Computational

Computational modeling and simulation

Increasing computational power is revolutionizing biology on all levels, not only by providing the means for analysis of new Big Data, but also through allowing virtual representation of biological molecules and systems. Modeling of protein structures and assemblies provides major insights into their dynamics and function, leading to better understanding of the molecular basis of disease and a means to design improved therapeutics.

IBBR maintains in-house HPC cluster with 10Gbit interconnectivity, hundreds of terabytes of file storage and on-demand expansion into the Amazon cloud which provides nearly limitless computing power. The cluster also maintains a front end set of visualization nodes running high end graphics capabilities for rendering and modeling macromolecular interactions.

  • Protein structure prediction. Modeling of protein three dimensional structure from amino acid sequence, molecular dynamics and other techniques to study molecular motion.
  • Protein structure-function modeling. IBBR researchers are developing methods to identify the effect of genetic variation on protein function and hence human disease. This includes analysis of the impact of genetic variants on protein function in rare Mendelian disease, in cancer, and in complex traits such as Crohn’s disease.
  • Modeling immune recognition. Immune recognition by antibodies and T cell receptors, highly important to biotherapeutics, vaccines, and disease research, is being actively explored. New algorithms are being developed to predict structures of TCRs and predict complexes of antibodies and TCRs with antigens.
  • Computational protein design. Vaccines and biotherapeutics are being engineered using computational structure-based design, allowing for alterations in stability, affinity, and binding specificity.

Software and database development

NMRPipe is a widely used and free software package for NMR data processing. The software is developed by Dr. Frank Delaglio and has been cited nearly 9,000 times in scientific journals. At the IBBR, Dr. Delaglio continues work to develop computational methods, software solutions, and scientific guidance to increase the effectiveness and applicability of NMR-based structural biology, drug discovery, and quality assurance of vaccines and biologic therapeutics.

The NMRPipe website hosted by IBBR is available at http://nmrpipe.org

Several other notable software projects being developed by IBBR computational biologists include: