January 27, 2022

Helpful Links

Installing Crystallography Software

CCP4 (includes Coot): https://www.ccp4.ac.uk/download/#os=macos

Phenix: https://phenix-online.org/download

Tips For DNA Oligos

Resuspending DNA Oligos (IDT DNA Tips)https://www.idtdna.com/pages/education/decoded/article/tips-for-resuspending-and-diluting-your-oligonucleotides

DNA Oligo Resuspension Calculator: https://www.idtdna.com/Calc/resuspension/

IDT DNA OligoAnalyzer (SS-structure, Tm, extinction coefficients etc.): https://www.idtdna.com/calc/analyzer

DNA and RNA Molecular Weights and Conversions: https://www.thermofisher.com/us/en/home/references/ambion-tech-support/rna-tools-and-calculators/dna-and-rna-molecular-weights-and-conversions.html

Crystallization Resources

Beamline Guides (MiTeGen):

All: https://www.mitegen.com/learn/beamline-guides/

ALS 8.2.2: https://www.mitegen.com/learn/beamline-guides/als-8-2-2/

NSLS II/AMX: https://www.mitegen.com/learn/beamline-guides/nsls-ii-amx-17-id-1/

Crystal Freezing


ProtParam- https://web.expasy.org/protparam/

A tool which allows the computation of various physical and chemical parameters for a given protein. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, and extinction coefficient. 

JANE- Journal Author Name Estimator – https://jane.biosemantics.org/index.php

Enter the title and/or abstract of your potential paper in the box, and Jane will compare it to find the best matching journals, authors or articles to help choose a place for submission.

PDBePISA (Proteins, Interfaces, Structures and Assemblies)– https://www.ebi.ac.uk/msd-srv/prot_int/pistart.html

Results include:

  • Structural and chemical properties of macromolecular surfaces and interfaces
  • probable quaternary structures (assemblies), their structural and chemical properties and probable dissociation pattern

PDBeFold- https://www.ebi.ac.uk/msd-srv/ssm/

A comparison with other protein matching services. PDBeFold is used as a structure search engine in PDBePISA. 

Dali – http://ekhidna2.biocenter.helsinki.fi/dali/

The Dali server is a network service for comparing protein structures in 3D.