Links
High-Performance Computing
Frequently Used Tools in Structural Biology
Chemix - Drawing for making figures
CryoFLARE: The FMI Live Analysis and Reconstruction Engine
CryoREAD: CryoREAD is a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
DeepTracer: "Ultra-fast, fully automated and accurate de novo macromolecular complex structure prediction and identification from 3D electron density maps using 3D deep learning."
EMReady - Improving the quality and interpretability of cryo-EM maps by local and non-local deep learning
EternaFold: RNA secondary structure prediction.
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.
Namdinator: Web-based molecular dynamics flexible fitting for cryo-EM modeling.
pdb-tools: a swiss army knife for manipulating and editing PDB files
RNAcentral: the non-coding RNA sequence database
RNAstructure @ Mathews Lab: RNA secondary structure prediction
Use IMOD to make movies (credits: Andrew Noske)
Warp - Advanced, real-time cryo-EM data pre-processing.
Visualization of Molecular Models
Illustrate: Non-photorealistic biomolecular illustration
PyMOL
UCSF ChimeraX
ChimeraX recipes and Python functions and structures for scripting
Links for Lab Recipes
Biochemical recipes - https://plchiulab.gitbook.io/biochemical-recipes/
Protein characterization procedures - https://plchiulab.gitbook.io/protein-characterization/
Recommended Books
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.