Search Results - "Jernigan, R.L."

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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Protein secondary structure prediction based on the GOR algorithm incorporating multiple sequence alignment information by KLOCZKOWSKI, A, TING, K.-L, JERNIGAN, R. L, GARNIER, J

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Possible alternative and extension to the use of dynamics for structure matching by Jernigan, R.L.

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Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation 1 1 Edited by B. Honig by Bahar, I., Jernigan, R.L.

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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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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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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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Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior by Keskin, O., Jernigan, R.L., Bahar, I.

“…We have investigated the similarities and differences in the computed dynamic fluctuations exhibited by six members of a protein fold family with a…”
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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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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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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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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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Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation11Edited by B. Honig 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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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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Distance-dependent dielectric constants and their application to double-helical DNA by Mazur, J, Jernigan, R L

“…Detailed studies of structures of biological macromolecules, even in simplified models, involve many costly and time-consuming calculations. Any thorough…”
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Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms by Mazur, J., Jernigan, R.L.

“…A new method, based on a space-fixed rotation axis, or local helix axis, is proposed for the calculation of the relative orientation variables for a sequence…”
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Interdependence of conformational variables in double-helical DNA by Sarai, A., Jernigan, R.L., Mazur, J.

“…DNA exhibits conformational polymorphism, with the details depending on the sequence and its environment. To understand the mechanisms of conformational…”
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Constructing optimal backbone segments for joining fixed DNA base pairs by Mazur, J., Jernigan, R.L., Sarai, A.

“…A method is presented to link a sequence of space-fixed base pairs by the sugar-phosphate segments of single nucleotides and to evaluate the effects in the…”
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Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins by Bahar, I., Jernigan, R.L.

“…The role played by non-homogeneous interactions in stabilizing cooperative structural changes in proteins was investigated by exhaustive simulations of all…”
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Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions by Bahar, I., Jernigan, R.L.

“…On-lattice simulations of two-dimensional self-avoiding chains subject to homogeneous intramolecular attractive interactions were performed as a model for…”
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