Lane Votapka

Title(s)	Sr Bioinfo Analyst, Molecular Biology
School	Vc-academic Affairs
Address	9500 Gilman Drive # La Jolla CA 92093
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Bibliographic

selected publications

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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Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics. J Chem Theory Comput. 2024 Nov 26; 20(22):9759-9769. Ojha AA, Votapka LW, Amaro RE. PMID: 39508322; PMCID: PMC11603602.

View in: PubMed Mentions: 1 Fields:
Bio Biochemistry Che Chemistry
Translation:Humans Cells
Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics. J Phys Chem Lett. 2024 Oct 24; 15(42):10473-10478. Votapka LW, Ojha AA, Asada N, Amaro RE. PMID: 39392497; PMCID: PMC11514002.

View in: PubMed Mentions: 2 Fields:
Che Chemistry
Translation:Cells
NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. J Chem Inf Model. 2024 Oct 28; 64(20):7966-7976. Stokely AM, Votapka LW, Hock MT, Teitgen AE, McCammon JA, McCulloch AD, Amaro RE. PMID: 39364881; PMCID: PMC12039534.

View in: PubMed Mentions: Fields:
Che Chemistry Med Medical Informatics
Translation:Cells
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: 4
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: 19
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: 9 Fields:
Che Chemistry Med Medical Informatics
Translation:Cells
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; PMCID: PMC9773147.

View in: PubMed Mentions: 5 Fields:
Che Chemistry
Translation:Cells
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: 15 Fields:
Che Chemistry Med Medical Informatics
Translation:Cells
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: 13
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: 35 Fields:
Che Chemistry
Translation:Cells
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: 22 Fields:
Che Chemistry
Translation:Cells
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: 33 Fields:
Com Computational Biology
Translation:Cells
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
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: 105 Fields:
Bio Biochemistry Che Chemistry
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: 60 Fields:
Bio Biochemistry Che Chemistry
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: 9 Fields:
Com Computational Biology
Translation:Cells
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
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: 54 Fields:
Bio Biology Sci Science
Translation:Cells