Comparison of CryoSPARC and RELION in Cryo-EM Single Particle Analysis
Open Access
- Author:
- Amjad, Wajid
- Area of Honors:
- Biochemistry and Molecular Biology
- Degree:
- Bachelor of Science
- Document Type:
- Thesis
- Thesis Supervisors:
- Susan Hafenstein, Thesis Supervisor
Santhosh Girirajan, Thesis Honors Advisor - Keywords:
- Structural virology
Cryo-EM
Cryo-EM Single Particle Analysis
Structural biology
Coxsackievirus B3 (CVB3) - Abstract:
- Since the development of cryo-electron microscopy (cryo-EM), a new tool for structural biologists emerged that eliminated some of the challenges presented by other techniques, such as X-ray crystallography. For example, the algorithms in the 3-D reconstructions using cryo-EM demonstrate the capability of providing structural information with tolerance to sample heterogeneity. Structure determination by single-particle cryo-EM has since become instrumental in the fields of virology, biochemistry, and progression in drug discovery pipelines. Single-particle analysis of cryo-EM data is facilitated through software program tools that are optimized to configure single-particle reconstructions. Among the frontiers of these software programs are cryoSPARC and RELION that operate in the Bayesian likelihood framework. Additionally, the framework surrounding these software programs is supported and further analyzed by an interactive visualization and analysis program called UCSF Chimera. CryoSPARC and RELION integrate similar job functions in their workflow, including but not limited to 2D classification, ab initio 3D classification, and CTF refinement. While the workflow of single-particle reconstruction refined by cryoSPARC and RELION has similarities, the framework behind these software tools has differences in the algorithm. We investigated the two software programs, cryoSPARC and RELION, in a comparative study to expand on the similarities and further elucidate the differences. The objective of this comparative study is to inspect the parameters utilized by the two software programs for jobs to evaluate the implications on the resolution of specimens.