Works matching IS 08873585 AND DT 2011 AND VI 79

Results: 315

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

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

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

Effects of the Val211Gly substitution on molecular dynamics of the CMY-2 cephalosporinase: Implications on hydrolysis of expanded-spectrum cephalosporins.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3180, doi. 10.1002/prot.23150

By:

Kotsakis, Stathis D.;
Tzouvelekis, Leonidas S.;
Petinaki, Efthymia;
Tzelepi, Eva;
Miriagou, Vivi

Publication type:

Article

Simulation of the β- to α-sheet transition results in a twisted sheet for antiparallel and an α-nanotube for parallel strands: Implications for amyloid formation.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3193, doi. 10.1002/prot.23154

By:

Hayward, Steven;
James Milner-White, E.

Publication type:

Article

A genetically encoded, high-signal-to-noise maltose sensor.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3025, doi. 10.1002/prot.23118

By:

Marvin, Jonathan S.;
Schreiter, Eric R.;
Echevarría, Ileabett M.;
Looger, Loren L.

Publication type:

Article

An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3221, doi. 10.1002/prot.23158

By:

Venken, Tom;
Krnavek, Daniela;
Münch, Jan;
Kirchhoff, Frank;
Henklein, Petra;
De Maeyer, Marc;
Voet, Arnout

Publication type:

Article

The structure, molecular dynamics, and energetics of centrin-melittin complex.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3132, doi. 10.1002/prot.23142

By:

Sosa, Liliana del Valle;
Alfaro, Elisa;
Santiago, Jorge;
Narváez, Daniel;
Rosado, Marie Cely;
Rodríguez, Aslin;
Gómez, Ana María;
Schreiter, Eric R.;
Pastrana-Ríos, Belinda

Publication type:

Article

The evolution of function in strictosidine synthase-like proteins.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3082, doi. 10.1002/prot.23135

By:

Hicks, Michael A.;
Barber, Alan E.;
Giddings, Lesley-Ann;
Caldwell, Jenna;
O'Connor, Sarah E.;
Babbitt, Patricia C.

Publication type:

Article

Characterization of PDZ domain-peptide interaction interface based on energetic patterns.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3208, doi. 10.1002/prot.23157

By:

Li, Nan;
Hou, Tingjun;
Ding, Bo;
Wang, Wei

Publication type:

Article

Antibody modeling assessment.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3050, doi. 10.1002/prot.23130

By:

Almagro, Juan C.;
Beavers, Mary Pat;
Hernandez-Guzman, Francisco;
Maier, Johannes;
Shaulsky, Jodi;
Butenhof, Kenneth;
Labute, Paul;
Thorsteinson, Nels;
Kelly, Kenneth;
Teplyakov, Alexey;
Luo, Jinquan;
Sweet, Raymond;
Gilliland, Gary L.

Publication type:

Article

Structural and biochemical analysis of mammalian methionine sulfoxide reductase B2.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3123, doi. 10.1002/prot.23141

By:

Aachmann, Finn L.;
Kwak, Geun-Hee;
Del Conte, Rebecca;
Kim, Hwa-Young;
Gladyshev, Vadim N.;
Dikiy, Alexander

Publication type:

Article

Crystal structure of a novel mitogen-activated protein kinase phosphatase, SKRP1.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3242, doi. 10.1002/prot.23156

By:

Wei, Chun Hua;
Ryu, Sun Young;
Jeon, Young Ho;
Yoon, Moon Young;
Jeong, Dae Gwin;
Kim, Seung Jun;
Ryu, Seong Eon

Publication type:

Article

Enhancing systematic protein-protein docking methods using ray casting: Application to ATTRACT.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3037, doi. 10.1002/prot.23127

By:

Li, Yi;
Cortés, Juan;
Siméon, Thierry

Publication type:

Article

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3108, doi. 10.1002/prot.23138

By:

Majumdar, Ritankar;
Railkar, Reema;
Dighe, Rajan R.

