ATPase is computer program for simulation actin.myosin ATPase cycle. The rate kinetic process for the ATP cycle can be described as a system of linear equations that define the rate of change in state concentration as a function of the instantaneous fluxes between the states. The mathematical descriptions of models are described in Mijailovich et al., 2017.
Thin filament regulation V320 is computer program package for simulation of stopped flow and titration experiment of myosin binding to regulated actin. The package includes McKillop Geeves (McK–G) three-state model and the Hill two-state cooperative model. The mathematical descriptions of models are described in Mijailovich et al., 2012. The models include three parameter estimation schemes for the estimation of model parameters (see Mijailovich et al., 2010) from traces of stopped-flow pyrene fluorescence transients of myosin-S1 fragment binding to regulated actin in solution titration experiments.
Also the package includes the complete actin.myosin ATPase cycle, and estimation parameters for that model. The descriptions of modeling the Actin.myosin ATPase Cross-Bridge Cycle for Skeletal and Cardiac Muscle Myosin Isoforms are described in Mijailovich et al., 2017.
You can run the program for various parameters estimation of ATPase model.
Presentation of results is currently not supported. Contents of files:
a_t.txt - experiment
kkk.dat - values of the estimated parameters
eee.dat - error match with an experiment
param_est.dat - sensitivity matrix
The components of the software include probabilistic (nonlinear ordinary differential equations (ODEs) and stochastic algorithms for both McK-G and Hill model. For model parameter estimation the package includes three methods namely quasi-Newton (QN), simulated annealing (SA) and Damped Least Squares (DLS) inversion method.
All of the code is freely available under the GNU General Public License.
Program Thin filament v320 contains few programs you can run:
Param. est. - MG Pro DLS
Param. Est. - MG Sto DLS
Param. Est. - HILL Sto DLS
Param. Est. - ATPase DLS
Parameter Optimization - SIMMAN
Parameter Optimization - Quasi-Newton
To start program, just unzip download and open file Thin_Filament_Regulation.exe. Three examples data are stored in example 1, example 2, and example 3.
Wemus is a web application for running MUSICO software. For limited use of this application, only Internet connection and Google Chrome are required. This application provides interface with MUSICO simulation platform and includes input of model parameters. After the calculations are completed, output data can be reviewed graphically or/and downloaded in text or graphic format.
For informative use and small size simulationsonly registration is required and login will be provided. Because the large simulations require significant computational resources (large cluster computers or super computers) and extensive computational time, a collaborative agreement needs to be arranged for such MUSICO users.
Instructions with example input for Musico simulation you can find here.
If you have problems with aplications, please contact us.