Ramanathan A - Search Results

1

Quasi-anharmonic analysis reveals intermediate states in the nuclear co-activator receptor binding domain ensemble.

Burger VM, Ramanathan A, Savol AJ, Stanley CB, Agarwal PK, Chennubhotla CS. Burger VM, et al. Among authors: ramanathan a. Pac Symp Biocomput. 2012:70-81. Pac Symp Biocomput. 2012. PMID: 22174264 Free PMC article.

2

Computational identification of slow conformational fluctuations in proteins.

Ramanathan A, Agarwal PK. Ramanathan A, et al. J Phys Chem B. 2009 Dec 31;113(52):16669-80. doi: 10.1021/jp9077213. J Phys Chem B. 2009. PMID: 19908896 Free PMC article.

3

An online approach for mining collective behaviors from molecular dynamics simulations.

Ramanathan A, Agarwal PK, Kurnikova M, Langmead CJ. Ramanathan A, et al. J Comput Biol. 2010 Mar;17(3):309-24. doi: 10.1089/cmb.2009.0167. J Comput Biol. 2010. PMID: 20377447

4

Discovering conformational sub-states relevant to protein function.

Ramanathan A, Savol AJ, Langmead CJ, Agarwal PK, Chennubhotla CS. Ramanathan A, et al. PLoS One. 2011 Jan 28;6(1):e15827. doi: 10.1371/journal.pone.0015827. PLoS One. 2011. PMID: 21297978 Free PMC article.

5

QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin.

Savol AJ, Burger VM, Agarwal PK, Ramanathan A, Chennubhotla CS. Savol AJ, et al. Among authors: ramanathan a. Bioinformatics. 2011 Jul 1;27(13):i52-60. doi: 10.1093/bioinformatics/btr248. Bioinformatics. 2011. PMID: 21685101 Free PMC article.

6

Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis.

Ramanathan A, Agarwal PK. Ramanathan A, et al. PLoS Biol. 2011 Nov;9(11):e1001193. doi: 10.1371/journal.pbio.1001193. Epub 2011 Nov 8. PLoS Biol. 2011. PMID: 22087074 Free PMC article.

7

Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase.

Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS. Ramanathan A, et al. Proteins. 2012 Nov;80(11):2536-51. doi: 10.1002/prot.24135. Epub 2012 Aug 8. Proteins. 2012. PMID: 22733562 Free PMC article.

Because post-simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are …

Because post-simulation analyses of such large trajectory datasets can be a limiting factor in obtaining biological insights, there i …

8

Protein conformational populations and functionally relevant substates.

Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Ramanathan A, et al. Acc Chem Res. 2014 Jan 21;47(1):149-56. doi: 10.1021/ar400084s. Epub 2013 Aug 29. Acc Chem Res. 2014. PMID: 23988159 Review.

9

Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization.

Castro JB, Ramanathan A, Chennubhotla CS. Castro JB, et al. Among authors: ramanathan a. PLoS One. 2013 Sep 18;8(9):e73289. doi: 10.1371/journal.pone.0073289. eCollection 2013. PLoS One. 2013. PMID: 24058466 Free PMC article.

10

Discovering Multi-Scale Co-Occurrence Patterns of Asthma and Influenza with Oak Ridge Bio-Surveillance Toolkit.

Ramanathan A, Pullum LL, Hobson TC, Stahl CG, Steed CA, Quinn SP, Chennubhotla CS, Valkova S. Ramanathan A, et al. Front Public Health. 2015 Aug 3;3:182. doi: 10.3389/fpubh.2015.00182. eCollection 2015. Front Public Health. 2015. PMID: 26284230 Free PMC article.

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