Publication type:

Article

Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3166, doi. 10.1002/prot.23149

By:

Tamamis, Phanourios;
Pierou, Panayiota;
Mytidou, Chrystalla;
Floudas, Christodoulos A.;
Morikis, Dimitrios;
Archontis, Georgios

Publication type:

Article

Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3067, doi. 10.1002/prot.23133

By:

Baiesi, Marco;
Seno, Flavio;
Trovato, Antonio

Publication type:

Article

How T cell receptors interact with peptide-MHCs: A multiple steered molecular dynamics study.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3007, doi. 10.1002/prot.23104

By:

Cuendet, Michel A.;
Zoete, Vincent;
Michielin, Olivier

Publication type:

Article

Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3144, doi. 10.1002/prot.23144

By:

Weißgraeber, Stephanie;
Hoffgaard, Franziska;
Hamacher, Kay

Publication type:

Article

The X-ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: Comparison of paralogous functions in B. thetaiotaomicron.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3099, doi. 10.1002/prot.23137

By:

Lu, Zhibing;
Dunaway-Mariano, Debra;
Allen, Karen N.

Publication type:

Article

Phosphorylation alters backbone conformational preferences of serine and threonine peptides.

Published in:

Proteins, 2011, v. 79, n. 11, p. 3155, doi. 10.1002/prot.23148

By:

Kim, Su-Yeon;
Jung, Youngae;
Hwang, Geum-Sook;
Han, Hogyu;
Cho, Minhaeng

Publication type:

Article

Evaluation of model quality predictions in CASP9.

Published in:

Proteins, 2011, v. 79, p. 91, doi. 10.1002/prot.23180

By:

Kryshtafovych, Andriy;
Fidelis, Krzysztof;
Tramontano, Anna

Publication type:

Article

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.

Published in:

Proteins, 2011, v. 79, p. 147, doi. 10.1002/prot.23111

By:

Xu, Dong;
Zhang, Jian;
Roy, Ambrish;
Zhang, Yang

Publication type:

Article

A multilayer evaluation approach for protein structure prediction and model quality assessment.

Published in:

Proteins, 2011, v. 79, p. 172, doi. 10.1002/prot.23184

By:

Zhang, Jingfen;
Wang, Qingguo;
Vantasin, Kittinun;
Zhang, Jiong;
He, Zhiquan;
Kosztin, Ioan;
Shang, Yi;
Xu, Dong

Publication type:

Article

Assessment of template based protein structure predictions in CASP9.

Published in:

Proteins, 2011, v. 79, p. 37, doi. 10.1002/prot.23177

By:

Mariani, Valerio;
Kiefer, Florian;
Schmidt, Tobias;
Haas, Juergen;
Schwede, Torsten

Publication type:

Article

CASP9 target classification.

Published in:

Proteins, 2011, v. 79, p. 21, doi. 10.1002/prot.23190

By:

Kinch, Lisa N.;
Shi, Shuoyong;
Cheng, Hua;
Cong, Qian;
Pei, Jimin;
Mariani, Valerio;
Schwede, Torsten;
Grishin, Nick V.

Publication type:

Article

Evaluation of disorder predictions in CASP9.

Published in:

Proteins, 2011, v. 79, p. 107, doi. 10.1002/prot.23161

By:

Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Moult, John;
Tramontano, Anna;
Kryshtafovych, Andriy

Publication type:

Article

Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method.

Published in:

Proteins, 2011, v. 79, p. 137, doi. 10.1002/prot.23120

By:

McGuffin, Liam J.;
Roche, Daniel B.

Publication type:

Article

Evaluation of residue-residue contact predictions in CASP9.

Published in:

Proteins, 2011, v. 79, p. 119, doi. 10.1002/prot.23160

By:

Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Tramontano, Anna;
Kryshtafovych, Andriy

Publication type:

Article