Works matching IS 08873585 AND DT 2011 AND VI 79
Results: 315
Is the prediction of p K<sub>a</sub> values by constant-pH molecular dynamics being hindered by inherited problems?
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- Proteins, 2011, v. 79, n. 12, p. 3437, doi. 10.1002/prot.23115
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Predicting extreme p K<sub>a</sub> shifts in staphylococcal nuclease mutants with constant pH molecular dynamics.
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- Proteins, 2011, v. 79, n. 12, p. 3276, doi. 10.1002/prot.23195
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Electrostatic p K<sub>a</sub> computations in proteins: Role of internal cavities.
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- Proteins, 2011, v. 79, n. 12, p. 3320, doi. 10.1002/prot.23092
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p K<sub>a</sub> predictions with a coupled finite difference Poisson-Boltzmann and Debye-Hückel method.
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- Proteins, 2011, v. 79, n. 12, p. 3374, doi. 10.1002/prot.23078
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Blind, one-eyed, or eagle-eyed? p K<sub>a</sub> calculations during blind predictions with staphylococcal nuclease.
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- Proteins, 2011, v. 79, n. 12, p. 3299, doi. 10.1002/prot.23110
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Energetics of charge-charge interactions between residues adjacent in sequence.
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- Proteins, 2011, v. 79, n. 12, p. 3494, doi. 10.1002/prot.23132
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Histidine in continuum electrostatics protonation state calculations.
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- Proteins, 2011, v. 79, n. 12, p. 3410, doi. 10.1002/prot.23114
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Toward accurate prediction of p K<sub>a</sub> values for internal protein residues: The importance of conformational relaxation and desolvation energy.
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- Proteins, 2011, v. 79, n. 12, p. 3364, doi. 10.1002/prot.23080
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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.
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- Proteins, 2011, v. 79, n. 12, p. 3249, doi. 10.1002/prot.23194
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Simulating electrostatic energies in proteins: Perspectives and some recent studies of p K<sub>a</sub>s, redox, and other crucial functional properties.
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- Proteins, 2011, v. 79, n. 12, p. 3469, doi. 10.1002/prot.23125
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Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol.
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- Proteins, 2011, v. 79, n. 12, p. 3356, doi. 10.1002/prot.23146
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Application of the Gaussian dielectric boundary in Zap to the prediction of protein p K<sub>a</sub> values.
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- Proteins, 2011, v. 79, n. 12, p. 3400, doi. 10.1002/prot.23079
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On the development of protein p K<sub>a</sub> calculation algorithms.
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- Proteins, 2011, v. 79, n. 12, p. 3287, doi. 10.1002/prot.23091
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Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interface.
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- Proteins, 2011, v. 79, n. 12, p. 3511, doi. 10.1002/prot.23095
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Protein electrostatics and p K<sub>a</sub> blind predictions; contribution from empirical predictions of internal ionizable residues.
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- Proteins, 2011, v. 79, n. 12, p. 3333, doi. 10.1002/prot.23113
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MCCE analysis of the p K<sub>a</sub>s of introduced buried acids and bases in staphylococcal nuclease.
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- Proteins, 2011, v. 79, n. 12, p. 3306, doi. 10.1002/prot.23124
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Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study.
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- Proteins, 2011, v. 79, n. 12, p. 3381, doi. 10.1002/prot.23136
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pH replica-exchange method based on discrete protonation states.
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- Proteins, 2011, v. 79, n. 12, p. 3420, doi. 10.1002/prot.23176
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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.
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- Proteins, 2011, v. 79, n. 12, p. 3485, doi. 10.1002/prot.23087
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Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions.
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- Proteins, 2011, v. 79, n. 12, p. 3500, doi. 10.1002/prot.23145
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Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase.
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- Proteins, 2011, v. 79, n. 12, p. 3448, doi. 10.1002/prot.23042
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Progress in the prediction of p K<sub>a</sub> values in proteins.
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- Proteins, 2011, v. 79, n. 12, p. 3260, doi. 10.1002/prot.23189
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Developing hybrid approaches to predict p K<sub>a</sub> values of ionizable groups.
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- Proteins, 2011, v. 79, n. 12, p. 3389, doi. 10.1002/prot.23097
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Calculation of p K<sub>a</sub> in proteins with the microenvironment modulated-screened coulomb potential.
