Browsing by Subject "protein"
Now showing items 21-30 of 30
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Protein dynamics and electron transfer: Electronic decoherence and non-Condon effects
(2005)We compute the autocorrelation function of the donor-acceptor tunneling matrix element 〈TDA(t)TDA(0)〉 for six Ru-azurin derivatives. Comparison of this decay time to the decay time of the time-dependent Franck-Condon factor ...
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Proteus and the design of ligand binding sites
(2016)This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...
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Article
Proton binding to proteins: A free-energy component analysis using a dielectric continuum model
(2005)Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. ...
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RAAS inhibition and the course of Alport syndrome
(2016)Alport syndrome (AS) is a hereditary progressive glomerulonephritis with a high life-time risk for end-stage renal disease (ESRD). Most patients will reach ESRD before the age of 30 years, while a subset of them with milder ...
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Recognition and discrimination of gases by the oxygen-sensing signal transducer protein HemAT as revealed by FTIR spectroscopy
(2006)The determination of ligand binding properties is a key step in our understanding of gas sensing and discrimination by gas sensory proteins. HemAT is a newly discovered signal transducer heme protein that recognizes O 2 ...
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A residue-pairwise generalized born scheme suitable for protein design calculations
(2005)We describe an efficient generalized Born (GB) approximation for proteins, in which the interaction energy between two amino acids depends on the whole protein structure, but can be accurately computed from residue-pairwise ...
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Review: Probing protein electron transfer mechanisms from the molecular to the cellular length scales
(2013)The mechanisms of bridge-mediated electron transfer (ET) reactions vary from coherent deep tunneling to thermally activated hopping. This short review focuses on some developments in the study of protein ET mechanisms at ...
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Screening of the PKD1 duplicated region reveals multiple single nucleotide polymorphisms and a de novo mutation in Hellenic polycystic kidney disease families.
(2000)Mutations in the PKD1 gene account for approximately 85% of cases with autosomal dominant polycystic kidney disease (ADPKD1
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Spectral density ratio based clustering methods for the binary segmentation of protein sequences: A comparative study
(2010)We compare several spectral domain based clustering methods for partitioning protein sequence data. The main instrument for this exercise is the spectral density ratio model, which specifies that the logarithmic ratio of ...
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