Some Other Tools

Online Tutorials and Related

• Bernhard Rupp’s Crystallography 101
• Statistical Descriptors in Crystallography
• Tutorial on Model Validation, from Uppsala
• Online Protein Crystallography Course, from MRC Cambridge
• Online Tutorial on Molecular Replacement, from Bart Hazes
• A Methods in Enzymolgy Paper (Older, but still applicable, guideline for refinement and model building practices)

Structural Databases

• RCSB Protein Data Bank - world wide repository
• HIC-Up-Database of Small Molecules/Ligands
• Viper - all the virus structures are collected here
• Nucleic Acid Database - world wide repository

Other Basic Database Tools

• Crystallization conditions database
• Info an amino acids, including substitutions
• NCBI - gateway for PubMed, Blast etc.
• ExPASy molecular biology server - collection of tools

Structural Analysis

• MolProbity - structure validation including C-alpha geometry and Glu/Asp/His rotamer determination
• Whatcheck - verify protein model stereochemistry and parameters (NOTE: this is the free portion from WhatIf)
• Procheck - verify protein model stereochemistry and parameters, with nice output
• WhatIf - more options than WhatCheck, but requires a license fee
• STAN (Structural Analysis Server) - checks for metals, cis-prolines, and interfaces with MOLMAN2, a geometry, and stereochemistry checker.

Crystallographic Applications on OSX

• Crystallographic Applications on OSX - an excellent resource for the Mac obsessed.

Miscellaneous Fun Things

•  ELVES - automated structure determination
•  PDB to MultiGif - upload your .pdb and get back a movie
•  Database of Molecular Movements - many premade movies (great for teaching tools!), and inputs to make your own.

Sources of stereoscopes for viewing stereofigures in 3-D

•  Berezin Stereo Photography Products
•  Hampton Research

Tips for improving crystal quality

Tips on mounting fragile needle-shaped crystals

Tips of cryoprotection of fragile crystals

Protocol for making Se-Met Proteins 

Non-Crystallographic Miscellaneous

• Links to Pathway and Other Databases - links to nomenclature as well as metabolic pathways and interaction servers
• ProteinProspector - for analysis of MS fingerprints

  * Comments are from Christine Bourne and do not represent the opinions of anyone but her.  But that doesn’t mean they aren’t right!