Search Results - "Dokholyan, N. V."

Molecular Dynamics Simulation of Amyloid β Dimer Formation by Urbanc, B., Cruz, L., Ding, F., Sammond, D., Khare, S., Buldyrev, S.V., Stanley, H.E., Dokholyan, N.V.

“…Recent experiments with amyloid β (A β) peptide indicate that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's…”
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p62-Dependent Phase Separation of Patient-Derived KEAP1 Mutations and NRF2 by Cloer, E. W., Siesser, P. F., Cousins, E. M., Goldfarb, D., Mowrey, D. D., Harrison, J. S., Weir, S. J., Dokholyan, N. V., Major, M. B.

“…Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a prosurvival gene…”
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An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity by Reynolds, J.A., Vishweshwaraiah, Y.L., Chirasani, V.R., Pritchard, J.R., Dokholyan, N.V.

“…Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal…”
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Small-world view of the amino acids that play a key role in protein folding by Vendruscolo, M, Dokholyan, N V, Paci, E, Karplus, M

“…We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called "key residues," act as…”
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Analysis of DNA sequences using methods of statistical physics by Buldyrev, S.V., Dokholyan, N.V., Goldberger, A.L., Havlin, S., Peng, C.-K., Stanley, H.E., Viswanathan, G.M.

“…We review the present status of the studies of DNA sequences using methods of statistical physics. We present evidence, based on systematic studies of the…”
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Computational approaches to understanding protein aggregation in neurodegeneration by Redler, Rachel L., Shirvanyants, David, Dagliyan, Onur, Ding, Feng, Kim, Doo Nam, Kota, Pradeep, Proctor, Elizabeth A., Ramachandran, Srinivas, Tandon, Arpit, Dokholyan, Nikolay V.

“…The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer＇s disease, Parkinson＇s disease, and…”
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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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Simple but predictive protein models by Ding, Feng, Dokholyan, Nikolay V.

“…The traditional approach to computational biophysics studies of molecular systems is brute force molecular dynamics simulations under the conditions of…”
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Parallel Folding Pathways in the SH3 Domain Protein by Lam, A.R., Borreguero, J.M., Ding, F., Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E., Shakhnovich, E.

“…The transition-state ensemble (TSE) is the set of protein conformations with an equal probability to fold or unfold. Its characterization is crucial for an…”
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Discrete molecular dynamics simulations of peptide aggregation by Peng, S, Ding, F, Urbanc, B, Buldyrev, S V, Cruz, L, Stanley, H E, Dokholyan, N V

“…We study the aggregation of peptides using the discrete molecular dynamics simulations. Specifically, at temperatures above the alpha-helix melting temperature…”
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Identifying the protein folding nucleus using molecular dynamics by Dokholyan, N V, Buldyrev, S V, Stanley, H E, Shakhnovich, E I

“…Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with…”
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Folding of Cu, Zn Superoxide Dismutase and Familial Amyotrophic Lateral Sclerosis by Khare, Sagar D., Ding, Feng, Dokholyan, Nikolay V.

“…Cu, Zn superoxide dismutase (SOD1) has been implicated in the familial form of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). It has been…”
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The architecture of the protein domain universe by Dokholyan, Nikolay V.

“…Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain…”
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Imprint of Evolution on Protein Structures by Tiana, Guido, Shakhnovich, Boris E., Dokholyan, Nikolay V., Shakhnovich, Eugene I., Wolynes, Peter G.

“…We attempt to understand the evolutionary origin of protein folds by simulating their divergent evolution with a three-dimensional lattice model. Starting from…”
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AlphaFold illuminates half of the dark human proteins by Binder, Jessica L., Berendzen, Joel, Stevens, Amy O., He, Yi, Wang, Jian, Dokholyan, Nikolay V., Oprea, Tudor I.

“…We investigate the use of confidence scores to evaluate the accuracy of a given AlphaFold (AF2) protein model for drug discovery. Prediction of accuracy is…”
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Using Protein Design for Homology Detection and Active Site Searches by Pei, Jimin, Dokholyan, Nikolay V., Shakhnovich, Eugene I., Grishin, Nick V.

“…We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure…”
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Hierarchy in social organization by Buldyrev, S.V, Dokholyan, N.V, Erramilli, S, Hong, M, Kim, J.Y, Malescio, G, Stanley, H.E

“…We find that area and population distributions of nations follow an inverse power-law, as is known for cities, but with a different exponent. To interpret this…”
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Discrete molecular dynamics studies of the folding of a protein-like model by Dokholyan, Nikolay V., Buldyrev, Sergey V., Stanley, H Eugene, Shakhnovich, Eugene I.

“…Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have…”
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Distributions of Dimeric Tandem Repeats in Non-coding and Coding DNA Sequences by DOKHOLYAN, NIKOLAY V., BULDYREV, SERGEY V., HAVLIN, SHLOMO, STANLEY, H.EUGENE

“…We study the length distribution functions for the 16 possible distinct dimeric tandem repeats in DNA sequences of diverse taxonomic partitions of GenBank…”
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Using percolation theory to predict oil field performance by King, P.R, Buldyrev, S.V, Dokholyan, N.V, Havlin, S, Lopez, E, Paul, G, Stanley, H.E

“…In this paper, we apply scaling laws from percolation theory to the problem of estimating the time for a fluid injected into an oilfield to breakthrough into a…”
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