Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations
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GNA2132 (Genome-derived Neisseria Antigen 2132) is a surface-exposed lipoprotein discovered by reverse vaccinology and expressed by genetically diverse Neisseria meningitidis strains (Pizza et al. 2000). The protein induces bactericidal antibodies against ...
The graph coloring problem is one of the most famous problems in graph theory and has a large range of applications. It consists in coloring the vertices of an undirected graph with a given number of colors such that two adjacent vertices get different col ...
The length of the Yersinia injectisome needle is determined by the protein YscP, which could act as a molecular ruler. The analysis of the correlation between the size of YscP and the needle length in seven wild-type strains of Yersinia enterocolitica rein ...
MicroRNAs (miRNAs) comprise a large set of short noncoding RNAs that bind to messenger RNAs (mRNAs) to reduce their translation into functional proteins. Computational prediction of miRNA targets is the first stage in the discovery and validation of new re ...
Because of the importance of helices in the secondary structure of proteins, we have undertaken a study of their spectroscopy, fragmentation patterns and conformations in the gas phase. In this work, we describe the effects of substitution at the N-terminu ...
2008
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Despite the establishment of design principles to optimize codon choice for heterologous expression vector design, the relationship between codon sequence and final protein yield remains poorly understood. In this work, we present a computational framework ...
Wiley-Blackwell2012
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Lysozyme can be electrochemically detected after adsorption at an electrified gel-water interface. Ex-situ characterization by electrostatic spray ionization mass spectrometry provides insights into the interfacial detection mechanism by allowing changes t ...
Royal Soc Chemistry2014
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Macrophage migration inhibitory factor (MIF) is a homotrimeric multifunctional proinflammatory cytokine that has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. Current therapeutic strategies for targeting MIF focus on ...
American Chemical Society2009
Proteins have the ability to assemble in multimeric states to perform their specific biological function. Unfortunately, characterizing experimentally these structures at atomistic resolution is usually difficult. For this reason, in silico methodologies a ...
EPFL2012
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In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic heterogeneity of force c ...
