Agarwal PK - Search Results

1

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: agarwal pk. Bioinformatics. 2011 Jul 1;27(13):i52-60. doi: 10.1093/bioinformatics/btr248. Bioinformatics. 2011. PMID: 21685101 Free PMC article.

2

Computational identification of slow conformational fluctuations in proteins.

Ramanathan A, Agarwal PK. Ramanathan A, et al. Among authors: agarwal pk. 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

Discovering conformational sub-states relevant to protein function.

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

4

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: agarwal pk. Pac Symp Biocomput. 2012:70-81. Pac Symp Biocomput. 2012. PMID: 22174264 Free PMC article.

5

Conformational Sub-states and Populations in Enzyme Catalysis.

Agarwal PK, Doucet N, Chennubhotla C, Ramanathan A, Narayanan C. Agarwal PK, et al. Methods Enzymol. 2016;578:273-97. doi: 10.1016/bs.mie.2016.05.023. Epub 2016 Jul 9. Methods Enzymol. 2016. PMID: 27497171 Free PMC article. Review.

6

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. Among authors: agarwal pk. Proteins. 2012 Nov;80(11):2536-51. doi: 10.1002/prot.24135. Epub 2012 Aug 8. Proteins. 2012. PMID: 22733562 Free PMC article.

7

Protein conformational populations and functionally relevant substates.

Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Ramanathan A, et al. Among authors: agarwal pk. 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.

8

Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily.

Narayanan C, Bernard DN, Bafna K, Gagné D, Chennubhotla CS, Doucet N, Agarwal PK. Narayanan C, et al. Among authors: agarwal pk. Structure. 2018 Mar 6;26(3):426-436.e3. doi: 10.1016/j.str.2018.01.015. Epub 2018 Feb 22. Structure. 2018. PMID: 29478822 Free PMC article.

9

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

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

10

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

Ramanathan A, Agarwal PK. Ramanathan A, et al. Among authors: agarwal pk. 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.

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