Protein Crystallography Links

03/14/08

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Genome and Proteome Databases

PDB.  The RCSB Protein Data Bank.  Repository of 3D structures of proteins (and nucleic acids).  We go here a lot.

NCBI (National Center for Biotechnology Information)  - Includes PubMed, BLAST, Genbank and other valuable resources.

ExPASy (Expert Protein Analysis System) - Includes Swiss-Prot, TrEMBL, and countless other valuable information and tools for protein science.

MK-BSGI (Monteal-Kingston Bacterial Structural Genomic Initiative) - Our lab is actively involved in contributing structural information to this bacterial structural genomics project)

MGC (Mammalian Gene Collection) - This is a database of publicly-available full-length I.M.A.G.E. cDNA clones.  As of March 2004, there are over 11000 human and 10000 mouse genes catalogued in this database, and they can all be ordered quite cheaply.

I.M.A.G.E. (Integrated Molecular Analysis of Genomes and their Expression) - This database of EST and cDNAs is the source of the clones catalogued in the MGC (see above).

Tutorials

Michael Sawaya's Crystallography Tutorials.  This is a collection of tutorials explaining what to do after you have collected a dataset.  A useful summary of some complicated things.

Tools

TMHMM (TransMembrane ) - This utility allows you to find transmembrane regions within your protein-of-interest.

NPS@ (Network Protein Sequence Analysis) - A secondary structure prediction tool that uses a 'Hierarchical Neural Network' method.

DisEMBL.  A program that estimates regions of disorder within a protein sequence.

GlobPlot. Gauges the tendency for disorder with a protein sequence

Synchrotrons

These are the synchrotrons our lab visits regularly:

APS (Advanced Photo Source) - at the Argonne National Laboratory outside Chicago, Illinois.

BNL (Brookhaven National Laboratory) - Home of NSLS (National Synchrotron Light Source) in Long Island, New York.

CHESS (Cornell High Energy Synchrotron Source) - in the Wilson Laboratory of Cornell University, Ithaca, New York.

 

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