18 hasil untuk "Burkhard Rost"
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Artikel Jurnal Teks lengkap
Alternative Protein-Protein Interfaces Are Frequent Exceptions
The intricate molecular details of protein-protein interactions (PPIs) are crucial for function. Therefore, measuring the same interacting protein pair again, we expect the same result. This work measured the similarity in the molecular details of interaction for the same and for homologous protein…
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Protein–Protein Interactions More Conserved within Species than across Species
Experimental high-throughput studies of protein–protein interactions are beginning to provide enough data for comprehensive computational studies. Today, about ten large data sets, each with thousands of interacting pairs, coarsely sample the interactions in fly, human, worm, and yeast. Another…
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Protein–Protein Interaction Hotspots Carved into Sequences
Protein–protein interactions, a key to almost any biological process, are mediated by molecular mechanisms that are not entirely clear. The study of these mechanisms often focuses on all residues at protein–protein interfaces. However, only a small subset of all interface residues is actually…
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Accelerating the Original Profile Kernel
One of the most accurate multi-class protein classification systems continues to be the profile-based SVM kernel introduced by the Leslie group. Unfortunately, its CPU requirements render it too slow for practical applications of large-scale classification tasks. Here, we introduce several software…
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Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines
RIKEN's FANTOM project has revealed many previously unknown coding sequences, as well as an unexpected degree of variation in transcripts resulting from alternative promoter usage and splicing. Ever more transcripts that do not code for proteins have been identified by transcriptome studies, in…
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Natively Unstructured Loops Differ from Other Loops
Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered…
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Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes
Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some…
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ProfPPIdb: Pairs of physical protein-protein interactions predicted for entire proteomes
Motivation: Protein-protein interactions (PPIs) play a key role in many cellular processes. Most annotations of PPIs mix experimental and computational data. The mix optimizes coverage, but obfuscates the annotation origin. Some resources excel at focusing on reliable experimental data. Here, we…
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Improved Disorder Prediction by Combination of Orthogonal Approaches
Disordered proteins are highly abundant in regulatory processes such as transcription and cell-signaling. Different methods have been developed to predict protein disorder often focusing on different types of disordered regions. Here, we present MD, a novel META-Disorder prediction method that…
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Predicted Molecular Effects of Sequence Variants Link to System Level of Disease
Developments in experimental and computational biology are advancing our understanding of how protein sequence variation impacts molecular protein function. However, the leap from the micro level of molecular function to the macro level of the whole organism, e.g. disease, remains barred. Here, we…
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ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus
Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola…
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ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature
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Artikel Jurnal Teks lengkap
NMR Structure of Lipoprotein YxeF from Bacillus subtilis Reveals a Calycin Fold and Distant Homology with the Lipocalin Blc from Escherichia coli
The soluble monomeric domain of lipoprotein YxeF from the Gram positive bacterium B. subtilis was selected by the Northeast Structural Genomics Consortium (NESG) as a target of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins. The…
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Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome
In the past, short protein-coding genes were often disregarded by genome annotation pipelines. Transcriptome sequencing (RNAseq) signals outside of annotated genes have usually been interpreted to indicate either ncRNA or pervasive transcription. Therefore, in addition to the transcriptome, the…
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Artikel Jurnal Teks lengkap
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)
Ancestral sequence reconstruction is a technique that is gaining widespread use in molecular evolution studies and protein engineering. Accurate reconstruction requires the ability to handle appropriately large numbers of sequences, as well as insertion and deletion (indel) events, but available…