Works matching IS 08873585 AND DT 2011 AND VI 79 AND IP 12

Results: 24

Electrostatic p Ka computations in proteins: Role of internal cavities.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3320, doi. 10.1002/prot.23092

By:

Meyer, Tim;
Kieseritzky, Gernot;
Knapp, Ernst-Walter

Publication type:

Article

Is the prediction of p Ka values by constant-pH molecular dynamics being hindered by inherited problems?

Published in:

Proteins, 2011, v. 79, n. 12, p. 3437, doi. 10.1002/prot.23115

By:

Machuqueiro, Miguel;
Baptista, António M.

Publication type:

Article

Predicting extreme p Ka shifts in staphylococcal nuclease mutants with constant pH molecular dynamics.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3276, doi. 10.1002/prot.23195

By:

Arthur, Evan J.;
Yesselman, Joseph D.;
Brooks, Charles L.

Publication type:

Article

p Ka predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3374, doi. 10.1002/prot.23078

By:

Jim Warwicker

Publication type:

Article

Blind, one-eyed, or eagle-eyed? p Ka calculations during blind predictions with staphylococcal nuclease.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3299, doi. 10.1002/prot.23110

By:

Czodrowski, Paul

Publication type:

Article

Energetics of charge-charge interactions between residues adjacent in sequence.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3494, doi. 10.1002/prot.23132

By:

Loladze, Vakhtang V.;
Makhatadze, George I.

Publication type:

Article

Histidine in continuum electrostatics protonation state calculations.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3410, doi. 10.1002/prot.23114

By:

Couch, Vernon;
Stuchebrukhov, Alexei

Publication type:

Article

Toward accurate prediction of p Ka values for internal protein residues: The importance of conformational relaxation and desolvation energy.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3364, doi. 10.1002/prot.23080

By:

Wallace, Jason A.;
Wang, Yuhang;
Shi, Chuanyin;
Pastoor, Kevin J.;
Nguyen, Bao-Linh;
Xia, Kai;
Shen, Jana K.

Publication type:

Article

The p Ka Cooperative: A collaborative effort to advance structure-based calculations of p Ka values and electrostatic effects in proteins.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3249, doi. 10.1002/prot.23194

By:

Nielsen, Jens E.;
Gunner, M. R.;
García-Moreno E., Bertrand

Publication type:

Article

Simulating electrostatic energies in proteins: Perspectives and some recent studies of p Kas, redox, and other crucial functional properties.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3469, doi. 10.1002/prot.23125

By:

Warshel, Arieh;
Dryga, Anatoly

Publication type:

Article

On the development of protein p Ka calculation algorithms.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3287, doi. 10.1002/prot.23091

By:

Carstensen, Tommy;
Farrell, Damien;
Huang, Yong;
Baker, Nathan A.;
Nielsen, Jens Erik

Publication type:

Article

Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3381, doi. 10.1002/prot.23136

By:

Williams, Sarah L.;
Blachly, Patrick G.;
McCammon, J. Andrew

Publication type:

Article

pH replica-exchange method based on discrete protonation states.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3420, doi. 10.1002/prot.23176

By:

Itoh, Satoru G.;
Damjanović, Ana;
Brooks, Bernard R.

Publication type:

Article

Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interface.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3511, doi. 10.1002/prot.23095

By:

Ensign, Daniel L.;
Webb, Lauren J.

Publication type:

Article

Protein electrostatics and p Ka blind predictions; contribution from empirical predictions of internal ionizable residues.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3333, doi. 10.1002/prot.23113

By:

Olsson, Mats H. M.

Publication type:

Article

MCCE analysis of the p Kas of introduced buried acids and bases in staphylococcal nuclease.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3306, doi. 10.1002/prot.23124

By:

Gunner, M. R.;
Zhu, Xuyu;
Klein, Max C.

