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sobolevnrm pka [72 articles]

Recent papers added to sobolevnrm library classified by the tag pka. You can also see everyone's pka.
  • An abnormal pKa value of internal histidine of the insulin molecule revealed by neutron crystallographic analysis
    Biochemical and Biophysical Research Communications, Vol. 376, No. 1. (2008), pp. 32-35.
    by Takuya Ishikawa, Toshiyuki Chatake, Yukio Morimoto, Mitsuru Maeda, Kazuo Kurihara, Ichiro Tanaka, Nobuo Niimura
    posted to structure pka by sobolevnrm on 2008-10-03 12:32:35 as read
  • FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins
    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 solvation pka electrostatics by sobolevnrm on 2008-09-17 12:42:50 as read
  • Very fast prediction and rationalization of p$K_a$ values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics (in press)
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to solvation software pka electrostatics bioinformatics by sobolevnrm on 2008-09-03 13:35:31 as read
  • Modeling Charged Protein Side Chains in Lipid Membranes
    Journal of General Physiology, Vol. 130, No. 2. (2007), pp. 237-240.
    by Toby W Allen
    posted to solvation pka biomembranes by sobolevnrm on 2008-09-03 13:35:31 as read
  • Electrostatic Contributions to the Stability of the GCN4 Leucine Zipper Structure
    Journal of Molecular Biology, Vol. 374, No. 1. (2007), pp. 206-19.
    by William M Matousek, Barbara Ciani, Carolyn A Fitch, Bertrand, Richard A Kammerer, Andrei T Alexandrescu
    posted to solvation pka electrostatics by sobolevnrm on 2008-09-02 12:34:10 as read
  • Electrostatics-defying interaction between arginine termini as a thermodynamic driving force in protein-protein interaction
    Proteins: Structure, Function, and Bioinformatics (in press)
    by Deepa Pednekar, Abhijit Tendulkar, Susheel Durani
    posted to protein-proteininteractions pka electrostatics by sobolevnrm on 2008-09-02 12:34:08 as **
  • Charged Protein Side Chain Movement in Lipid Bilayers Explored with Free Energy Simulation
    Vol. Volume 60 (2008), pp. 405-459.
    by Libo Li, Igor Vorobyov, Sudha Dorairaj, Toby W Allen, Scott E Feller
    posted to biomembranes electrostatics pka review solvation by sobolevnrm on 2008-08-28 13:07:44 as read
  • notes Ionization of phospholipids and phospholipid-supported interfacial lateral diffusion of protons in membrane model systems
    Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1031, No. 1. (1990)
    by Tocanne, J Teissie
    posted to biomembranes electrostatics pka by sobolevnrm on 2008-08-23 16:23:22 as read
  • Direct Evidence for Deprotonation of a Lysine Side Chain Buried in the Hydrophobic Core of a Protein
    Journal of the American Chemical Society, Vol. 130, No. 21. (2008)
    by Yuki Takayama, Carlos A Castañeda, Michael Chimenti, Bertrand García-Moreno, Junji Iwahara
    posted to electrostatics pka solvation by sobolevnrm on 2008-08-21 12:18:41 as read
  • Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
    Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (2008)
    by Haipeng Gong, Glen Hocky, Karl F Freed
    posted to electrostatics pka solvation by sobolevnrm on 2008-08-18 12:41:33 as read
  • Prediction of interaction sites from apo 3D structures when the holo conformation is different
    Proteins: Structure, Function, and Bioinformatics, Vol. 72, No. 3. (2008), pp. 980-992.
