Search Results - "Shakhnovich, EI"

Physics and Evolution of Thermophilic Adaptation by Berezovsky, Igor N., Shakhnovich, Eugene I., Fersht, Alan R.

“…Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their…”
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Proteins with selected sequences fold into unique native conformation by Shakhnovich, EI

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Topological Determinants of Protein Folding by Dokholyan, Nikolay V., Li, Lewyn, Ding, Feng, Shakhnovich, Eugene I.

“…The folding of many small proteins is kinetically a two-state process that represents overcoming the major free-energy barrier. A kinetic characteristic of a…”
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The Ensemble Folding Kinetics of Protein G from an All-Atom Monte Carlo Simulation by Shimada, Jun, Shakhnovich, Eugene I.

“…Protein G is folded with an all-atom Monte Carlo simulation by using a$G\bar o$potential. When folding is monitored by using burial of the lone tryptophan in…”
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Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function by Mirny, Leonid A., Shakhnovich, Eugene I.

“…Here, we provide an analysis of molecular evolution of five of the most populated protein folds: immunoglobulin fold, oligonucleotide-binding fold, Rossman…”
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Theoretical studies of protein-folding thermodynamics and kinetics by Shakhnovich, Eugene I

“…Recently, protein-folding models have advanced to the point where folding simulations of protein-like chains of reasonable length (up to 125 amino acids) are…”
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Understanding hierarchical protein evolution from first principles by Dokholyan, N V, Shakhnovich, E I

“…We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of…”
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Structural determinant of protein designability by England, Jeremy L, Shakhnovich, Eugene I

“…Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in…”
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SMall Molecule Growth 2001 (SMoG2001):  An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions by Ishchenko, Alexey V, Shakhnovich, Eugene I

“…Computational lead design procedures require fast and accurate scoring functions to rank millions of generated virtual ligands for protein targets. In this…”
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A Simple Physical Model for Scaling in Protein-Protein Interaction Networks by Deeds, Eric J., Ashenberg, Orr, Shakhnovich, Eugene I.

“…It has recently been demonstrated that many biological networks exhibit a "scale-free" topology, for which the probability of observing a node with a certain…”
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Expanding Protein Universe and Its Origin from the Biological Big Bang by Dokholyan, Nikolay V., Shakhnovich, Boris, Shakhnovich, Eugene I.

“…The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. With the large number of protein structures identified…”
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The folding thermodynamics and kinetics of crambin using an all-atom monte carlo simulation by Shimada, Jun, Kussell, Edo L., Shakhnovich, Eugene I.

“…We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all…”
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How to Derive a Protein Folding Potential? A New Approach to an Old Problem by Mirny, Leonid A., Shakhnovich, Eugene I.

“…In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by an optimization procedure that…”
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SMoG:  de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence by DeWitte, Robert S, Shakhnovich, Eugene I

“…In this paper, we present SMoG (Small Molecule Growth), a novel, straightforward method for de novo lead design and the evidence for its effectiveness. It is…”
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Molecular Dynamics Simulation of the SH3 Domain Aggregation Suggests a Generic Amyloidogenesis Mechanism by Ding, Feng, Dokholyan, Nikolay V., Buldyrev, Sergey V., Stanley, H.Eugene, Shakhnovich, Eugene I.

“…We use molecular dynamics simulation to study the aggregation of Src SH3 domain proteins. For the case of two proteins, we observe two possible aggregation…”
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Reconstruction of the src-SH3 Protein Domain Transition State Ensemble using Multiscale Molecular Dynamics Simulations by Ding, Feng, Guo, Weihua, Dokholyan, Nikolay V., Shakhnovich, Eugene I., Shea, Joan-Emma

“…We use an integrated computational approach to reconstruct accurately the transition state ensemble (TSE) for folding of the src-SH3 protein domain. We first…”
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Constructing, Verifying, and Dissecting the Folding Transition State of Chymotrypsin Inhibitor 2 with All-Atom Simulations by Li, Lewyn, Shakhnovich, Eugene I.

“…Experimentally, protein engineering and ϕ-value analysis is the method of choice to characterize the structure in folding transition state ensemble (TSE) of…”
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Entropic stabilization of proteins and its proteomic consequences by Berezovsky, Igor N, Chen, William W, Choi, Paul J, Shakhnovich, Eugene I

“…Evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. However,…”
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Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble by Ding, Feng, Dokholyan, Nikolay V., Buldyrev, Sergey V., Stanley, H. Eugene, Shakhnovich, Eugene I.

“…The concept of the protein transition state ensemble (TSE), a collection of the conformations that have 50% probability to convert rapidly to the folded state…”
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Evidence for the role of PrPC helix 1 in the hydrophilic seeding of prion aggregates by Morrissey, M. P., Shakhnovich, E. I.

“…Prions are mammalian proteins (PrPs) with a unique pathogenic property: a nonendogenous isoform PrP Sc can catalyze conversion of the endogenous PrP C isoform…”
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