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Lane Votapka
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Year
POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics
JD Durrant, L Votapka, J S°rensen, RE Amaro
Journal of chemical theory and computation 10 (11), 5047-5056, 2014
2392014
Weighted implementation of suboptimal paths (WISP): an optimized algorithm and tool for dynamical network analysis
AT Van Wart, J Durrant, L Votapka, RE Amaro
Journal of chemical theory and computation 10 (2), 511-517, 2014
1702014
Mechanism of 150-cavity formation in influenza neuraminidase
RE Amaro, RV Swift, L Votapka, WW Li, RC Walker, RM Bush
Nature communications 2 (1), 388, 2011
1492011
SEEKR: simulation enabled estimation of kinetic rates, a computational tool to estimate molecular kinetics and its application to trypsin–benzamidine binding
LW Votapka, BR Jagger, AL Heyneman, RE Amaro
The Journal of Physical Chemistry B 121 (15), 3597-3606, 2017
1002017
Multiscale estimation of binding kinetics using Brownian dynamics, molecular dynamics and milestoning
LW Votapka, RE Amaro
PLoS computational biology 11 (10), e1004381, 2015
722015
Two relations to estimate membrane permeability using milestoning
LW Votapka, CT Lee, RE Amaro
The Journal of Physical Chemistry B 120 (33), 8606-8616, 2016
422016
Bridging scales through multiscale modeling: a case study on protein kinase A
BW Boras, SP Hirakis, LW Votapka, RD Malmstrom, RE Amaro, ...
Frontiers in physiology 6, 250, 2015
272015
A computational assay that explores the hemagglutinin/neuraminidase functional balance reveals the neuraminidase secondary site as a novel anti-influenza target
RE Amaro, PU Ieong, G Huber, A Dommer, AC Steven, RM Bush, ...
ACS central science 4 (11), 1570-1577, 2018
262018
SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine
LW Votapka, AM Stokely, AA Ojha, RE Amaro
Journal of chemical information and modeling 62 (13), 3253-3262, 2022
222022
SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx
SH Kim, FL Kearns, MA Rosenfeld, L Votapka, L Casalino, M Papanikolas, ...
Cell Reports Physical Science 4 (4), 2023
182023
Multistructural hot spot characterization with FTProd
L Votapka, RE Amaro
Bioinformatics 29 (3), 393-394, 2013
182013
Gaussian accelerated molecular dynamics in OpenMM
MM Copeland, HN Do, L Votapka, K Joshi, J Wang, RE Amaro, Y Miao
The Journal of Physical Chemistry B 126 (31), 5810-5820, 2022
112022
Selectivity and ranking of tight-binding JAK-STAT inhibitors using Markovian milestoning with Voronoi tessellations
AA Ojha, A Srivastava, LW Votapka, RE Amaro
Journal of Chemical Information and Modeling 63 (8), 2469-2482, 2023
72023
Positively bound: remapping of increased positive charge drives SARS-CoV-2 spike evolution to optimize its binding to cell surface receptors
SH Kim, FL Kearns, MA Rosenfeld, L Votapka, L Casalino, M Papanikolas, ...
American Chemical Society (ACS), 2022
72022
DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi
LW Votapka, L Czapla, M Zhenirovskyy, RE Amaro
Communications in Computational Physics 13 (1), 256-268, 2013
72013
Brownian dynamics simulations of biomolecular diffusional association processes
A Mu˝iz‐Chicharro, LW Votapka, RE Amaro, RC Wade
Wiley Interdisciplinary Reviews: Computational Molecular Science 13 (3), e1649, 2023
52023
QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations
AA Ojha, LW Votapka, RE Amaro
Chemical Science 14 (45), 13159-13175, 2023
32023
Variable ligand-and receptor-binding hot spots in key strains of influenza neuraminidase
L Votapka, Í Demir, RV Swift, RC Walker, RE Amaro
Journal of Molecular and Genetic Medicine: an International Journal ofá…, 2012
32012
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Multiscale Approach for the Calculation of Protein-Ligand Association and Dissociation Kinetics
BR Jagger, LW Votapka, RE Amaro
Biophysical Journal 114 (3), 42a, 2018
22018
Numerical and Computational Solutions for Biochemical Kinetics, Druggability, and Simulation
LW Votapka
University of California, San Diego, 2016
12016
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Articles 1–20