    by Leonel F Murga, Mary J Ondrechen, Dagmar Ringe
    posted to bioinformatics electrostatics pka structure by sobolevnrm on 2008-08-11 15:19:27 as read
  • Calculation of Solvation Free Energies of Charged Solutes Using Mixed Cluster/Continuum Models
    Journal of Physical Chemistry B (in press)
    by Vyacheslav S Bryantsev, Mamadou S Diallo, William
    posted to multiscale pka solvation by sobolevnrm on 2008-08-03 16:29:40 as read
  • Large-scale modulation of thermodynamic protein folding barriers linked to electrostatics
    Proceedings of the National Academy of Sciences, Vol. 105, No. 25. (2008), pp. 8625-8630.
    by oyvind Halskau, Raul P Jimenez, Beatriz I Molero, Jarl Underhaug, Victor Muñoz, Aurora Martinez, Jose
    posted to electrostatics pka proteinfolding by sobolevnrm on 2008-08-02 17:53:53 as read
  • Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin
    Biophysical Journal, Vol. 95, No. 3. (2008), pp. 1080-1088.
    by Changge Ji, Ye Mei, John ZH Zhang
    posted to electrostatics pka by sobolevnrm on 2008-08-02 17:53:53 as read
  • Potential of Mean Force and pKa Profile Calculation for a Lipid Membrane-Exposed Arginine Side Chain
    Journal of Physical Chemistry B (in press)
    by Libo Li, Igor Vorobyov, Toby W Allen
    posted to biomembranes electrostatics pka solvation by sobolevnrm on 2008-08-02 17:53:53 as read
  • pKa of Residue 66 in Staphylococal nuclease. I. Insights from QM/MM Simulations with Conventional Sampling
    Journal of Physical Chemistry B, Vol. 112, No. 28. (2008), pp. 8387-8397.
    by Nilanjan Ghosh, Qiang Cui
    posted to molecularsimulation pka solvation by sobolevnrm on 2008-08-02 17:53:52 as read
  • Very fast prediction and rationalization of p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values for protein-ligand complexes
    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 on 2008-07-22 11:48:46 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane
    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 on 2008-07-16 16:02:20 as read along with 2 people and 1 group softsimu rok baker-group
  • Membrane Organization and Ionization Behavior of the Minor but Crucial Lipid Ceramide-1-Phosphate
    Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4320-4330.
    by Edgar E Kooijman, Jesus Sot, Montes, Alicia Alonso, Arne Gericke, Ben de Kruijff, Satyendra Kumar, Felix M Goni
    posted to biomembranes pka by sobolevnrm on 2008-07-08 12:07:18 as read along with 1 person and 1 group paulschlesinger baker-group
  • Calculation of the aqueous solvation free energy of the proton
    The Journal of Chemical Physics, Vol. 109, No. 12. (1998), pp. 4852-4863.
    by GJ Tawa, IA Topol, SK Burt, RA Caldwell, AA Rashin
    posted to electrostatics pka solvation by sobolevnrm on 2008-06-30 12:27:13 as read along with 1 group baker-group
  • Improved p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> prediction: Combining empirical and semimicroscopic methods
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Gernot Kieseritzky, EW Knapp
    posted to bioinformatics electrostatics pka solvation by sobolevnrm on 2008-06-27 18:08:01 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Benchmarking pKa Prediction Methods for Residues in Proteins
    J. Chem. Theory Comput., Vol. 4, No. 6. (10 June 2008), pp. 951-966.
    by Courtney L Stanton, Kendall N Houk
    posted to electrostatics pka solvation by sobolevnrm on 2008-06-27 11:54:41 as read along with 1 group baker-group
  • A buried lysine that titrates with a normal pKa : Role of conformational flexibility at the protein-water interface as a determinant of pKa values
    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 on 2008-06-05 11:59:31 as read along with 3 people and 2 groups zfekete skoddet RamuAnandakrishnan baker-group Nielsen group
  • Electrostatic Effects in a Network of Polar and Ionizable Groups in Staphylococcal Nuclease
    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 on 2008-06-03 17:12:13 as read along with 1 group baker-group
  • Mapping Local Protein Electrostatics by EPR of pH-Sensitive Thiol-Specific Nitroxide
    Biochemistry, Vol. 47, No. 20. (20 May 2008), pp. 5626-5637.