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- Proteins, 2011, v. 79, n. 12, p. 3346, doi. 10.1002/prot.23098
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Effects of the Val211Gly substitution on molecular dynamics of the CMY-2 cephalosporinase: Implications on hydrolysis of expanded-spectrum cephalosporins.
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- Proteins, 2011, v. 79, n. 11, p. 3180, doi. 10.1002/prot.23150
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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.
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- Proteins, 2011, v. 79, n. 11, p. 3193, doi. 10.1002/prot.23154
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A genetically encoded, high-signal-to-noise maltose sensor.
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- Proteins, 2011, v. 79, n. 11, p. 3025, doi. 10.1002/prot.23118
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An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor.
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- Proteins, 2011, v. 79, n. 11, p. 3221, doi. 10.1002/prot.23158
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The structure, molecular dynamics, and energetics of centrin-melittin complex.
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- Proteins, 2011, v. 79, n. 11, p. 3132, doi. 10.1002/prot.23142
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The evolution of function in strictosidine synthase-like proteins.
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- Proteins, 2011, v. 79, n. 11, p. 3082, doi. 10.1002/prot.23135
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Characterization of PDZ domain-peptide interaction interface based on energetic patterns.
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- Proteins, 2011, v. 79, n. 11, p. 3208, doi. 10.1002/prot.23157
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Antibody modeling assessment.
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- Proteins, 2011, v. 79, n. 11, p. 3050, doi. 10.1002/prot.23130
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Structural and biochemical analysis of mammalian methionine sulfoxide reductase B2.
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- Proteins, 2011, v. 79, n. 11, p. 3123, doi. 10.1002/prot.23141
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Crystal structure of a novel mitogen-activated protein kinase phosphatase, SKRP1.
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- Proteins, 2011, v. 79, n. 11, p. 3242, doi. 10.1002/prot.23156
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Enhancing systematic protein-protein docking methods using ray casting: Application to ATTRACT.
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- Proteins, 2011, v. 79, n. 11, p. 3037, doi. 10.1002/prot.23127
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Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies.
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- Proteins, 2011, v. 79, n. 11, p. 3108, doi. 10.1002/prot.23138
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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.
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- Proteins, 2011, v. 79, n. 11, p. 3166, doi. 10.1002/prot.23149
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Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity.
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- Proteins, 2011, v. 79, n. 11, p. 3067, doi. 10.1002/prot.23133
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How T cell receptors interact with peptide-MHCs: A multiple steered molecular dynamics study.
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- Proteins, 2011, v. 79, n. 11, p. 3007, doi. 10.1002/prot.23104
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Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase.
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- Proteins, 2011, v. 79, n. 11, p. 3144, doi. 10.1002/prot.23144
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Assessment of template based protein structure predictions in CASP9.
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- Proteins, 2011, v. 79, p. 37, doi. 10.1002/prot.23177
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Phosphorylation alters backbone conformational preferences of serine and threonine peptides.
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- Proteins, 2011, v. 79, n. 11, p. 3155, doi. 10.1002/prot.23148
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Evaluation of model quality predictions in CASP9.
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- Proteins, 2011, v. 79, p. 91, doi. 10.1002/prot.23180
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Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.
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- Proteins, 2011, v. 79, p. 147, doi. 10.1002/prot.23111
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A multilayer evaluation approach for protein structure prediction and model quality assessment.
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- Proteins, 2011, v. 79, p. 172, doi. 10.1002/prot.23184
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The X-ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: Comparison of paralogous functions in B. thetaiotaomicron.
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- Proteins, 2011, v. 79, n. 11, p. 3099, doi. 10.1002/prot.23137
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CASP9 target classification.
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- Proteins, 2011, v. 79, p. 21, doi. 10.1002/prot.23190
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Evaluation of disorder predictions in CASP9.
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- Proteins, 2011, v. 79, p. 107, doi. 10.1002/prot.23161
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Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method.
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- Proteins, 2011, v. 79, p. 137, doi. 10.1002/prot.23120
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Evaluation of residue-residue contact predictions in CASP9.
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- Proteins, 2011, v. 79, p. 119, doi. 10.1002/prot.23160
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