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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get more information

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.

Get full text

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…”
Get full text