    by Maxim A Voinov, Andres Ruuge, Vladimir A Reznikov, Igor A Grigor&#x2019;ev, Alex I Smirnov
    posted to electrostatics pka solvation by sobolevnrm on 2008-05-27 01:52:16 as read along with 1 person and 2 groups skoddet baker-group Nielsen group
  • Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups
    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 on 2008-05-05 11:14:27 as read along with 2 people and 1 group paulschlesinger onufriev baker-group
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins (in press)
    by M Machuqueiro, AM Baptista
    posted to molecular_dynamics pka solvation by sobolevnrm on 2008-04-30 11:14:29 as read along with 1 group baker-group
  • Analysing the pH-dependent properties of proteins using pKa calculations
    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 on 2008-04-24 15:00:23 as read along with 1 group baker-group
  • Recent advances in implicit solvent-based methods for biomolecular simulations
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Jianhan Chen, Brooks, Jana Khandogin
    posted to electrostatics nonpolar pka solvation by sobolevnrm on 2008-04-15 11:47:07 as read along with 2 people and 1 group choonpeng onufriev baker-group
  • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    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 on 2008-04-03 11:57:01 as read along with 4 people and 1 group mijogiffin dmobley sunhwan boris_aguilar baker-group
  • Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel
    PLoS Computational Biology, Vol. 3, No. 2. (2007), e22.
    by DL Bostick, Brooks
    posted to biomembranes ion_channels pka solvation by sobolevnrm on 2008-04-01 12:19:18 as read along with 1 group baker-group
  • On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel.
    Biophys J, Vol. 92, No. 12. (15 June 2007)
    by DL Bostick, CL Brooks
    posted to biomembranes ion_channels pka by sobolevnrm on 2008-04-01 12:16:21 as read along with 1 person and 1 group paulschlesinger baker-group
  • Proton Binding to Proteins: p<i>K</i><sub>a</sub> Calculations with Explicit and Implicit Solvent Models
    J. Am. Chem. Soc., Vol. 126, No. 13. (7 April 2004), pp. 4167-4180.
    by T Simonson, J Carlsson, DA Case
    posted to electrostatics molecular_dynamics pka solvation by sobolevnrm on 2008-03-28 10:50:31 as read along with 3 people and 1 group 6rheology RamuAnandakrishnan dmobley baker-group
  • Electrostatic effects in unfolded staphylococcal nuclease
    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 on 2008-02-26 12:16:44 as read along with 1 group baker-group
  • Does Arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations
    Biophys. J. (16 January 2008), biophysj.107.122945.
    by Jejoong Yoo, Qiang Cui
    posted to biomembranes electrostatics pka solvation by sobolevnrm on 2008-02-25 12:11:49 as read along with 2 people and 1 group paulschlesinger sunhwan baker-group
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Miguel Machuqueiro, António M Baptista
    posted to molecular_dynamics pka by sobolevnrm on 2008-02-25 12:09:47 as read along with 2 people and 1 group sunhwan skoddet baker-group
  • Is Arginine Charged in a Membrane?
    Biophys. J., Vol. 94, No. 2. (15 January 2008), pp. L11-13.
    by Libo Li, Igor Vorobyov, Alexander D Mackerell, Toby W Allen
    posted to biomembranes electrostatics pka solvation by sobolevnrm on 2008-01-31 12:54:26 as read along with 1 group baker-group
  • Residue-Specific pKa Determination of Lysine and Arginine Side Chains by Indirect 15N and 13C NMR Spectroscopy: Application to apo Calmodulin
