ABI Sustaining: Maintaining CHARMM-GUI to Support the Biomolecular Modeling and Simulation Community

Lehigh University, Bethlehem PA

Investigators

Abstract

Researchers who study how biomolecules flex or shift shape over time use very sophisticated algorithms as tools to understand different aspects of structure, motion and interaction. These tools are part of larger software applications that capture how the whole system behaves, including atoms and molecules that are in both the environment and the biomolecules. As researchers model larger volumes with more components, over longer study intervals, keeping track of all the elements in the system and their properties is becoming a major hurdle, even for relatively well-experienced computational biologists. The grand challenge is to maintain accuracy and reproducibility while efficiently carrying out these complex simulations in order to solve practical problems. The goal of this project is to assist two classes of researchers: experts who know how to set up the conditions and want to save and share them, and non-experts who need guidance in setting up all of the inputs and perhaps some help with interpreting the results. These challenges have been addressed by CHARMM-GUI, in that users can interactively set up complex biomolecular systems and easily understand what files must be input in order to carry out state-of-the-art biomolecular simulations. The interface is not limited to the CHARMM simulation package, despite the name, but also encompasses GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. This project aims to maintain the unique scope of the CHARMM-GUI interface application while improving the consistency of the code base to make it easier to maintain the tool going forward, and to make it easier to add new functionality that works correctly by including test suites. The project's overarching goal is to help students and researchers carry out innovative and novel biomolecular modeling and simulation research to acquire novel insight into structures, dynamics, and underlying mechanisms for the biomolecular systems of interest through availability of an excellent tool, excellent documentation with tutorials, Webinars and videos, and a user forum. The main objective of this project is to ensure ongoing maintenance for the operation of CHARMM-GUI (http://www.charmm-gui.org), a web-based graphical user interface (GUI). This will require code changes to make it a robust, sustainable web-based cyberinfrastructure that supports both expert and non-expert users from a broad range of disciplines to easily build and simulate complex biological systems. Over the past 10 years, CHARMM-GUI has proven that such a web-based GUI provides an ideal platform to build complex biological systems interactively, and prepare simulation inputs with well-established and reproducible simulation protocols. While the modules in CHARMM-GUI are all functional, similar to most academic software, they have been developed by different students and postdocs, which requires substantial code cleaning and quality control to guarantee CHARMM-GUI's sustainable operations. So, this project will (AIM 1) maintain and Improve CHARMM-GUI and (AIM 2) improve Usability. This project also seeks to foster synergistic scientific research and education by providing a well-maintained, web-based cyberinfrastructure resource to students and researchers in multiple simulation communities for any general biomolecular simulations as well as advanced modeling and simulation.