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Results: 1 to 20 of 177

1.

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

Mei Y, Xu L, Mowrey DD, Mendez Giraldez R, Wang Y, Pasek DA, Dokholyan NV, Meissner G.

J Biol Chem. 2015 May 21. pii: jbc.M115.659672. [Epub ahead of print]

2.

iFoldRNA v2: folding RNA with constraints.

Krokhotin A, Houlihan K, Dokholyan NV.

Bioinformatics. 2015 Apr 24. pii: btv221. [Epub ahead of print]

PMID:
25910700
3.

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

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E.

RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16.

4.

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

Krokhotin A, Dokholyan NV.

Methods Enzymol. 2015;553:65-89. doi: 10.1016/bs.mie.2014.10.052. Epub 2015 Feb 3.

PMID:
25726461
5.

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

Brown KA, Zou Y, Shirvanyants D, Zhang J, Samanta S, Mantravadi PK, Dokholyan NV, Deiters A.

Chem Commun (Camb). 2015 Apr 4;51(26):5702-5. doi: 10.1039/c4cc09442e.

PMID:
25716548
6.

Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator.

Proctor EA, Kota P, Aleksandrov AA, He L, Riordan JR, Dokholyan NV.

Chem Sci. 2015 Feb;6(2):1237-1246.

PMID:
25685315
7.

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

Convertino M, Samoshkin A, Gauthier J, Gold MS, Maixner W, Dokholyan NV, Diatchenko L.

Prog Neuropsychopharmacol Biol Psychiatry. 2014 Dec 6. pii: S0278-5846(14)00235-8. doi: 10.1016/j.pnpbp.2014.11.009. [Epub ahead of print]

PMID:
25485963
8.

RNA tertiary structure analysis by 2'-hydroxyl molecular interference.

Homan PJ, Tandon A, Rice GM, Ding F, Dokholyan NV, Weeks KM.

Biochemistry. 2014 Nov 4;53(43):6825-33. doi: 10.1021/bi501218g. Epub 2014 Oct 23.

PMID:
25341083
9.

Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal.

Hasan SS, Proctor EA, Yamashita E, Dokholyan NV, Cramer WA.

Biophys J. 2014 Oct 7;107(7):1620-8. doi: 10.1016/j.bpj.2014.08.003.

PMID:
25296314
10.

Single-molecule correlated chemical probing of RNA.

Homan PJ, Favorov OV, Lavender CA, Kursun O, Ge X, Busan S, Dokholyan NV, Weeks KM.

Proc Natl Acad Sci U S A. 2014 Sep 23;111(38):13858-63. doi: 10.1073/pnas.1407306111. Epub 2014 Sep 9.

11.

Potentiator ivacaftor abrogates pharmacological correction of ΔF508 CFTR in cystic fibrosis.

Cholon DM, Quinney NL, Fulcher ML, Esther CR Jr, Das J, Dokholyan NV, Randell SH, Boucher RC, Gentzsch M.

Sci Transl Med. 2014 Jul 23;6(246):246ra96. doi: 10.1126/scitranslmed.3008680.

12.

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

Nedd S, Redler RL, Proctor EA, Dokholyan NV, Alexandrova AN.

J Mol Biol. 2014 Dec 12;426(24):4112-24. doi: 10.1016/j.jmb.2014.07.016. Epub 2014 Jul 30.

PMID:
25083917
13.

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

Kota P, Buchner G, Chakraborty H, Dang YL, He H, Garcia GJ, Kubelka J, Gentzsch M, Stutts MJ, Dokholyan NV.

J Biol Chem. 2014 Aug 15;289(33):23029-42. doi: 10.1074/jbc.M114.570952. Epub 2014 Jun 28.

PMID:
24973914
14.

Pore dynamics and conductance of RyR1 transmembrane domain.

Shirvanyants D, Ramachandran S, Mei Y, Xu L, Meissner G, Dokholyan NV.

Biophys J. 2014 Jun 3;106(11):2375-84. doi: 10.1016/j.bpj.2014.04.023.

PMID:
24896116
15.

Discrete molecular dynamics can predict helical prestructured motifs in disordered proteins.

Szöllősi D, Horváth T, Han KH, Dokholyan NV, Tompa P, Kalmár L, Hegedűs T.

PLoS One. 2014 Apr 24;9(4):e95795. doi: 10.1371/journal.pone.0095795. eCollection 2014.

16.

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

Thompson PM, Tolbert CE, Shen K, Kota P, Palmer SM, Plevock KM, Orlova A, Galkin VE, Burridge K, Egelman EH, Dokholyan NV, Superfine R, Campbell SL.

Structure. 2014 May 6;22(5):697-706. doi: 10.1016/j.str.2014.03.002. Epub 2014 Mar 27.

17.

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

Redler RL, Fee L, Fay JM, Caplow M, Dokholyan NV.

Biochemistry. 2014 Apr 15;53(14):2423-32. doi: 10.1021/bi500158w. Epub 2014 Apr 2.

18.

Intrinsic disorder mediates cooperative signal transduction in STIM1.

Furukawa Y, Teraguchi S, Ikegami T, Dagliyan O, Jin L, Hall D, Dokholyan NV, Namba K, Akira S, Kurosaki T, Baba Y, Standley DM.

J Mol Biol. 2014 May 15;426(10):2082-97. doi: 10.1016/j.jmb.2014.03.006. Epub 2014 Mar 17.

19.

Computational approaches to understanding protein aggregation in neurodegeneration.

Redler RL, Shirvanyants D, Dagliyan O, Ding F, Kim DN, Kota P, Proctor EA, Ramachandran S, Tandon A, Dokholyan NV.

J Mol Cell Biol. 2014 Apr;6(2):104-15. doi: 10.1093/jmcb/mju007. Epub 2014 Mar 11. Review.

20.

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

Kimura S, Caldarini M, Broglia RA, Dokholyan NV, Tiana G.

Proteins. 2014 Apr;82(4):633-9. doi: 10.1002/prot.24440. Epub 2013 Nov 22.

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