Find Research Output

Search concepts
Selected Filters

Publication Year

  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011

Author

  • Nikolay Dokholyan
2017

Transmembrane helical interactions in the CFTR channel pore

Das, J., Aleksandrov, A. A., Cui, L., He, L., Riordan, J. R. & Dokholyan, N. V., Jun 2017, In : PLoS computational biology. 13, 6, e1005594.

Research output: Contribution to journalArticle

7 Scopus citations
2016

A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase

Hadi-Alijanvand, H., Proctor, E. A., Ding, F., Dokholyan, N. V. & Moosavi-Movahedi, A. A., May 1 2016, In : Proteins: Structure, Function and Bioinformatics. 84, 5, p. 611-623 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

Chandrasekaran, S. N., Das, J., Dokholyan, N. V. & Carter, C. W., Jan 1 2016, In : Structural Dynamics. 3, 1, 012101.

Research output: Contribution to journalArticle

13 Scopus citations

A Phosphomimetic Mutation Stabilizes SOD1 and Rescues Cell Viability in the Context of an ALS-Associated Mutation

Fay, J. M., Zhu, C., Proctor, E. A., Tao, Y., Cui, W., Ke, H. & Dokholyan, N. V., Nov 1 2016, In : Structure. 24, 11, p. 1898-1906 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

Applications of Discrete Molecular Dynamics in biology and medicine

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

Research output: Contribution to journalReview article

26 Scopus citations

Computational modeling of small molecule ligand binding interactions and affinities

Convertino, M. & Dokholyan, N. V., May 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 23-32 10 p. (Methods in Molecular Biology; vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Controlling Allosteric Networks in Proteins

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

Research output: Contribution to journalReview article

63 Scopus citations
9 Scopus citations

Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications

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

Research output: Contribution to journalReview article

25 Scopus citations

Engineering extrinsic disorder to control protein activity in living cells

Dagliyan, O., Tarnawski, M., Chu, P. H., Shirvanyants, D., Schlichting, I., Dokholyan, N. V. & Hahn, K. M., Dec 16 2016, In : Science. 354, 6318, p. 1441-1444 4 p.

Research output: Contribution to journalArticle

66 Scopus citations

Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit coupling

Shobair, M., Dagliyan, O., Kota, P., Dang, Y. L., He, H., Stutts, M. J. & Dokholyan, N. V., Feb 19 2016, In : Journal of Biological Chemistry. 291, 8, p. 3682-3692 11 p.

Research output: Contribution to journalArticle

6 Scopus citations

Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins

Jacob, R. B., Michaels, K. C., Anderson, C. J., Fay, J. M. & Dokholyan, N. V., Nov 15 2016, In : Scientific reports. 6, 37175.

Research output: Contribution to journalArticle

3 Scopus citations

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

Proctor, E. A., Fee, L., Tao, Y., Redler, R. L., Fay, J. M., Zhang, Y., Lv, Z., Mercer, I. P., Deshmukh, M., Lyubchenko, Y. L. & Dokholyan, N. V., Jan 19 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 3, p. 614-619 6 p.

Research output: Contribution to journalArticle

45 Scopus citations

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

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

Research output: Contribution to journalReview article

40 Scopus citations

Protein Destabilization as a Common Factor in Diverse Inherited Disorders

Redler, R. L., Das, J., Diaz, J. R. & Dokholyan, N., Jan 1 2016, In : Journal Of Molecular Evolution. 82, 1, p. 11-16 6 p.

Research output: Contribution to journalLetter

15 Scopus citations

Restoration of R117H CFTR folding and function in human airway cells through combination treatment with VX-809 and VX-770

Gentzsch, M., Ren, H. Y., Houck, S. A., Quinney, N. L., Cholon, D. M., Sopha, P., Chaudhry, I. G., Das, J., Dokholyan, N. V., Randell, S. H. & Cyr, D. M., Jan 1 2016, In : American Journal of Physiology - Lung Cellular and Molecular Physiology. 311, 3, p. L550-L559

Research output: Contribution to journalArticle

12 Scopus citations
2015

ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations

Williams, B., Convertino, M., Das, J. & Dokholyan, N. V., Jan 1 2015, In : PLoS computational biology. 11, 10, e1004359.

