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Items: 1 to 20 of 181

1.

Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.

Liu J, Sankar K, Wang Y, Jia K, Jernigan RL.

Biophys J. 2017 Apr 25;112(8):1561-1570. doi: 10.1016/j.bpj.2017.03.004.

PMID:
28445748
2.

Altered dynamics upon oligomerization corresponds to key functional sites.

Mishra SK, Sankar K, Jernigan RL.

Proteins. 2017 Aug;85(8):1422-1434. doi: 10.1002/prot.25302. Epub 2017 Apr 27.

PMID:
28383162
3.

Knowledge-based entropies improve the identification of native protein structures.

Sankar K, Jia K, Jernigan RL.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2928-2933. doi: 10.1073/pnas.1613331114. Epub 2017 Mar 6.

4.

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information.

Kandoi G, Leelananda SP, Jernigan RL, Sen TZ.

Methods Mol Biol. 2017;1484:35-44. doi: 10.1007/978-1-4939-6406-2_4.

PMID:
27787818
5.

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape.

Manibog K, Sankar K, Kim SA, Zhang Y, Jernigan RL, Sivasankar S.

Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):E5711-20. doi: 10.1073/pnas.1604012113. Epub 2016 Sep 12.

6.

Fold-specific sequence scoring improves protein sequence matching.

Leelananda SP, Kloczkowski A, Jernigan RL.

BMC Bioinformatics. 2016 Aug 30;17(1):328. doi: 10.1186/s12859-016-1198-z.

7.

Predicting Designability of Small Proteins from Graph Features of Contact Maps.

Leelananda SP, Jernigan RL, Kloczkowski A.

J Comput Biol. 2016 May;23(5):400-11. doi: 10.1089/cmb.2015.0209.

8.

Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.

Chopra N, Wales TE, Joseph RE, Boyken SE, Engen JR, Jernigan RL, Andreotti AH.

PLoS Comput Biol. 2016 Mar 24;12(3):e1004826. doi: 10.1371/journal.pcbi.1004826. eCollection 2016 Mar.

9.

Distributions of experimental protein structures on coarse-grained free energy landscapes.

Sankar K, Liu J, Wang Y, Jernigan RL.

J Chem Phys. 2015 Dec 28;143(24):243153. doi: 10.1063/1.4937940.

10.

Ribosome Mechanics Informs about Mechanism.

Zimmermann MT, Jia K, Jernigan RL.

J Mol Biol. 2016 Feb 27;428(5 Pt A):802-810. doi: 10.1016/j.jmb.2015.12.003. Epub 2015 Dec 11. Review.

11.

Clusters of Structurally Similar MHC I HLA-A2 Molecules, Found with a New Method, Suggest Mechanisms of T-Cell Receptor Avidity.

Rashin AA, Jernigan RL.

Biochemistry. 2016 Jan 12;55(1):167-85. doi: 10.1021/acs.biochem.5b01077. Epub 2015 Dec 21.

PMID:
26600404
12.

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

Na H, Jernigan RL, Song G.

PLoS Comput Biol. 2015 Oct 16;11(10):e1004542. doi: 10.1371/journal.pcbi.1004542. eCollection 2015 Oct.

13.

ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli.

Jiang F, An C, Bao Y, Zhao X, Jernigan RL, Lithio A, Nettleton D, Li L, Wurtele ES, Nolan LK, Lu C, Li G.

Infect Immun. 2015 Sep;83(9):3545-54. doi: 10.1128/IAI.00312-15. Epub 2015 Jun 22.

14.

Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.

Katebi AR, Jernigan RL.

Biochemistry. 2015 Jun 9;54(22):3543-54. doi: 10.1021/acs.biochem.5b00042. Epub 2015 May 27.

PMID:
25982518
15.

The use of experimental structures to model protein dynamics.

Katebi AR, Sankar K, Jia K, Jernigan RL.

Methods Mol Biol. 2015;1215:213-36. doi: 10.1007/978-1-4939-1465-4_10.

16.

A conserved isoleucine maintains the inactive state of Bruton's tyrosine kinase.

Boyken SE, Chopra N, Xie Q, Joseph RE, Wales TE, Fulton DB, Engen JR, Jernigan RL, Andreotti AH.

J Mol Biol. 2014 Oct 23;426(21):3656-69. doi: 10.1016/j.jmb.2014.08.018. Epub 2014 Sep 2.

17.

Elastic network models capture the motions apparent within ensembles of RNA structures.

Zimmermann MT, Jernigan RL.

RNA. 2014 Jun;20(6):792-804. doi: 10.1261/rna.041269.113. Epub 2014 Apr 23.

18.

Factors correlating with significant differences between X-ray structures of myoglobin.

Rashin AA, Domagalski MJ, Zimmermann MT, Minor W, Chruszcz M, Jernigan RL.

Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):481-91. doi: 10.1107/S1399004713028812. Epub 2014 Jan 29.

19.

The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality.

Katebi AR, Jernigan RL.

Protein Sci. 2014 Feb;23(2):213-28. doi: 10.1002/pro.2407. Epub 2013 Dec 31.

20.

Computational and experimental characterization of RNA cubic nanoscaffolds.

Afonin KA, Kasprzak W, Bindewald E, Puppala PS, Diehl AR, Hall KT, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA.

Methods. 2014 May 15;67(2):256-65. doi: 10.1016/j.ymeth.2013.10.013. Epub 2013 Nov 1.

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