Citations ========= On this page, you will find a list of BibTex format citations for easy citing. Main SEEKR2 Paper ----------------- If you wish to cite SEEKR2, please cite the following paper:: @article{votapka2022seekr2, title={SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine}, author={Votapka, Lane W and Stokely, Andrew M and Ojha, Anupam A and Amaro, Rommie E}, journal={Journal of chemical information and modeling}, volume={62}, number={13}, pages={3253--3262}, year={2022}, publisher={ACS Publications} } Dependencies ------------ One should also cite SEEKR2's dependencies:: @Article{Hunter:2007, Author = {Hunter, J. D.}, Title = {Matplotlib: A 2D graphics environment}, Journal = {Computing in Science \& Engineering}, Volume = {9}, Number = {3}, Pages = {90--95}, abstract = {Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.}, publisher = {IEEE COMPUTER SOC}, doi = {10.1109/MCSE.2007.55}, year = 2007 } @article{van2011numpy, title={The NumPy array: a structure for efficient numerical computation}, author={Van Der Walt, Stefan and Colbert, S Chris and Varoquaux, Gael}, journal={Computing in Science \& Engineering}, volume={13}, number={2}, pages={22--30}, year={2011}, publisher={AIP Publishing}, doi={10.1109/MCSE.2011.37} } @Misc{JOP+01, author = {Eric Jones and Travis Oliphant and Pearu Peterson and others}, title = {{SciPy}: Open source scientific tools for {Python}}, year = {2001--}, url = "http://www.scipy.org/", note = {[Online; accessed 2015-07-13]} } @article{doi:10.1021/acs.jctc.9b01211, author = {Swinburne, Thomas D. and Wales, David J.}, title = {Defining, Calculating, and Converging Observables of a Kinetic Transition Network}, journal = {Journal of Chemical Theory and Computation}, volume = {16}, number = {4}, pages = {2661-2679}, year = {2020}, doi = {10.1021/acs.jctc.9b01211}, note ={PMID: 32155072}, } Other SEEKR Papers ------------------ One may also optionally cite one or more of the following papers:: @article{ojha2023qmrebind, title={QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations}, author={Ojha, Anupam Anand and Votapka, Lane William and Amaro, Rommie Elizabeth}, journal={Chemical Science}, volume={14}, number={45}, pages={13159--13175}, year={2023}, publisher={Royal Society of Chemistry} } @article{doi:10.1021/acs.jcim.2c01589, author = {Ojha, Anupam Anand and Srivastava, Ambuj and Votapka, Lane William and Amaro, Rommie E.}, title = {Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations}, journal = {Journal of Chemical Information and Modeling}, volume = {63}, number = {8}, pages = {2469-2482}, year = {2023}, doi = {10.1021/acs.jcim.2c01589}, note ={PMID: 37023323} } @article{votapka2017seekr, title={SEEKR: simulation enabled estimation of kinetic rates, a computational tool to estimate molecular kinetics and its application to trypsin--benzamidine binding}, author={Votapka, Lane W and Jagger, Benjamin R and Heyneman, Alexandra L and Amaro, Rommie E}, journal={The Journal of Physical Chemistry B}, volume={121}, number={15}, pages={3597--3606}, year={2017}, publisher={ACS Publications} } @article{jagger2020predicting, title={Predicting ligand binding kinetics using a Markovian milestoning with voronoi tessellations multiscale approach}, author={Jagger, Benjamin R and Ojha, Anupam A and Amaro, Rommie E}, journal={Journal of Chemical Theory and Computation}, volume={16}, number={8}, pages={5348--5357}, year={2020}, publisher={ACS Publications} } @article{doi:10.1021/acs.jpclett.8b02047, author = {Jagger, Benjamin R. and Lee, Christopher T. and Amaro, Rommie E.}, title = {Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach}, journal = {The Journal of Physical Chemistry Letters}, volume = {9}, number = {17}, pages = {4941-4948}, year = {2018}, doi = {10.1021/acs.jpclett.8b02047}, note ={PMID: 30070844}, } @article{10.1371/journal.pcbi.1004381, doi = {10.1371/journal.pcbi.1004381}, author = {Votapka, Lane W. AND Amaro, Rommie E.}, journal = {PLOS Computational Biology}, publisher = {Public Library of Science}, title = {Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning}, year = {2015}, month = {10}, volume = {11}, url = {https://doi.org/10.1371/journal.pcbi.1004381}, pages = {1-24}, abstract = {The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2−, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.}, number = {10}, }