Votapka LW - Search Results

1

Bridging scales through multiscale modeling: a case study on protein kinase A.

Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD. Boras BW, et al. Among authors: votapka lw. Front Physiol. 2015 Sep 9;6:250. doi: 10.3389/fphys.2015.00250. eCollection 2015. Front Physiol. 2015. PMID: 26441670 Free PMC article. Review.

2

Mechanism of 150-cavity formation in influenza neuraminidase.

Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. Amaro RE, et al. Nat Commun. 2011 Jul 12;2:388. doi: 10.1038/ncomms1390. Nat Commun. 2011. PMID: 21750542 Free PMC article.

3

Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase.

Votapka L, Demir O, Swift RV, Walker RC, Amaro RE. Votapka L, et al. J Mol Genet Med. 2012;6:293-300. doi: 10.4172/1747-0862.1000052. Epub 2012 May 25. J Mol Genet Med. 2012. PMID: 22872804 Free PMC article.

4

Multistructural hot spot characterization with FTProd.

Votapka L, Amaro RE. Votapka L, et al. Bioinformatics. 2013 Feb 1;29(3):393-4. doi: 10.1093/bioinformatics/bts689. Epub 2012 Nov 29. Bioinformatics. 2013. PMID: 23202744 Free PMC article.

5

Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis.

Van Wart AT, Durrant J, Votapka L, Amaro RE. Van Wart AT, et al. J Chem Theory Comput. 2014 Feb 11;10(2):511-517. doi: 10.1021/ct4008603. Epub 2014 Jan 14. J Chem Theory Comput. 2014. PMID: 24803851 Free PMC article.

6

POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.

Durrant JD, Votapka L, Sørensen J, Amaro RE. Durrant JD, et al. J Chem Theory Comput. 2014 Nov 11;10(11):5047-5056. doi: 10.1021/ct500381c. Epub 2014 Sep 29. J Chem Theory Comput. 2014. PMID: 25400521 Free PMC article.

7

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.

Votapka LW, Amaro RE. Votapka LW, et al. PLoS Comput Biol. 2015 Oct 27;11(10):e1004381. doi: 10.1371/journal.pcbi.1004381. eCollection 2015 Oct. PLoS Comput Biol. 2015. PMID: 26505480 Free PMC article.

8

Two Relations to Estimate Membrane Permeability Using Milestoning.

Votapka LW, Lee CT, Amaro RE. Votapka LW, et al. J Phys Chem B. 2016 Aug 25;120(33):8606-16. doi: 10.1021/acs.jpcb.6b02814. Epub 2016 May 27. J Phys Chem B. 2016. PMID: 27154639 Free PMC article.

9

SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

Votapka LW, Jagger BR, Heyneman AL, Amaro RE. Votapka LW, et al. J Phys Chem B. 2017 Apr 20;121(15):3597-3606. doi: 10.1021/acs.jpcb.6b09388. Epub 2017 Mar 3. J Phys Chem B. 2017. PMID: 28191969 Free PMC article.

10

A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target.

Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW. Amaro RE, et al. Among authors: votapka lw. ACS Cent Sci. 2018 Nov 28;4(11):1570-1577. doi: 10.1021/acscentsci.8b00666. Epub 2018 Nov 9. ACS Cent Sci. 2018. PMID: 30555910 Free PMC article.

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