Search Results - "Jernigan, R. L."

Non-coding RNA in raw and commercially processed milk and putative targets related to growth and immune-response by Shome, S, Jernigan, R L, Beitz, D C, Clark, S, Testroet, E D

“…Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, or an exocrine manner…”
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Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model by Atilgan, A.R., Durell, S.R., Jernigan, R.L., Demirel, M.C., Keskin, O., Bahar, I.

“…Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent…”
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Molecular Mechanisms of Chaperonin GroEL−GroES Function by Keskin, O, Bahar, I, Flatow, D, Covell, D. G, Jernigan, R. L

“…The dynamics of the GroEL−GroES complex is investigated with a coarse-grained model. This model is one in which single-residue points are connected to other…”
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Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation by Bahar, I, Jernigan, R L

“…Residue-specific potentials between pairs of side-chains and pairs of side-chain-backbone interaction sites have been generated by collecting radial…”
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Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence by Kloczkowski, A., Ting, K.-L., Jernigan, R.L., Garnier, J.

“…We have modified and improved the GOR algorithm for the protein secondary structure prediction by using the evolutionary information provided by multiple…”
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Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model by Bahar, I, Wallqvist, A, Covell, D. G, Jernigan, R. L

“…Recently, we developed a simple analytical model based on local residue packing densities and the distribution of tertiary contacts for describing the…”
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Protein sequence entropy is closely related to packing density and hydrophobicity by Liao, H., Yeh, W., Chiang, D., Jernigan, R.L., Lustig, B.

“…We investigated the correlation between the Shannon information entropy, ‘sequence entropy’, with respect to the local flexibility of native globular proteins…”
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Efficient Characterization of Collective Motions and Interresidue Correlations in Proteins by Low-Resolution Simulations by Bahar, I, Erman, B, Haliloglu, T, Jernigan, R. L

“…A low-resolution model is used together with recently developed knowledge-based potentials for exploring the dynamics of proteins. Configurations are generated…”
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A role for surface hydrophobicity in protein‐protein recognition by Young, L., Jernigan, R.L., Covell, D.G.

“…The role of hydrophobicity as a determinant of protein‐protein interactions is examined. Surfaces of apo‐protein targets comprising 9 classes of enzymes, 7…”
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RNABindR: a server for analyzing and predicting RNA-binding sites in proteins by Terribilini, Michael, Sander, Jeffry D, Lee, Jae-Hyung, Zaback, Peter, Jernigan, Robert L, Honavar, Vasant, Dobbs, Drena

“…Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a…”
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Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches by Bahar, I., Kaplan, M., Jernigan, R.L.

“…A statistical analysis of known structures is made for an assessment of the utility of short‐range energy considerations. For each type of amino acid, the…”
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Identification of kinetically hot residues in proteins by Demirel, Melik C., Atilgan, Ali Rana, Bahar, Ivet, Jernigan, Robert L., Erman, Burak

“…A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in…”
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Sequence-Dependent B↔A Transition in DNA Evaluated with Dimeric and Trimeric Scales by Tolstorukov, M.Y., Ivanov, V.I., Malenkov, G.G., Jernigan, R.L., Zhurkin, V.B.

“…Experimental data on the sequence-dependent B↔A conformational transition in 24 oligo- and polymeric duplexes yield optimal dimeric and trimeric scales for…”
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Static and Statistical Bending of DNA Evaluated by Monte Carlo Simulations by Zhurkin, V. B., Ulyanov, N. B., Gorin, A. A., Jernigan, R. L.

“…To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5·T5and…”
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Empirical solvent‐mediated potentials hold for both intra‐molecular and inter‐molecular inter‐residue interactions by Keskin, O., Bahar, I., Jernigan, R. L., Badretdinov, A. Y., Ptitsyn, O. B.

“…Whether knowledge‐based intra‐molecular inter‐residue potentials are valid to represent inter‐molecular interactions taking place at protein‐protein interfaces…”
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A preference‐based free‐energy parameterization of enzyme‐inhibitor binding. Applications to HIV‐1‐protease inhibitor design by Wallqvist, A., Jernigan, R.L., Covell, D.G.

“…The interface between protein receptor‐ligand complexes has been studied with respect to their binary interatomic interactions. Crystal structure data have…”
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Ideal architecture of residue packing and its observation in protein structures by Raghunathan, G., Jernigan, R. L.

“…A simple model of sphere packing has been investigated as an ideal model for long‐range interactions for the packing of non‐bonded residues in protein…”
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A parallel DNA triplex as a model for the intermediate in homologous recombination by Zhurkin, V B, Raghunathan, G, Ulyanov, N B, Camerini-Otero, R D, Jernigan, R L

“…Parallel DNA triplexes considered to be putative intermediates in homologous recombination, are studied by means of theoretical conformational analysis. These…”
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Possible alternative and extension to the use of dynamics for structure matching: Comment on “Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments” by C. Micheletti by Jernigan, R.L.

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Sequence dependence of DNA conformational flexibility by Sarai, A, Mazur, J, Nussinov, R, Jernigan, R. L

“…By using conformational free energy calculations, we have studied the sequence dependence of flexibility and its anisotropy along various conformational…”
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