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.


Primer Prim’er – PCR Primer Design Software

Northeast Structural Genomics Consortium

Primer Prim'er (Everett et al., 2004) is a PCR primer design tool that completely automates the primer design process. Primer Prim'er generates vector specific PCR primer sets for target amplification and cloning. Both restriction endonuclease and viral recombination cloning strategies are supported.

Details

http://www-nmr.cabm.rutgers.edu/bioinformatics/Primer_Primer/


ProFunc: fully automated structure-based function prediction

Midwest Center for Structural Genomics

The aim of the ProFunc server is to help identify the likely biochemical function of a protein from its three-dimensional structure. ProFunc has been developed jointly with the Midwest Center for Structural Genomics (MCSG) and European Bioinformatics Institute (EBI).

Details

http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/


ProKnow server for function prediction

Integrated Center for Structure and Function Innovation

A server is available at http://proknow.mbi.ucla.edu/ that can predict the functions of, and annotate, a protein structure.

Details

http://proknow.mbi.ucla.edu/


ProLinks database for functional linkage prediction

Integrated Center for Structure and Function Innovation

A database is available at http://services.mbi.ucla.edu/prolinks/ that can infer functional linkages between pairs of genome-encoded proteins.

Details

http://services.mbi.ucla.edu/prolinks/


Protein function annotation by homology-based inference

Midwest Center for Structural Genomics

The BioSapiens Network has developed tools to address all stages of characterizing genes and proteins from their sequence. Here we review progress in the automated prediction of protein function based on protein sequence and structure.

Details

http://www.biosapiens.info/page.php.html


PubServer: literature searches by homology

Joint Center for Structural Genomics

PubServer, available at http://pubserver.burnham.org/, is a tool to automatically collect, filter, and analyze publications associated with groups of homologous proteins.

Details

http://pubserver.burnham.org/


Pxs Crystallization Score and Prediction Server

Northeast Structural Genomics Consortium

Pxs (Protein Crystal Structure Propensity) estimates the probability that an amino acid sequence will produce a crystal structure. Using data generated by the NESG, we determined that several individual sequence features were statistically predictive of high quality protein crystals.

Details

http://www.nesg.org/PXS