Machine Learning-assisted Lipid Phase Analysis (MLLPA) is a new Python 3 module developed to analyze phase domains in lipid membrane based on molecular states. Reading standard simulation coordinate and trajectory files, the software first composition of by using machine learning tools label each individual molecules with respect their state, then decompose box Voronoi tessellations local envir...

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation o...

This work aims to explore theoretically the molecular mechanisms of ligand binding to proteins through the use of molecular dynamics simulations. The binding of sodium dodecyl sulfate (SDS) to cobra cardio toxin A3 (CTX A3) and thiourea (TOU) to lysozyme have been chosen as the two model systems. Data acquisitions were made by Gromacs software. To begin with, the collisions of ligand molecules ...