Research output: Contribution to journalArticle

12 Scopus citations

Channel gating dependence on pore lining helix glycine residues in skeletal muscle ryanodine receptor

Mei, Y., Xu, L., Mowrey, D. D., Giraldez, R. M., Wang, Y., Pasek, D. A., Dokholyan, N. V. & Meissner, G., Jul 10 2015, In : Journal of Biological Chemistry. 290, 28, p. 17535-17545 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models

Krokhotin, A. & Dokholyan, N. V., 2015, Methods in Enzymology. Academic Press Inc., p. 65-89 25 p. (Methods in Enzymology; vol. 553).

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

COMT gene locus: New functional variants

Meloto, C. B., Segall, S. K., Smith, S., Parisien, M., Shabalina, S. A., Rizzatti-Barbosa, C. M., Gauthier, J., Tsao, D., Convertino, M., Piltonen, M. H., Slade, G. D., Fillingim, R. B., Greenspan, J. D., Ohrbach, R., Knott, C., Maixner, W., Zaykin, D., Dokholyan, N. V., Reenila, I., Mannisto, P. T. & 1 others, Diatchenko, L., Oct 2015, In : Pain. 156, 10, p. 2072-2083 12 p.

Research output: Contribution to journalArticle

15 Scopus citations

Differences in the Antinociceptive Effects and Binding Properties of Propranolol and Bupranolol Enantiomers

Martin, L. J., Piltonen, M. H., Gauthier, J., Convertino, M., Acland, E. L., Dokholyan, N., Mogil, J. S., Diatchenko, L. & Maixner, W., Jan 1 2015, In : Journal of Pain. 16, 12, p. 1321-1333 13 p.

Research output: Contribution to journalArticle

12 Scopus citations

Differential regulation of 6- and 7-Transmembrane helix variants of μ-opioid receptor in response to morphine stimulation

Convertino, M., Samoshkin, A., Viet, C. T., Gauthier, J., Fraine, S. P. L., Sharif-Naeini, R., Schmidt, B. L., Maixner, W., Diatchenko, L. & Dokholyan, N. V., Nov 10 2015, In : PloS one. 10, 11, e0142826.

Research output: Contribution to journalArticle

9 Scopus citations

iFoldRNA v2: Folding RNA with constraints

Krokhotin, A., Houlihan, K. & Dokholyan, N. V., Feb 6 2015, In : Bioinformatics. 31, 17, p. 2891-2893 3 p.

Research output: Contribution to journalArticle

25 Scopus citations

Light-cleavable rapamycin dimer as an optical trigger for protein dimerization

Brown, K. A., Zou, Y., Shirvanyants, D., Zhang, J., Samanta, S., Mantravadi, P. K., Dokholyan, N. V. & Deiters, A., Apr 4 2015, In : Chemical Communications. 51, 26, p. 5702-5705 4 p.

Research output: Contribution to journalArticle

21 Scopus citations

Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX

Wang, L., Xie, L., Ramachandran, S., Lee, Y. Y., Yan, Z., Zhou, L., Krajewski, K., Liu, F., Zhu, C., Chen, D. J., Strahl, B. D., Jin, J., Dokholyan, N. V. & Chen, X., Jul 24 2015, In : Chemistry and Biology. 22, 7, p. 849-861 13 p., 3066.

Research output: Contribution to journalArticle

9 Scopus citations

Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator

Proctor, E. A., Kota, P., Aleksandrov, A. A., He, L., Riordan, J. R. & Dokholyan, N. V., Feb 1 2015, In : Chemical Science. 6, 2, p. 1237-1246 10 p.

Research output: Contribution to journalArticle

28 Scopus citations

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

Miao, Z., Adamiak, R. W., Blanchet, M. F., Boniecki, M., Bujnicki, J. M., Chen, S. J., Cheng, C., Chojnowski, G., Chou, F. C., Cordero, P., Cruz, J. A., Ferré-D'Amaré, A. R., Das, R., Ding, F., Dokholyan, N. V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M. & 20 others, Major, F., Mann, T. H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K. J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xiao, Y., Xu, X., Zhang, J., Zhao, P., Zok, T. & Westhof, E., Jun 1 2015, In : RNA (New York, N.Y.). 21, 6, p. 1066-1084 19 p.

