Links

Arizona State University

• Arizona State University

• School of Molecular Sciences

• The Biodesign Institute

• LeRoy Eyring Center for Solid State Science (LECSSS)

• ASU Research Computing Facility

Cryo-EM Community

• 3DEM

• EMPIAR (Electron Microscopy Pilot Image Archive)

• NRAMM (Natinoal Resource for Automated Molecular Microscopy)

• PNCC (Pacific Northwest Center for Cryo-EM)

Structural Biology Community

• Chemistry at HARvard Macromolecular Mechanics (CHARMM)

• Deutsches Elektronen-Synchrotron (DESY)

• The Human Protein Atlas

• SBGrid Consortium

• Theoretical and Computational Biophysics Group @ UIUC

High-Performance Computing

• HPC on Mac OS X

• SPIDER (System for Processing Image Data from Electron microscopy and Related fields)

Frequently Used Tools in Structural Biology

• 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

• CIF Editor

• https://cryoem101.org/

• 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."

• EMDA Toolkit. 

• EMReady - Improving the quality and interpretability of cryo-EM maps by local and non-local deep learning

• EternaFold: RNA secondary structure prediction. 

• Expasy

• FindMySequence - "A neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM."

• GEMMI

• HOLE

• IPLT (Image Processing Library & Toolbox)

• 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. 

• Orientations of proteins in membranes (OPM) database

• PDB standard file format

• pdb-tools: a swiss army knife for manipulating and editing PDB files

• explainshell.com

• RNAcentral: the non-coding RNA sequence database

• RNAstructure @ Mathews Lab: RNA secondary structure prediction

• SSDraw

• Use IMOD to make movies (credits: Andrew Noske)

• TEM Simulator

• Warp  - Advanced, real-time cryo-EM data pre-processing. 

Visualization of Molecular Models

• BioRender

• Illustrate: Non-photorealistic biomolecular illustration

• POV-Ray

PyMOL

• PyMOL script depository

• APBS plugin

• PyVOL

UCSF ChimeraX

• UCSF ChimeraX Tutorials

• 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.