Pawel A. Penczek, PhD

Areas of Interest

Research Interests

Research Information

Structural determination of proteins and molecular assemblies

We are interested in the determination of three-dimensional structures of large macromolecular complexes with low or non-existing symmetry in single-particle form using stain and cryo-electron microscopy (cryo-EM), and computer image processing techniques.

Unconstrained by crystal packing, the molecule in a single particle specimen can be thought to exhibit the entire range of native conformations. The ability to find the structure of each conformer is one of the most important potential assets of 3D cryo-EM of single particles. On the other hand, the realization of high resolution for each of these conformers poses daunting problems of data collection and processing, considering the statistical requirements stated before. Therefore, we are also interested in the development of efficient and robust computational methods of structure refinement and structure validation in the presence of multiple conformational or binding states.

We develop, in collaboration with other groups, a single particle software package SPARX (Hohn, et al). SPARX is provided free of charge as a service to the scientific community and its main features include:

1. SPARX is supported by a Wiki-based interactive documentation.
2. New generation of 2D and 3D alignment protocols.
3. Abinitiostructure determination programs.
4. Advanced code for multivariate statistical analysis (PCA, Varimax)
5. Extensive C++ library of general and EM_specific image operations with Python bindings, thus accessible to Python programmers.
6. All structure determination applications written as user transparent Python scripts.

Selected Publications:
Hattne, J., Martynowycz, M.W., Penczek,
P.A. & Gonen, T., 2016. MicroED with the Falcon III direct electron detector. IUCrJ, 6:921-926.