Research output: Contribution to journalArticle

79 Scopus citations

Structural and functional interactions between six-transmembrane μ-opioid receptors and β2-adrenoreceptors modulate opioid signaling

Samoshkin, A., Convertino, M., Viet, C. T., Wieskopf, J. S., Kambur, O., Marcovitz, J., Patel, P., Stone, L. S., Kalso, E., Mogil, J. S., Schmidt, B. L., Maixner, W., Dokholyan, N. V. & Diatchenko, L., Dec 11 2015, In : Scientific reports. 5, 18198.

Research output: Contribution to journalArticle

15 Scopus citations

μ-Opioid receptor 6-transmembrane isoform: A potential therapeutic target for new effective opioids

Convertino, M., Samoshkin, A., Gauthier, J., Gold, M. S., Maixner, W., Dokholyan, N. & Diatchenko, L., Oct 1 2015, In : Progress in Neuro-Psychopharmacology and Biological Psychiatry. 62, p. 61-67 7 p.

Research output: Contribution to journalArticle

14 Scopus citations
2014

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. V., Apr 2014, In : Journal of Molecular Cell Biology. 6, 2, p. 104-115 12 p.

Research output: Contribution to journalReview article

19 Scopus citations

Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive

Nedd, S., Redler, R. L., Proctor, E. A., Dokholyan, N. V. & Alexandrova, A. N., Dec 12 2014, In : Journal of Molecular Biology. 426, 24, p. 4112-4124 13 p.

Research output: Contribution to journalArticle

25 Scopus citations

Cystic fibrosis: Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis

Cholon, D. M., Quinney, N. L., Fulcher, M. L., Esther, C. R., Das, J., Dokholyan, N. V., Randell, S. H., Boucher, R. C. & Gentzsch, M., Jul 23 2014, In : Science Translational Medicine. 6, 246, 246ra96.

Research output: Contribution to journalArticle

182 Scopus citations

Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins

Szöllosi, D., Horváth, T., Han, K. H., Dokholyan, N. V., Tompa, P., Kalmár, L. & Hegedus, T., Apr 24 2014, In : PloS one. 9, 4, e95795.

Research output: Contribution to journalArticle

16 Scopus citations

Erratum: Correctors of dF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein (FASEB Journal (2013) 27 (536 -545) DOI:10.1096/fj.12-216119)

He, L., Kota, P., Aleksandrov, A. A., Cui, L., Jensen, T., Dokholyan, N. V. & Riordan, J. R., Jun 2014, In : FASEB Journal. 28, 6, 1 p.

Research output: Contribution to journalComment/debate

Identification of an actin binding surface on vinculin that mediates mechanical cell and focal adhesion properties

Thompson, P. M., Tolbert, C. E., Shen, K., Kota, P., Palmer, S. M., Plevock, K. M., Orlova, A., Galkin, V. E., Burridge, K., Egelman, E. H., Dokholyan, N. V., Superfine, R. & Campbell, S. L., May 6 2014, In : Structure. 22, 5, p. 697-706 10 p.

Research output: Contribution to journalArticle

25 Scopus citations

Intrinsic disorder mediates cooperative signal transduction in STIM1

Furukawa, Y., Teraguchi, S., Ikegami, T., Dagliyan, O., Jin, L., Hall, D., Dokholyan, N., Namba, K., Akira, S., Kurosaki, T., Baba, Y. & Standley, D. M., May 15 2014, In : Journal of Molecular Biology. 426, 10, p. 2082-2097 16 p.

Research output: Contribution to journalArticle

17 Scopus citations

Non-native soluble oligomers of Cu/Zn superoxide dismutase (SOD1) contain a conformational epitope linked to cytotoxicity in amyotrophic lateral sclerosis (ALS)

Redler, R. L., Fee, L., Fay, J. M., Caplow, M. & Dokholyan, N., Apr 15 2014, In : Biochemistry. 53, 14, p. 2423-2432 10 p.

Research output: Contribution to journalArticle

19 Scopus citations

Pore dynamics and conductance of RyR1 transmembrane domain

Shirvanyants, D., Ramachandran, S., Mei, Y., Xu, L., Meissner, G. & Dokholyan, N., Jun 3 2014, In : Biophysical journal. 106, 11, p. 2375-2384 10 p.

