Search Results - "Shakhnovich, E.I."

Structural Similarity Enhances Interaction Propensity of Proteins by Lukatsky, D.B., Shakhnovich, B.E., Mintseris, J., Shakhnovich, E.I.

“…We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of…”
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What can Disulfide Bonds Tell Us about Protein Energetics, Function and Folding: Simulations and Bioninformatics Analysis by Abkevich, V.I., Shakhnovich, E.I.

“…We study the impact of disulfide bonds on protein stability and folding. Using lattice model simulations, we show that formation of a disulfide bond stabilizes…”
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Impact of Local and Non-local Interactions on Thermodynamics and Kinetics of Protein Folding by Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I.

“…To address the question of how the geometry of a protein's native conformation affects its folding and stability, we studied three model 36-mers on a cubic…”
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The role of cotranslation in protein folding: a lattice model study by Morrissey, M.P., Ahmed, Z., Shakhnovich, E.I.

“…Computational studies of protein folding have implicitly assumed that folding occurs from a denatured state comprised of the entire protein. Cotranslational…”
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A new approach to the design of stable proteins by Shakhnovich, E I, Gutin, A M

“…We propose a simple algorithm to design a sequence which fits a given protein structure with a given energy. The algorithm is a modification of the Metropolis…”
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Identification of a Conserved Aggregation-Prone Intermediate State in the Folding Pathways of Spc-SH3 Amyloidogenic Variants by Krobath, H., Estácio, S.G., Faísca, P.F.N., Shakhnovich, E.I.

“…We compared the folding pathways of selected mutational variants of the α-spectrin SH3 domain (Spc-SH3) by using a continuum model that combines a full…”
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Hiking in the energy landscape in sequence space: A bumpy road to good folders by Tiana, G., Broglia, R.A., Shakhnovich, E.I.

“…With the help of a simple 20‐letter lattice model of heteropolymers, we investigated the energy landscape in the space of designed good‐folder sequences…”
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Statistical mechanics of random heteropolymers by Sfatos, C.D., Shakhnovich, E.I.

“…We review analytical theories of random heteropolymers which investigates the freezing and the microphase separation transitions. Due to the heterogeneity of…”
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Adsorption-Freezing Transition for Random Heteropolymers near Disordered 2D Manifolds due to "Pattern Matching" by Srebnik, S, Chakraborty, AK, Shakhnovich, EI

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Analysis of knowledge-based protein–ligand potentials using a self-consistent method by SHIMADA, J., ISHCHENKO, A.V., SHAKHNOVICH, E.I.

“…We propose a self-consistent approach to analyze knowledge-based atom–atom potentials used to calculate protein–ligand binding energies. Ligands complexed to…”
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Theory of kinetic partitioning in protein folding with possible applications to prions by Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I.

“…This study focuses on the phenomenon of kinetic partitioning when a polypeptide chain has two ground‐state conformations, one of which is kinetically more…”
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Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach by Shakhnovich, E I, Gutin, A M

“…A replica approach analogous to that used in spin glass systems is implemented to study the configurational space of a heteropolymeric model of protein with a…”
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Microphase Ordering in Melts of Randomly Grafted Copolymers by Qi, Shuyan, Chakraborty, Arup K., Wang, Hao, Lefebvre, Amy A., Balsara, Nitash P., Shakhnovich, Eugene I., Xenidou, Maria, Hadjichristidis, Nikos

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Domains in folding of model proteins by Abkevich, V.I., Gutin, A.M., Shakhnovich, E.I.

“…By means of Monte Carlo simulation, we investigated the equilibrium between folded and unfolded states of lattice model proteins. The amino acid sequences were…”
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Adsorption of random copolymers on disordered surfaces by Bratko, D., Chakraborty, Arup K., Shakhnovich, E.I.

“…Monte Carlo simulations are used to study adsorption of random heteropolymers on disordered substrates. The adsorbent surface is modelled as an impenetrable…”
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Energy profile of the space of model protein sequences by Tiana, G, Broglia, R A, Shakhnovich, E I

“…A numerical study of the energy landscape of the space of model proteinsequences is carried out. As a consequence of the heterogeneity of thecontact energies…”
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Exhaustive enumeration of protein conformations using experimental restraints by Dewitte, R.S., Michnick, S.W., Shakhnovich, E.I.

“…We present an efficient new algorithm that enumerates all possible conformations of a protein that satisfy a given set of distance restraints. Rapid growth of…”
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Influence of point mutations on protein structure: probability of a neutral mutation by Shakhnovich, E I, Gutin, A M

“…We investigate the probability X that a random mutation (i.e. the substitution in a random site of one amino acid residue by randomly chosen residue) will be a…”
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Protein folding kinetics in the dense phase by Leopold, P.E., Shakhnovich, E.I.

“…The standard theoretical approach to the protein folding problem uses the thermodynamic hypothesis to justify the assumption that proteins fold to the global…”
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