Collaboratory for Structural Nanobiology
In collaboration with the Imaging and Visualization Group, the SAMM Group is developing a computational methods to study the electronic properties of proteins and nanomaterial through The Collaboratory for Structural Nanobiology.
|Contact Information:||Dr. Igor Topol (301)846-1989
Dr. Raul Cachau (301)846-6062
Quantum Mechanical Modeling of Proteins
New semi-empirical quantum mechanical techniques can be used to model the electronic properties of proteins.
Drug design / Ultra-high resolution structure analysis
Protonation, tautomerism and multiple error sources, including limitations in current analysis methods, conspire against the full knowledge of the conformation of molecules bound to biological targets. New procedures, combining the prowess of ultra-high resolution and ab-initio quantum mechanical methods may soon overcome these limitations and offer a new, quantitated view of the ligand binding process.
In collaboration with Dr. Marc C. Nicklaus, Head, Computer-Aided Drug Design (CADD) Group, CCR, we are performing the analysis and interpretation of strutural data at ultra-high resolution using custom tools. In particular, we are examining isoamide bonds / protein backbones and Ras inhibitors. This involves the exploration of the adaptation of QM codes to the study of electron densities at ultra-high resolution.
Protein nanocarriers modelling and 3D reconstruction
There is a pressing need to develop new methods for the characterization of unaltered (i.e. not unstained) soft nanomaterials. Low voltage EM offers an alternative method to achieve this goal. The image processing algorithms for EM are, however, adapted to the high energy regime. We are in the process of developing new methods to produce statistical analysis of soft nanoparticles size and shape distribution and 3D reconstruction using LVEM. We are planning to use LVEM data to obtain a 3D reconstruction of soft nanoparticles and apply detailed modelling tools to study the assembling mechanism.
This project is in its initial phase and is in collaboration with Dr. Nadya I. Tarasova, Cancer and Inflammation Program, Head, Synthetic Biologics Core, CCR.