Search Results - "Dima, R I"

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors by Zhmurov, A., Dima, R. I., Kholodov, Y., Barsegov, V.

“…Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and…”
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Emerging ideas on the molecular basis of protein and peptide aggregation by Thirumalai, D, Klimov, DK, Dima, RI

“…Several neurodegenerative diseases are associated with the unfolding and subsequent fibrillization of proteins. Although neither the assembly mechanism nor the…”
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Exploring protein aggregation and self‐propagation using lattice models: Phase diagram and kinetics by Dima, R.I., Thirumalai, D.

“…Many seemingly unrelated neurodegenerative disorders, such as amyloid and prion diseases, are associated with propagating fibrils whose structures are…”
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Order Statistics Theory of Unfolding of Multimeric Proteins by Zhmurov, A., Dima, R.I., Barsegov, V.

“…Dynamic force spectroscopy has become indispensable for the exploration of the mechanical properties of proteins. In force-ramp experiments, performed by…”
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Exploring the propensities of helices in PrP(C) to form beta sheet using NMR structures and sequence alignments by Dima, R I, Thirumalai, D

“…Neurodegenerative diseases induced by transmissible spongiform encephalopathies are associated with prions. The most spectacular event in the formation of the…”
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Scoring functions in protein folding and design by DIMA, RUXANDRA I., BANAVAR, JAYANTH R., MARITAN, AMOS

“…We present an analysis of the assumptions behind some of the most commonly used methods for evaluating the goodness of the fit between a sequence and a…”
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Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures by Dima, Ruxandra I., Hyeon, Changbong, Thirumalai, D.

“…A crucial step in the determination of the three-dimensional native structures of RNA is the prediction of their secondary structures, which are stable…”
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Protein Threading by Learning by Chang, Iksoo, Cieplak, Marek, Dima, Ruxandra I., Maritan, Amos, Banavar, Jayanth R.

“…By using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen…”
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Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back by Chen, Jie, Dima, Ruxandra I., Thirumalai, D.

“…Escherichia coli dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate to tetrahydrofolate. During the catalytic cycle, DHFR undergoes…”
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Statistical Mechanics of Protein-Like Heteropolymers by Dima, Ruxandra I., Banavar, Jayanth R., Cieplak, Marek, Maritan, Amos

“…A strategy is outlined for obtaining the free energy of a typical designed heteropolymer. The design procedure considers the probability that the target…”
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Asymmetry in the Shapes of Folded and Denatured States of Proteins by Dima, Ruxandra I, Thirumalai, D

“…The asymmetry in the shapes of folded and unfolded states are probed using two parameters, Δ (a measure of the sphericity) and S that describes the shape (S >…”
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Determination of network of residues that regulate allostery in protein families using sequence analysis by Dima, Ruxandra I., Thirumalai, D.

“…Allosteric interactions between residues that are spatially apart and well separated in sequence are important in the function of multimeric proteins as well…”
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Probing the instabilities in the dynamics of helical fragments from mouse PrPC by Dima, Ruxandra I, Thirumalai, D

“…The first step in the formation of the protease resistant form (PrP Sc ) of prion proteins involves a conformational transition of the monomeric cellular form…”
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Exploring the Propensities of Helices in PrPC to Form β Sheet Using NMR Structures and Sequence Alignments by Dima, R.I., Thirumalai, D.

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Proteins associated with diseases show enhanced sequence correlation between charged residues by Dima, Ruxandra I., Thirumalai, D.

“…Motivation: Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The…”
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Langevin dynamics simulations of biomolecules on graphics processors by Zhmurov, A, Dima, R. I, Kholodov, Y, Barsegov, V

“…Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical…”
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