Principal component analysis is a standard approach to study conformational changes in biological molecules, in particular when the free energy lanscape has only one global minima. PCAlipids is a Python-based software that performs complete quantitative analysis of conformations and dynamics of lipids or other small molecules. The information about the approach can be found in the following papers:
- Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids, Buslaev, Mustafin & Gushchin, BBA-Biomem. 2020
- Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules, Buslaev & Gushchin, Sci. Rep. 2017
- Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations, Buslaev et al., JCTC 2016
You can find the information on installation and a brief tutorial here.
If you have any questions about using the PCALipids, please contact:
- Khalid Mustafin - developer of PCAlipids; code-related questions
- Pavel Buslaev - [email protected] applying PCAlipids, developer of PCAlipids
- Ivan Gushchin - [email protected] general questions & supervision