Greg Pintilie

Contact NCMI

Email Us:

gregp@slac.stanford.edu

wahc@stanford.edu

 

Research

We study and extend computational methods to discover the structure and function of molecular complexes. Molecular complexes are the building blocks and machinery in every living cell. The methods we've focused on and some examples are:

  • Segmentation and analysis of 3D density maps from Cryo-Electron Microscopy
    • Extension of methods from computer vision, e.g. segmentation via watersheds, and clustering via scale-space analysis.
    • Modeling of protein structures based on Cryo-EM density maps
    • Quantification of density map quality using fitted models and statistical scores (e.g. Z-scores, Q-scores).
    • Tools we have developed: Segger, ModelZ, MapQ
  • Molecular Dynamics methods for building and fitting atomic models to CryoEM maps
    • Use of methods such as NAMD and MDFF
    • Interpretation of results, modeling uncertainty
  • Animation of macromolecular complexes
    • Key-framing, transform interpolation, atomic model and volume morphing.
    • Chimera plugin for creating movies: BioMovie

 

COVID-19 related:

Spike Proteins (Open/Closed), ACE2 Receptor Spike Proteins with Antibodies Spike Proteins (Open) and ACE2 Receptor
Sources:EMD:21452, PDB:6vxx, EMD:21457, PDB:6vw1 Sources:EMD:21452, PDB:6vxx, EMD:0403, PDB:6vw1 Sources:EMD:21452, PDB:6vxx, EMD:30039, PDB:6m17

Rendered with UCSF Chimera, In SLAC News, On Youtube

 

Publications

 

    
    
    
    
    
    
    
    
 
 
  • EMDataBank Unified Data Resource for 3DEM
  • C. Lawson, A. Patwardhan, M. Baker, C, Hryc, E.S. Garcia, B. Hudson, I. Lagerstedt, S. Ludtke, G. Pintilie, R. Sala, J. Westbrook, H. Berman, G. Kleywegt, and W. Chiu
  • Nucleic Acids Research, vol. 44, no. D1, pp. D396-403, Jan. 2016
 
   
 

Art