein by flbarroso on 2009-07-15 03:34:14 as
	Electrostatic Interactions in Aliphatic Dicarboxylic Acids: A Computational Route to the Determination of pKa Shifts [My Copy] Journal of the American Chemical Society, Vol. 116, No. 18. (1 September 1994), pp. 8238-8240. by E. Rajasekaran, B. Jayaram, B. Honig posted to electrostatics pka by flbarroso on 2009-07-15 03:33:41 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 electrostatics pb pka by flbarroso on 2009-07-15 03:32:37 as along with 4 people scampos onufriev dfgreen RamuAnandakrishnan
	Electrostatic Interactions in Macromolecules: Theory and Applications [My Copy] Annual Review of Biophysics and Biophysical Chemistry, Vol. 19, No. 1. (1990), pp. 301-332. by K. A. Sharp, B. Honig posted to electrostatics pb pka by flbarroso on 2009-07-15 03:31:31 as along with 3 people scampos dfgreen RamuAnandakrishnan
	Improving macromolecular electrostatics calculations [My Copy] Protein Eng., Vol. 12, No. 8. (1 August 1999), pp. 657-662. by J. E. Nielsen, K. V. Andersen, B. Honig, et al.R. W. W. Hooft, G. Klebe, G. Vriend, R. C. Wade posted to electrostatics lysozyme pb pka sod by flbarroso on 2009-07-15 03:30:59 as along with 1 person and 1 group cat_worth structural_bioinformatics
	Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program [My Copy] Computer Physics Communications, Vol. 91, No. 1-3. (02 September 1995), pp. 57-95. by J. Madura posted to continnum electrostatics pb pka by flbarroso on 2009-07-15 00:41:56 as along with 2 people and 2 groups barry sim82 structural_bioinformatics Bioinformatics
	Long-range surface charge-charge interactions in proteins. Comparison of experimental results with calculations from a theoretical method. [My Copy] Journal of molecular biology, Vol. 232, No. 2. (20 July 1993), pp. 574-583. by R. Loewenthal, J. Sancho, T. Reinikainen, A. R. Fersht posted to barnase electrostatics pb pka protein-protein by flbarroso on 2009-07-06 16:41:35 as
	Theoretical Calculation of pKa Reveals an Important Role of Arg205 in the Activity and Stability of Streptomyces sp. N174 Chitosanase [My Copy] J. Biol. Chem. (26 May 2000), M002574200. by Tamo Fukamizo, Andre H. Juffer, Hans H. Vogel, et al.Yuji Honda, Hugo Tremblay, Isabelle Boucher, Witold A. Neugebauer, Ryszard Brzezinski posted to pka by franklu310 on 2009-07-06 09:45:34 as
	Theoretical prediction of pKa values for methacrylic acid oligomers using combined quantum mechanical and continuum solvation methods. [My Copy] The journal of physical chemistry. A, Vol. 112, No. 49. (11 December 2008), pp. 12687-12694. by H. Dong, H. Du, X. Qian posted to pka by franklu310 on 2009-07-02 02:08:04 as

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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
biomembranes	17
review	17
pb	16
docking	14
molecular_dynamics	14
ltp	13
epac	12
nmr	12
camkii	11
bioinformatics	10
compartments	10
pkc	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
catalysis	5
darpp-32	5
enzyme	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
molecular_simulation	4
nonpolar	4
protein-protein_interactions	4
statistical_mechanics	4
synaptic_plasticity	4
thrombin	4
yak1	4
allostery	3
ampar_p	3
benchmark	3
calmodulin	3
camp-pka	3
campssenseur	3
design	3
design-drug	3
dhk	3
dictyostelium	3
drug	3
dynamics	3
gb	3
glast	3
glt-1	3
glutamate_transporters	3
glutamate_uptake	3
gpa2	3
havealook	3
hiv	3
kt	3
mapk	3
mc	3
mcce	3
myoglobin	3
nucleic_acids	3
pi3k	3
propka	3
qmmm	3
tcrmr	3
8-pcpt-2-o-me-camp	2
nitric-oxide	2
protein_dynamics	2
serotonin	2
striatum	2

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