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Research Output 1994 2019

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Review article
2019
9 Citations (Scopus)

Allostery in Its Many Disguises: From Theory to Applications

Wodak, S. J., Paci, E., Dokholyan, N., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J. P., Bolhuis, P. G., Vreede, J., Faccioli, P. & 19 others, Orioli, S., Ravasio, R., Yan, L., Brito, C., Wyart, M., Gkeka, P., Rivalta, I., Palermo, G., McCammon, J. A., Panecka-Hofman, J., Wade, R. C., Di Pizio, A., Niv, M. Y., Nussinov, R., Tsai, C. J., Jang, H., Padhorny, D., Kozakov, D. & McLeish, T., Apr 2 2019, In : Structure. 27, 4, p. 566-578 13 p.

Research output: Contribution to journalReview article

Allosteric Regulation
Biological Phenomena
Education
Drug Design
Signal Transduction
2016
23 Citations (Scopus)

Applications of Discrete Molecular Dynamics in biology and medicine

Proctor, E. A. & Dokholyan, N., Apr 1 2016, In : Current Opinion in Structural Biology. 37, p. 9-13 5 p.

Research output: Contribution to journalReview article

Molecular Dynamics Simulation
Medicine
Microcomputers
Proteostasis Deficiencies
Petroleum Pollution
50 Citations (Scopus)

Controlling Allosteric Networks in Proteins

Dokholyan, N., Jun 8 2016, In : Chemical Reviews. 116, 11, p. 6463-6487 25 p.

Research output: Contribution to journalReview article

Proteins
Ligands
Cystic Fibrosis Transmembrane Conductance Regulator
Biological systems
Binding Sites
21 Citations (Scopus)

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications

Allen, S. E., Dokholyan, N. & Bowers, A. A., Jan 15 2016, In : ACS Chemical Biology. 11, 1, p. 10-24 15 p.

Research output: Contribution to journalReview article

Biological Products
Scaffolds
Pharmaceutical Chemistry
Point contacts
Proteins
35 Citations (Scopus)

Pharmacological Chaperones: Design and Development of New Therapeutic Strategies for the Treatment of Conformational Diseases

Convertino, M., Das, J. & Dokholyan, N., Jun 17 2016, In : ACS Chemical Biology. 11, 6, p. 1471-1489 19 p.

Research output: Contribution to journalReview article

Pharmacology
Protein folding
Poisons
Protein Folding
Bioactivity
2014
14 Citations (Scopus)

Computational approaches to understanding protein aggregation in neurodegeneration

Redler, R. L., Shirvanyants, D., Dagliyan, O., Ding, F., Kim, D. N., Kota, P., Proctor, E. A., Ramachandran, S., Tandon, A. & Dokholyan, N., Jan 1 2014, In : Journal of Molecular Cell Biology. 6, 2, p. 104-115 12 p.

Research output: Contribution to journalReview article

Proteins
Poisons
Amyotrophic Lateral Sclerosis
Information Systems
Neurodegenerative Diseases
2012
93 Citations (Scopus)

The interface of protein structure, protein biophysics, and molecular evolution

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L. J., De Koning, A. P. J., Dokholyan, N., Echave, J., Elofsson, A., Gerloff, D. L., Goldstein, R. A., Grahnen, J. A., Holder, M. T., Lakner, C., Lartillot, N., Lovell, S. C., Naylor, G., Perica, T. & 13 others, Pollock, D. D., Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjølander, K., Sunyaev, S., Teufel, A. I., Thorne, J. L., Thornton, J. W., Weinreich, D. M. & Whelan, S., Jun 1 2012, In : Protein Science. 21, 6, p. 769-785 17 p.

Research output: Contribution to journalReview article

Biophysics
Molecular Evolution
Proteins
Biochemistry
Intrinsically Disordered Proteins
2011

Approaches for probing the sequence space of substrates recognized by molecular chaperones

Kota, P. & Dokholyan, N., Mar 1 2011, In : Methods. 53, 3, p. 318-324 7 p.

Research output: Contribution to journalReview article

Molecular Chaperones
Neurodegenerative Diseases
Substrates
Neurodegenerative diseases
Neurons
2010
51 Citations (Scopus)

Regulation of the epithelial Na+ channel and airway surface liquid volume by serine proteases

Gaillard, E. A., Kota, P., Gentzsch, M., Dokholyan, N., Stutts, M. J. & Tarran, R., Jun 1 2010, In : Pflugers Archiv European Journal of Physiology. 460, 1, p. 1-17 17 p.

Research output: Contribution to journalReview article

Epithelial Sodium Channels
Serine Proteases
Mucus
Liquids
Bridge clearances
2008
15 Citations (Scopus)

Probing protein aggregation using discrete molecular dynamics

Sharma, S., Ding, F. & Dokholyan, N., May 1 2008, In : Frontiers in Bioscience. 13, 12, p. 4795-4808 14 p.

Research output: Contribution to journalReview article

Molecular Dynamics Simulation
Molecular dynamics
Agglomeration
Proteins
Aptitude
60 Citations (Scopus)

Protein folding: Then and now

Chen, Y., Ding, F., Nie, H., Serohijos, A. W., Sharma, S., Wilcox, K. C., Yin, S. & Dokholyan, N., Jan 1 2008, In : Archives of Biochemistry and Biophysics. 469, 1, p. 4-19 16 p.

Research output: Contribution to journalReview article

Protein folding
Protein Folding
Cell Engineering
Thermodynamics
Proteins
2007
21 Citations (Scopus)

Molecular mechanisms of polypeptide aggregation in human diseases

Khare, S. D. & Dokholyan, N., Dec 1 2007, In : Current Protein and Peptide Science. 8, 6, p. 573-579 7 p.

Research output: Contribution to journalReview article

Agglomeration
Peptides
Proteins
Amyloid
Association reactions
2006
61 Citations (Scopus)

Studies of folding and misfolding using simplified models

Dokholyan, N., Feb 1 2006, In : Current Opinion in Structural Biology. 16, 1, p. 79-85 7 p.

Research output: Contribution to journalReview article

Biological Phenomena
Protein Conformation
Molecular Dynamics Simulation
Computer Simulation
Proteins