Lane Votapka

Title(s)Sr Bioinfo Analyst, Division of Biological Science
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci. 2023 Nov 22; 14(45):13159-13175. Ojha AA, Votapka LW, Amaro RE. PMID: 38023523; PMCID: PMC10664576.
      View in: PubMed   Mentions:
    2. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. Cell Rep Phys Sci. 2023 Apr 19; 4(4):101346. Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. PMID: 37077408; PMCID: PMC10080732.
      View in: PubMed   Mentions: 4  
    3. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J Chem Inf Model. 2023 04 24; 63(8):2469-2482. Ojha AA, Srivastava A, Votapka LW, Amaro RE. PMID: 37023323; PMCID: PMC10131228.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    4. Gaussian Accelerated Molecular Dynamics in OpenMM. J Phys Chem B. 2022 08 11; 126(31):5810-5820. Copeland MM, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. PMID: 35895977.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    5. SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J Chem Inf Model. 2022 07 11; 62(13):3253-3262. Votapka LW, Stokely AM, Ojha AA, Amaro RE. PMID: 35759413; PMCID: PMC9277580.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    6. A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. ACS Cent Sci. 2018 Nov 28; 4(11):1570-1577. Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW. PMID: 30555910; PMCID: PMC6276040.
      View in: PubMed   Mentions: 14  
    7. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. J Phys Chem B. 2017 04 20; 121(15):3597-3606. Votapka LW, Jagger BR, Heyneman AL, Amaro RE. PMID: 28191969; PMCID: PMC5562489.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    8. Two Relations to Estimate Membrane Permeability Using Milestoning. J Phys Chem B. 2016 08 25; 120(33):8606-16. Votapka LW, Lee CT, Amaro RE. PMID: 27154639; PMCID: PMC5002937.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    9. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput Biol. 2015 Oct; 11(10):e1004381. Votapka LW, Amaro RE. PMID: 26505480; PMCID: PMC4624728.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    10. Bridging scales through multiscale modeling: a case study on protein kinase A. Front Physiol. 2015; 6:250. Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD. PMID: 26441670; PMCID: PMC4563169.
      View in: PubMed   Mentions: 10  
    11. POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics. J Chem Theory Comput. 2014 Nov 11; 10(11):5047-5056. Durrant JD, Votapka L, Sørensen J, Amaro RE. PMID: 25400521; PMCID: PMC4230373.
      View in: PubMed   Mentions: 103     Fields:    
    12. Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. J Chem Theory Comput. 2014 Feb 11; 10(2):511-517. Van Wart AT, Durrant J, Votapka L, Amaro RE. PMID: 24803851; PMCID: PMC3958135.
      View in: PubMed   Mentions: 61     Fields:    
    13. Multistructural hot spot characterization with FTProd. Bioinformatics. 2013 Feb 01; 29(3):393-4. Votapka L, Amaro RE. PMID: 23202744; PMCID: PMC3562065.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    14. Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase. J Mol Genet Med. 2012; 6:293-300. Votapka L, Demir O, Swift RV, Walker RC, Amaro RE. PMID: 22872804; PMCID: PMC3410406.
      View in: PubMed   Mentions: 2  
    15. Mechanism of 150-cavity formation in influenza neuraminidase. Nat Commun. 2011 Jul 12; 2:388. Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM. PMID: 21750542; PMCID: PMC3144582.
      View in: PubMed   Mentions: 57     Fields:    Translation:Cells
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