Boltz-1 - Boltz-1 predicts the 3D structure of proteins, RNA, DNA, and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.
Chemix - Drawing for making figures
Confidence map calculated using false discovery rate.
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."
ModelCraft: Automated model building of proteins and nucleic acids in X-ray crystallography and cryo-EM.
The Molecular Modeling Toolkit (MMTK): an open source program library for molecular simulation applications.
Moorhen: molecular modeling on the web.
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.
Illustrate: Non-photorealistic biomolecular illustration
ChimeraX recipes and Python functions and structures for scripting
Biochemical recipes - https://plchiulab.gitbook.io/biochemical-recipes/
Protein characterization procedures - https://plchiulab.gitbook.io/protein-characterization/
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.