Publication type:

Article

Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3356, doi. 10.1002/prot.23146

By:

Song, Yifan

Publication type:

Article

Estimating the p Ka values of basic and acidic side chains in ion channels using electrophysiological recordings: A robust approach to an elusive problem.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3485, doi. 10.1002/prot.23087

By:

Cymes, Gisela D.;
Grosman, Claudio

Publication type:

Article

Calculation of p Ka in proteins with the microenvironment modulated-screened coulomb potential.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3346, doi. 10.1002/prot.23098

By:

Shan, Jufang;
Mehler, Ernest L.

Publication type:

Article

Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3500, doi. 10.1002/prot.23145

By:

Meng, Wenli;
Raleigh, Daniel P.

Publication type:

Article

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3448, doi. 10.1002/prot.23042

By:

Polydorides, Savvas;
Amara, Najette;
Aubard, Caroline;
Plateau, Pierre;
Simonson, Thomas;
Archontis, Georgios

Publication type:

Article

Progress in the prediction of p Ka values in proteins.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3260, doi. 10.1002/prot.23189

By:

Alexov, Emil;
Mehler, Ernest L.;
Baker, Nathan;
M. Baptista, António;
Huang, Yong;
Milletti, Francesca;
Erik Nielsen, Jens;
Farrell, Damien;
Carstensen, Tommy;
Olsson, Mats H. M.;
Shen, Jana K.;
Warwicker, Jim;
Williams, Sarah;
Word, J. Michael

Publication type:

Article

Developing hybrid approaches to predict p Ka values of ionizable groups.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3389, doi. 10.1002/prot.23097

By:

Witham, Shawn;
Talley, Kemper;
Wang, Lin;
Zhang, Zhe;
Sarkar, Subhra;
Gao, Daquan;
Yang, Wei;
Alexov, Emil

Publication type:

Article

Application of the Gaussian dielectric boundary in Zap to the prediction of protein p Ka values.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3400, doi. 10.1002/prot.23079

By:

Word, J. Michael;
Nicholls, Anthony

Publication type:

Article

Works matching IS 08873585 AND DT 2011 AND VI 79 AND IP 12

Electrostatic p K<sub>a</sub> computations in proteins: Role of internal cavities.

Is the prediction of p K<sub>a</sub> values by constant-pH molecular dynamics being hindered by inherited problems?

Predicting extreme p K<sub>a</sub> shifts in staphylococcal nuclease mutants with constant pH molecular dynamics.

p K<sub>a</sub> predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.

Blind, one-eyed, or eagle-eyed? p K<sub>a</sub> calculations during blind predictions with staphylococcal nuclease.

Energetics of charge-charge interactions between residues adjacent in sequence.

Histidine in continuum electrostatics protonation state calculations.

Toward accurate prediction of p K<sub>a</sub> values for internal protein residues: The importance of conformational relaxation and desolvation energy.

The p K<sub>a</sub> Cooperative: A collaborative effort to advance structure-based calculations of p K<sub>a</sub> values and electrostatic effects in proteins.

Simulating electrostatic energies in proteins: Perspectives and some recent studies of p K<sub>a</sub>s, redox, and other crucial functional properties.

On the development of protein p K<sub>a</sub> calculation algorithms.

Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study.

pH replica-exchange method based on discrete protonation states.

Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interface.

Protein electrostatics and p K<sub>a</sub> blind predictions; contribution from empirical predictions of internal ionizable residues.

MCCE analysis of the p K<sub>a</sub>s of introduced buried acids and bases in staphylococcal nuclease.

Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol.

Estimating the p K<sub>a</sub> values of basic and acidic side chains in ion channels using electrophysiological recordings: A robust approach to an elusive problem.

Calculation of p K<sub>a</sub> in proteins with the microenvironment modulated-screened coulomb potential.

Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions.

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase.

Progress in the prediction of p K<sub>a</sub> values in proteins.

Developing hybrid approaches to predict p K<sub>a</sub> values of ionizable groups.

Application of the Gaussian dielectric boundary in Zap to the prediction of protein p K<sub>a</sub> values.