    J. Am. Chem. Soc., Vol. 129, No. 51. (26 December 2007), pp. 15805-15813.
    by I Andre, S Linse, FAA Mulder
    posted to nmr pka by sobolevnrm on 2008-01-31 12:52:27 as read along with 1 group baker-group
  • UNIT 8.11 Structure-Based pKa Calculations Using Continuum Electrostatics Methods
    Current Protocols in Bioinformatics (2006)
    by CA Fitch, García-Moreno
    posted to electrostatics pka solvation by sobolevnrm on 2008-01-28 14:41:56 as read along with 1 group baker-group
  • Probing electric fields in proteins in solution by NMR spectroscopy
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Mathias AS Hass, Malene R Jensen, Jens J Led
    posted to electrostatics nmr pka solvation by sobolevnrm on 2008-01-27 14:41:30 as read along with 1 group baker-group
  • Optimizing pKa computation in proteins with pH adapted conformations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Gernot Kieseritzky, Ernst-Walter Knapp
    posted to electrostatics pka solvation by sobolevnrm on 2008-01-07 13:00:01 as read along with 3 people and 1 group sim82 RamuAnandakrishnan boris_aguilar baker-group
  • Protein-protein binding is often associated with changes in protonation state
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron C Mason, Jan H Jensen
    posted to electrostatics pka protein-protein_interactions solvation by sobolevnrm on 2007-12-17 12:40:07 as read along with 5 people and 3 groups csrocha bicko chad_davis RamuAnandakrishnan barry baker-group structural_bioinformatics McCammon
  • Linking folding with aggregation in Alzheimer's beta-amyloid peptides
    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 molecular_dynamics pka protein_folding by sobolevnrm on 2007-11-08 13:04:01 as read along with 1 group baker-group
  • Ligand Effects on the Protein Ensemble: Unifying the Descriptions of Ligand Binding, Local Conformational Fluctuations, and Protein Stability
    Methods in Cell Biology, Vol. 84 (2008), pp. 871-91.
    by ST Whitten, Garc\ia BE Moreno, VJ Hilser
    posted to pka solvation by sobolevnrm on 2007-10-30 12:33:51 as read
  • New and Original pKa Prediction Method Using Grid Molecular Interaction Fields
    J. Chem. Inf. Model. (2 October 2007)
    by F Milletti, L Storchi, G Sforna, G Cruciani
    posted to pka solvation drugdesign by sobolevnrm on 2007-10-08 12:24:55 as read along with 1 person and 1 group sim82 baker-group
  • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    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 solvation by sobolevnrm on 2007-10-04 13:17:49 as read along with 2 people and 2 groups barry skoddet structural_bioinformatics baker-group
  • Role of Flexibility and Polarity as Determinants of the Hydration of Internal Cavities and Pockets in Proteins
    Biophys. J., Vol. 93, No. 8. (15 October 2007), pp. 2791-2804.
    by Ana Damjanovic, Jamie L Schlessman, Carolyn A Fitch, Angel E Garcia, Garcia-Moreno
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-23 21:18:26 as read along with 1 group baker-group
  • Electrostatic Contributions to the Stability of the GCN4 Leucine Zipper Structure
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by William M Matousek, Barbara Ciani, Carolyn A Fitch, Bertrand E Garcia-Moreno, Richard A Kammerer, Andrei T Alexandrescu
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-17 01:56:00 as read along with 1 person and 1 group cjeans baker-group
  • Protonation free energy levels in complex molecular systems
    Biopolymers, Vol. 9999, No. 9999. (2007), NA.
    by Jan M Antosiewicz
    posted to electrostatics pka solvation by sobolevnrm on 2007-09-06 13:15:31 as read along with 1 person and 2 groups barry baker-group McCammon
  • Electrostatic Polarization Is Crucial for Reproducing pKa Shifts of Carboxylic Residues in Turkey Ovomucoid Third Domain
    Journal of Physical Chemistry B (in press)
    by CM Macdermaid, GA Kaminski
    posted to electrostatics pka by sobolevnrm on 2007-07-12 13:25:50 as read along with 1 group baker-group
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