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Group: baker-group - with tag pka [52 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag pka
  • 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 to the group baker-group on 2008-07-22 11:48:46 as read along with 1 person RamuAnandakrishnan
  • 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 to the group baker-group on 2008-07-16 16:02:21 as read along with 2 people softsimu rok
  • 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 to the group baker-group on 2008-07-08 12:07:18 as read along with 1 person paulschlesinger
  • 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 to the group baker-group on 2008-06-30 12:27:13 as read
  • 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 to the group baker-group on 2008-06-27 18:08:01 as read along with 1 person RamuAnandakrishnan
  • 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 to the group baker-group on 2008-06-27 11:54:41 as read along with 1 person 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
    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 read 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
    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 read
  • 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 to the group baker-group on 2008-05-27 01:52:16 as read 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
    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 read along with 2 people paulschlesinger onufriev
  • 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 to the group baker-group on 2008-04-30 11:14:29 as read
  • 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 to the group baker-group on 2008-04-24 15:00:23 as read
  • 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 to the group baker-group on 2008-04-15 11:47:07 as read along with 2 people choonpeng onufriev
  • 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 to the group baker-group on 2008-04-03 11:57:02 as read along with 4 people mijogiffin dmobley sunhwan boris_aguilar
  • 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 to the group baker-group on 2008-04-01 12:19:18 as read
  • 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 to the group baker-group on 2008-04-01 12:16:21 as read along with 1 person paulschlesinger
  • 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 to the group baker-group on 2008-03-28 10:50:31 as read along with 3 people 6rheology RamuAnandakrishnan dmobley
  • 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 to the group baker-group on 2008-02-26 12:16:44 as read
  • 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 to the group baker-group on 2008-02-25 12:11:49 as read along with 2 people paulschlesinger sunhwan
  • 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 to the group baker-group on 2008-02-25 12:09:47 as read along with 2 people sunhwan skoddet
  • 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 to the group baker-group on 2008-01-31 12:54:26 as read
  • 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 to the group baker-group on 2008-01-31 12:52:28 as read
  • 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 to the group baker-group on 2008-01-28 14:41:56 as read
  • 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 to the group baker-group on 2008-01-27 14:41:30 as read
  • Optimizing pK<SUB><FONT SIZE='-1'>A</FONT></SUB> 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 to the group baker-group on 2008-01-07 13:00:01 as read along with 3 people sim82 RamuAnandakrishnan boris_aguilar
  • 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 to the group baker-group on 2007-12-17 12:40:08 as read along with 5 people and 2 groups onufriev csrocha bicko RamuAnandakrishnan barry 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 to the group baker-group on 2007-11-08 13:04:01 as read along with 1 person onufriev
  • 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 drug_design pka solvation by sobolevnrm to the group baker-group on 2007-10-08 12:24:55 as read along with 1 person sim82
  • 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 to the group baker-group on 2007-10-04 13:17:49 as read along with 3 people and 1 group onufriev barry skoddet structural_bioinformatics
  • 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 to the group baker-group on 2007-09-23 21:18:26 as read
  • 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 solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-09-17 01:56:00 as read along with 1 person cjeans
  • Protonation free energy levels in complex molecular systems
    Biopolymers, Vol. 9999, No. 9999. (2007), NA.
    by Jan M Antosiewicz
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-09-06 13:15:31 as read along with 1 person and 1 group barry 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 pka electrostatics by sobolevnrm to the group baker-group on 2007-07-12 13:25:50 as read
  • A statistical approach to the prediction of pKa values in proteins
    Proteins (in press)
    by Y He, J Xu, XM Pan
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-07-02 13:18:45 as read
  • PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    Nucleic Acids Research (in press)
    by TJ Dolinsky, P Czodrowski, H Li, JE Nielsen, JH Jensen, G Klebe, NA Baker
    posted to solvation software pka by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • Molecular simulation with variable protonation states at constant pH
    Journal of Chemical Physics, Vol. 126 (2007)
    by HA Stern
    posted to solvation pka molecular_simulation by sobolevnrm to the group baker-group on 2007-05-25 14:38:05 as read
  • Accurate, conformation-dependent predictions of solvent effects on protein ionization constants
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 12. (2007), pp. 4898-903.
    by P Barth, T Alber, PB Harbury
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:49 as read
  • High Apparent Dielectric Constant Inside a Protein Reflects Structural Reorganization Coupled to the Ionization of an Internal Asp
    Biophysical Journal, Vol. 92, No. 6. (2007), pp. 2041-53.
    by DA Karp, AG Gittis, MR Stahley, CA Fitch, WE Stites, Garc\ia
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:29 as read
  • Calculation of pKas in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides
    Journal of Molecular Biology, Vol. 366, No. 5. (2007), pp. 1475-96.
    by CL Tang, E Alexov, AM Pyle, B Honig
    posted to solvation pka nucleic_acids electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:05 as read
  • Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments
    Journal of Molecular Biology, Vol. 367, No. 5. (2007), pp. 1347-56.
    by P Czodrowski, CA Sotriffer, G Klebe
    posted to thrombin protein-ligand_interactions pka by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Benchmarking pKa prediction
    BMC Biochemistry, Vol. 7 (2006)
    by MN Davies, CP Toseland, DS Moss, DR Flower
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Solution pH Alters Mechanical and Electrical Properties of Phosphatidylcholine Membranes: Relation between Interfacial Electrostatics, Intramembrane Potential and Bending Elasticity
    Biophysical Journal (in press)
    by Y Zhou, RM Raphael
    posted to solvation pka electrostatics biomembranes by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Redesigning protein pKa values
    Protein Science, Vol. 16, No. 2. (2007), pp. 239-49.
    by Tynan BM Connolly, JE Nielsen
    posted to solvation protein_engineering pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:36:04 as read
  • Electrostatic Potential Energy within a Protein Monitored by Metal Charge-Dependent Hydrogen Exchange
    Biophysical Journal, Vol. 91, No. 11. (2006), pp. L93-5.
    by JS Anderson, DM Lemaster, G Hernã!'ndez
    posted to pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:24:57 as read
  • Electrostatic Contributions to Residue-Specific Protonation Equilibria and Proton Binding Capacitance for a Small Protein
    Biochemistry, Vol. 45, No. 47. (2006), pp. 13993-402.
    by S Lindman, S Linse, FAA Mulder, I Andrã\copyright
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:24:56 as read
  • 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), pp. 111-42.
    by JF Tocanne, J Teissiã\copyright
    posted to pka electrostatics biomembranes by sobolevnrm to the group baker-group on 2007-05-25 14:23:20 as read
  • Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes
    Proteins, Vol. 65, No. 2. (2006), pp. 424-37.
    by P Czodrowski, I Dramburg, CA Sotriffer, G Klebe
    posted to protein-ligand_interactions pka by sobolevnrm to the group baker-group on 2007-05-25 14:23:18 as read
  • Electrostatic Properties of Protein-Protein Complexes
    Biophysical Journal, Vol. 91, No. 5. (2006), pp. 1724-36.
    by PJ Kundrotas, E Alexov
    posted to solvation protein-protein_interactions pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:18 as read
  • The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations
    Proteins, Vol. 64, No. 4. (2006), pp. 829-44.
    by M Kato, AV Pisliakov, A Warshel
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
  • Toward the Accurate First-Principles Prediction of Ionization Equilibria in Proteins
    Biochemistry, Vol. 45, No. 31. (2006), pp. 9363-73.
    by J Khandogin, Iii
    posted to solvation pka electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:23:17 as read
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