Yoichi Murakami

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MOTIVATION The limited availability of protein structures often restricts the functional annotation of proteins and the identification of their protein-protein interaction sites. Computational methods to identify interaction sites from protein sequences alone are, therefore, required for unraveling the functions of many proteins. This article describes a(More)
We have developed a new method to predict protein- protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of shape complementarity weighted by the conservation of the(More)
MOTIVATION All eukaryotic proteomes are characterized by a significant percentage of proteins of unknown function. Comp-utational function prediction methods are therefore essential as initial steps in the function annotation process. This article describes an annotation method (PiRaNhA) for the prediction of RNA-binding residues (RBRs) from protein(More)
The PiRaNhA web server is a publicly available online resource that automatically predicts the location of RNA-binding residues (RBRs) in protein sequences. The goal of functional annotation of sequences in the field of RNA binding is to provide predictions of high accuracy that require only small numbers of targeted mutations for verification. The PiRaNhA(More)
UNLABELLED SHARP2 is a flexible web-based bioinformatics tool for predicting potential protein-protein interaction sites on protein structures. It implements a predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. Six parameters are calculated: solvation potential, hydrophobicity,(More)
The optical transition energies E and E of single walled carbon nanotubes SWNTs sus pended in air have been investigated for species by photoluminescence and excitation spectro scopies We have studied the environmental e ects in photoluminescence by comparing our results with those for the SWNTs wrapped by sodium dodecyl sulfate SDS as reported by Weisman(More)
Patient Age, y/sex Occupation Hospital Days with fever after possible tick bite Symptom onset Fever Rash Additional symptom/sign Underlying disorder Laboratory findings (reference values)† Treatment 1 87/F Farmer A 5 d after working on farm 2010 May 39.7C Yes Malaise Hypertension, hyperlipidemia WBC, 8.7 × 10 cells/L (3.5–9.2 × 10 cells/L); Plt, 196 × 10(More)
Films of vertically aligned single-walled carbon nanotubes (SWNTs) with a few μm thickness were grown by catalytic chemical vapor deposition (CVD) on quartz substrates. Low-temperature CVD from ethanol was performed by using densely mono-dispersed Co-Mo catalyst of ≈ 1.0 – 2.0 nm prepared on quartz substrates by a dip-coating method. Continuous reduction of(More)
Anisotropic optical absorption properties of single-walled carbon nanotubes (SWNTs) are determined from a vertically aligned SWNT film for 0.5-6 eV. Absorption peaks at 4.5 and 5.25 eV are found to exhibit remarkable polarization dependence and have relevance to optical properties of graphite. A method for determining a nematic order parameter for an(More)
Abstract Near-infrared fluorescence measurements were performed on single-walled carbon nanotubes (SWNTs) catalytically synthesized from alcohol under various experimental conditions (alcohol catalytic CVD method, ACCVD). The chirality distribution was determined by measuring the fluorescence emitted from separated SWNTs as a function of excitation(More)