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Simulation-Enabled Estimation of Kinetic Rates (SEEKR): a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory.
lvotapka/seekr
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########################################## ### ###### ###### ### ### ##### ##### ## # ## # ## # ## # ## ## ## ## # ## # ## #### #### ### ## # ## ## ## ### ##### ##### ## # ## # ## # ## # ### ###### ###### ### ## ### # ########################################## ####### # # ### ## ######### ## ### # # ####### SEEKR: Simulation-Enabled Estimation of Kinetic Rates Introduction ------------ SEEKR (http:https://amarolab.ucsd.edu/seekr/) is a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. Instructions ------------ SEEKR is designed to be run on Linux. Obtain SEEKR by cloning the Git repository on github git clone https://github.com/lvotapka/seekr.git Or, go to the URL https://github.com/lvotapka/seekr and click the "Clone or download" button and save to a place in your computer. From there, open seekr/doc/manual.txt to get started. Files ----- This is a description of the folders in the base seekr/ directory. doc/ - Find detailed information about the installation, usage, tutorials, and troubleshooting of SEEKR in this folder test/ - Most of the tests in SEEKR are integrated directly into the scripts, but some tests are run externally, and are included in this directory. tools/ - A number of non-essential scripts are included in this directory that may be useful for calculations, preparations, and analysis. website/ - a full copy of the SEEKR website Getting Help ------------ Need help? Check out the documentation at http:https://amarolab.ucsd.edu/seekr/ or that is located in seekr/doc/manual.txt Also, you can make comments, submit issues, and talk to real people at the Github site: http:https://github.com/lvotapka/seekr
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Simulation-Enabled Estimation of Kinetic Rates (SEEKR): a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory.
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