Web-based Resources


There are several online resources that can assist in the various stages of structure production listed below. Tools in the PSI Structural Biology Knowledgebase can also help with the analysis of protein sequences and structures.


Downloadable datasets for the crystallographic methods development community

Joint Center for Structural Genomics

JCSG has created a unique repository of X-ray crystallographic datasets for the structures it has solved and deposited in PDB, which includes x-ray diffraction images, as well as processed data.

Details

http://www.jcsg.org/datasets-info.shtml


FoXS: a web server for rapid computation and fitting of SAXS profiles

New York Structural Genomics Research Consortium

FoXS (Fast X-Ray Scattering) is a rapid method for computing a SAXS profile of a given structure and for matching of the computed and experimental profiles.

Details

http://salilab.org/foxs


FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies

Midwest Center for Structural Genomics

FunTree is a new web resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies.

Details

www.ebi.ac.uk/thorton-srv/databases/FunTree


GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains

Midwest Center for Structural Genomics

GeMMA (Genome Modelling and Model Annotation) is a new approach to automatic functional subfamily classification within families and superfamilies of protein sequences.

Details

http://www.biochem.ucl.ac.uk/cgi-bin/dlee/GeMMA


Gene Composer

Accelerated Technologies Center for Gene to 3D Structure

Gene Composer(TM) software suite for computer-aided construct engineering and expression-optimized synthetic gene design is available for download at http://www.genecomposer.net.

Details

http://www.genecomposer.net


Gene amplification and cloning

Midwest Center for Structural Genomics

Gene amplification and cloning steps are automated in a 96-well format, but the methods described in this review can be scaled down. The availability of genomic DNA from commercial sources, such as ATCC and DSMZ, along with web-enabled oligo design and LIC cloning help accelerate these steps in the pipeline.

Details

http://tools.bio.anl.gov/bioJAVA/index.jsp


Gene3D

Midwest Center for Structural Genomics

Gene3D is a comprehensive resource containing domain and functional annotations for most available protein sequences.

Details

http://gene3d.biochem.ucl.ac.uk/