Why ProLint?

Role and purpose of the web server

ProLint is a complete webserver that takes input data, analyses the underlying interaction and visualizes the results, without requiring any input from the user. ProLint is also a webservice in that it can store results and allow users world-wide to interact with the data regardless of their knowledge of Molecular Dynamics (MD) Simulations or coding experience. Hosting and sharing of data files is done free of charge. Finally, ProLint serves as a stand-alone program. It is easy to install and set up and the code will be made freely available on GitHub. Interested users can download the code and use the webserver locally.

ProLint as a webserver and webservice has four core objectives. These are listed below and explained in more detail in the following sections.

  1. -  Powerful and customizable analysis of protein-lipid contacts
  2. -  Modern and beautiful visualization
  3. -  Data sharing and accessibility
  4. -  Automation of protein-lipid contact generation

Powerful and customizable analysis of protein-lipid contacts

Currently, the time it takes to analyze and interpret data usually exceeds the time to set up and perform MD Simulations. Add to this the continuing trend of increased system sizes, simulated for longer time scales and the need for a much bigger set of proteins, it becomes clear how analysis and visualization of protein-lipid contacts can become a significant bottleneck. It is worth noting here that the challenge is not large files in itself (i.e. the raw size of output files) as these can be usually trimmed down quite significantly without losing much information. Rather the challenge lies in the increasing complexity of the interaction networks involved in simulating more and more compositionally compolex systems. ProLint aims to bridge this gap between data generation and obtaining important insight on what is happening in the simulation.

Modern and beautiful visualization to gain quick insight

ProLint provides a fully-fledged visualization library that quickly and effortlessly displays protein-lipid interactions. It uses modern visualization libraries like Bokeh , D3.js , NGL Viewer , and Three.js in the background. The set of visualization applications that are supported by ProLint are distinct in the sense that each one offers a different insight into the calculated interaction network between lipids and proteins.

Data sharing and accessibility

Scientific journals usually have rigid restrictions on the number and type of graphical elements allowed and researchers must try to limit themselves to only what they believe to be the most relevant details of their work. This leads to an inefficient and incomplete presentation of the experiments and/or simulations performed and unintentional bias in only presenting positive and confirming results. Obtaining the original data that was used in published works is also a significant challenge. ProLint allows for contact information to be extracted from simulated systems and stored in small files that can be easily downloaded and shared and made publicly available.

Automation of protein-lipid contact generation

Following the trend in lipid-protein interactions, it is clear that it will become increasingly important to automate the generation of protein-lipid contacts for any arbitrary protein. Such tools will allow us to study how membrane proteins interact with their lipid environment and elucidate the importance of lipids in regulating and/or modulating the activity of embedded membrane proteins. Developing such automation protocols is an essential step in creating lipid-protein interaction databases - which will be the next major step in the field. ProLint is a perfectly suited tool that can be used as part of such automation pipelines.