Collaborative Molecular Modeling

Molecular modeling is an essential part of modern biology, pharmacy, materials science, and a variety of further disciplines. One of the most important tasks in molecular modeling is the faithful and intuitive visualization of three-dimensional molecular structures and their properties, and the interaction with and simulation of the displayed molecular entities. Today, molecular modeling is usually performed in large interdisciplinary teams that are often spread out over the globe.

Existing tools and applications are today inherently single-user, with limited – or usually no – support for collaborative workflows. This Intel VCI project investigates ways to assist drug designers with modern rendering techniques by greatly improved visual perception of three-dimensional molecular properties, and with 3D-internet and collaboration techniques by unlocking the potential of interdisciplinary, virtual cooperation.

We build on three areas of previous and ongoing research:

  • Extend the BALL and BALLView for collaborative use: accommodate concurrent read and edit access by multiple users and enable the synchronized viewing and editing of molecular scenes in multiple BALLView instances, with Web-based users contributing edits, comments or annotations concurrently.
  • Renderer extension and update protocols: the project uses the XML3D approach to fully integrate 3D molecular objects into the Web browser DOM, and XML3D’s integration of advanced renderers into common Web browsers from the same project. We investigate how to support the rendering of dynamic geometries that are generated or modified on-the-fly in this framework, guaranteeing optimal build and run time performance for each case and platform. A second area of work is the definition of efficient update protocols – the molecular objects and their annotations are frequently changing, and updates have to be sent to all parties participating in a session. Techniques from virtual worlds or MMORG might be applicable here.
  • Distributed information integration and conflict resolution: significant topics here are ensuring data confidentiality and security, for which approaches from Grid/Cloud research will be investigated, and the management and reconciliation of conflicting edits to the shared structural or annotation data. A second line of work will exploit the potential of combining knowledge gained from BALL/BALLView or Web services with the three-dimensional geometries transported via XML3D. We plan to integrate sequence and structural annotation on a semantic level with a focus on two use-cases: GPCR coupling and nuclear receptors.


Project team

Principal Investigator
Prof. Dr. Andreas Hildebrandt

Researcher
Stefan Nickels, M.Sc.