Frequently Used Tools in Structural Biology
CryoFLARE: The FMI Live Analysis and Reconstruction Engine
DeepTracer: "Ultra-fast, fully automated and accurate de novo macromolecular complex structure prediction and identification from 3D electron density maps using 3D deep learning."
FindMySequence - "A neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM."
The Molecular Modeling Toolkit (MMTK): an open source program library for molecular simulation applications.
Warp - Advanced, real-time cryo-EM data pre-processing.
EMReady - Improving the quality and interpretability of cryo-EM maps by local and non-local deep learning
Chemix - Drawing for making figures
Use IMOD to make movies (credits: Andrew Noske)
Blankenship, Robert E. Molecular Mechanisms of Photosynthesis. 2nd ed., Wiley Blackwell, 2014.
Cantor and Schimmel. Biophysical Chemistry. Freeman, 1980.
Duda, R.O., Hart, P.E., and Stork, D.G. Pattern Classification. 2nd ed., John Wiley & Sons, 2001.
Goodman, J.W. Introduction to Fourier Optics. 4th ed., W.H. Freeman, 2017.
Kirkland, E.J. Advanced Computing in Electron Microscopy. 2nd ed., Springer, 2010.
Spence, John C.H. High-Resolution Electron Microscopy. 4th ed., Oxford University Press, 2013.