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Determination of atomic desolvation energies from the structures of crystallized proteins.
We estimated effective atomic contact energies (ACE), the desolvation free energies required to transfer atoms from water to a protein's interior, using an adaptation of a method introduced by S.Expand
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The detection and classification of membrane-spanning proteins.
Discriminant analysis can be used to precisely classify membrane proteins as integral or peripheral and to estimate the odds that the classification is correct. Specifically, using 102 membraneExpand
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Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.
Protein segments that form amphipathic alpha-helices in their native state have periodic variation in the hydrophobicity values of the residues along the segment, with a 3.6 residue per cycle periodExpand
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VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
We report on new capabilities of VisANT--an integrative software platform for the visualization, mining, analysis and modeling of the biological networks--which extend the application of GO in network visualization, analysis, inference. Expand
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Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network
We integrate 16 genomic features to construct an evidence-weighted functional-linkage network comprising 21,657 human genes. The functional-linkage network is used to prioritize candidate genes forExpand
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Towards the identification of essential genes using targeted genome sequencing and comparative analysis
BackgroundThe identification of genes essential for survival is of theoretical importance in the understanding of the minimal requirements for cellular life, and of practical importance in theExpand
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VisANT: an online visualization and analysis tool for biological interaction data
We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. Expand
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An immunodominant epitope of the human immunodeficiency virus envelope glycoprotein gp160 recognized by class I major histocompatibility complex molecule-restricted murine cytotoxic T lymphocytes.
Because cytotoxic T lymphocytes (CTL) may be important for preventing direct cell-to-cell transmission of human immunodeficiency virus (HIV), the agent responsible for acquired immunodeficiencyExpand
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Two complementary methods for predicting peptides binding major histocompatibility complex molecules.
We describe two methods for predicting whether a given peptide will bind to an MHC and apply them to these peptides. Expand
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Identification of a microRNA panel for clear-cell kidney cancer.
OBJECTIVES To identify a robust panel of microRNA signatures that can classify tumor from normal kidney using microRNA expression levels. Mounting evidence suggests that microRNAs are key players inExpand
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