Browsing by Subject "protein"
Now showing items 1-20 of 30
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Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation
(2007)Modifications on histones control important biological processes through their effects on chromatin structure. Methylation at lysine 4 on histone H3 (H3K4) is found at the 5′ end of active genes and contributes to ...
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BioTextQuest+: A knowledge integration platform for literature mining and concept discovery
(2014)The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific ...
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CHARMM: The biomolecular simulation program
(2009)CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, ...
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A comparative study on filtering protein secondary structure prediction
(2012)Filtering of Protein Secondary Structure Prediction (PSSP) aims to provide physicochemically realistic results, while it usually improves the predictive performance. We performed a comparative study on this challenging ...
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Computational protein design: The proteus software and selected applications
(2013)We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...
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Computational sidechain placement and protein mutagenesis with implicit solvent models
(2007)Structure prediction and computational protein design should benefit from accurate solvent models. We have applied implicit solvent models to two problems that are central to this area. First, we performed sidechain placement ...
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Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis
(2015)The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA) + rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorly understood. Here we ...
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Electron transfer mechanisms
(1998)The tunneling pathway framework description of protein electron transfer reactions has prompted a lively discussion of how structure and evolution influence electron transfer rates. Recent protein and model system experiments, ...
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Familial Mediterranean fever associated pyrin mutations in Greece
(2003)Objective: To search for pyrin mutations associated with familial Mediterranean fever (FMF) in Greece. Patients and methods: 62 patients fulfilling the Tel Hashomer diagnostic criteria for definite (33) or probable (29) ...
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Fluctuations in biological and bioinspired electron-transfer reactions
(2010)Central to theories of electron transfer (ET) is the idea that nuclear motion generates a transition state that enables electron flow to proceed, but nuclear motion also induces fluctuations in the donor-acceptor (DA) ...
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Free energy simulations come of age: Protein-ligand recognition
(2002)In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide ...
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Genomic approaches that aid in the identification of transcription factor target genes
(2004)It is well-established that deregulation of the transcriptional activity of many different genes has been causatively linked to human diseases. In cancer, altered patterns of gene expression are often the result of the ...
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In vivo, site-specific, covalent conjugation of quantum dots to proteins via split-intein splicing
(2012)The ability to target proteins with nanostructures and/or nanodevices in vivo is important for understanding and controlling their biological function. Quantum dots (QDs) serve as an ideal model nanostructure due to their ...
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Making the Connection: Ciliary Adhesion Complexes Anchor Basal Bodies to the Actin Cytoskeleton
(2014)Cilia have been associated with diverse developmental and physiological processes, and defects in cilia underlie a number of genetic conditions. Several lines of evidence support a critical role of the actin cytoskeleton ...
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Neuralized Encodes a Peripheral Membrane Protein Involved in Delta Signaling and Endocytosis
(2001)Activation of the Notch (N) receptor involves an intracellular proteolytic step triggered by shedding of the extracellular N domain (N-EC) upon ligand interaction. The ligand Dl has been proposed to effect this N-EC shedding ...
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Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins
(1995)The simplest views of long-range electron transfer utilize flat one-dimensional barrier tunneling models, neglecting structural details of the protein medium. The pathway model of protein electron transfer reintroduces ...
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The Polycomb Group Protein SUZ12 regulates histone H3 lysine 9 methylation and HP1α distribution
(2007)Regulation of histone methylation is critical for proper gene expression and chromosome function. Suppressor of Zeste 12 (SUZ12) is a requisite member of the EED/EZH2 histone methyltransferase complexes, and is required ...
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Polypeptide Amino Acid Composition and Isoelectric Point. 1. A Closed-Form Approximation
(1995)Two analytical expressions correlating explicitly polyampholyte isoelectric point to acid-base composition are derived and presented. The utility and limitations of these equations for the determination of the isoelectric ...
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Protein complexation with acrylic polyampholytes
(1994)The interaction of dilute mixtures of proteins and ABC triblock methacrylic polyampholytes at different values of pH was investigated turbidimetrically. The onset of interaction was manifested by large changes in turbidity ...