Research output: Contribution to journalArticle

6 Scopus citations

RNA tertiary structure analysis by 2?-Hydroxyl molecular interference

Homan, P. J., Tandon, A., Rice, G. M., Ding, F., Dokholyan, N. V. & Weeks, K. M., Nov 4 2014, In : Biochemistry. 53, 43, p. 6825-6833 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Series preface

Dokholyan, N., Jan 1 2014, Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods. CRC Press, p. xi

Research output: Chapter in Book/Report/Conference proceedingForeword/postscript

Single-molecule correlated chemical probing of RNA

Homan, P. J., Favorov, O. V., Lavender, C. A., Kursun, O., Ge, X., Busan, S., Dokholyan, N. V. & Weeks, K. M., Sep 23 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 38, p. 13858-13863 6 p.

Research output: Contribution to journalArticle

56 Scopus citations

The maturation of HIV-1 protease precursor studied by discrete molecular dynamics

Kimura, S., Caldarini, M., Broglia, R. A., Dokholyan, N. V. & Tiana, G., Apr 2014, In : Proteins: Structure, Function and Bioinformatics. 82, 4, p. 633-639 7 p.

Research output: Contribution to journalArticle

9 Scopus citations

The N-terminal domain allosterically regulates cleavage and activation of the epthelial sodium channel

Kota, P., Buchner, G., Chakraborty, H., Dang, Y. L., He, H., Garcia, G. J. M., Kubelka, J., Gentzsch, M., Stutts, M. J. & Dokholyan, N. V., Aug 15 2014, In : Journal of Biological Chemistry. 289, 33, p. 23029-23042 14 p.

Research output: Contribution to journalArticle

8 Scopus citations

Traffic within the cytochrome b6f lipoprotein complex: Gating of the quinone portal

Hasan, S. S., Proctor, E. A., Yamashita, E., Dokholyan, N. V. & Cramer, W. A., Oct 7 2014, In : Biophysical journal. 107, 7, p. 1620-1628 9 p.

Research output: Contribution to journalArticle

11 Scopus citations
2013

Correction: Thermal unfolding pathway of PHD2 catalytic domain in three different PHD2 species: Computational approaches (PLoS ONE)

Hadi-Alijanvand, H., Proctor, E. A., Goliaei, B., Dokholyan, N. & Moosavi-Movahedi, A. A., Apr 22 2013, In : PloS one. 8, 4

Research output: Contribution to journalComment/debate

Correctors of δF508 CFTR restore global conformational maturation without thermally stabilizing the mutant protein

He, L., Kota, P., Aleksandrov, A. A., Cui, L., Jensen, T., Dokholyan, N. V. & Riordan, J. R., Feb 2013, In : FASEB Journal. 27, 2, p. 536-545 10 p.

Research output: Contribution to journalArticle

81 Scopus citations

Dynamics intrinsic to cystic fibrosis transmembrane conductance regulator function and stability

Chong, P. A., Kota, P., Dokholyan, N. V. & Forman-Kay, J. D., Mar 1 2013, In : Cold Spring Harbor Perspectives in Medicine. 3, 3, a009522.

Research output: Contribution to journalArticle

23 Scopus citations

Highly covarying residues have a functional role in antibody constant domains

Proctor, E. A., Kota, P., Demarest, S. J., Caravella, J. A. & Dokholyan, N. V., May 1 2013, In : Proteins: Structure, Function and Bioinformatics. 81, 5, p. 884-895 12 p.

Research output: Contribution to journalArticle

4 Scopus citations

Identification of novel integrin binding partners for calcium and integrin binding protein 1 (CIB1): Structural and thermodynamic basis of CIB1 promiscuity

Freeman, T. C., Black, J. L., Bray, H. G., Dagliyan, O., Wu, Y. I., Tripathy, A., Dokholyan, N. V., Leisner, T. M. & Parise, L. V., Oct 8 2013, In : Biochemistry. 52, 40, p. 7082-7090 9 p.

Research output: Contribution to journalArticle

12 Scopus citations
29 Scopus citations