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.


Construct design and optimization

Northeast Structural Genomics Consortium

Construct design and optimization are critical to the success of the structure determination pipeline. The NESG employs a variety of freely available tools and algorithms during the selection and design of constructs. The DisMeta Server, developed by the NESG, provides a centralized point of access to many of these programs.

Details

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


DBAli: A Database of Structure Alignments

This site contains an up-to-date all-against-all comparison of protein structures.

Details

http://salilab.org/DBAli/


Dali Server: Conservation Mapping in 3D

The Dali server is a network service for comparing protein structures in 3D. Submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB) and receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.

Details

http://ekhidna.biocenter.helsinki.fi/dali_server/start


Data dissemination

Midwest Center for Structural Genomics

The MCSG has developed and maintains a public website (www.mcsg.anl.gov) which provides an interactive interface to the MCSG database and lists the targets, their status, and provides information about deposited structures.

Details

http://www.mcsg.anl.gov


Determination and application of empirically derived detergent phase boundaries to effectively crystallize membrane proteins

Membrane Protein Structural Biology Consortium

We have carried out dye-based detergent phase partitioning studies using different combinations of 10 polyethylene glycols (PEG), 11 salts, and 11 detergents to generate a significant amount of chemically diverse phase boundary data. The resulting curves were used to guide the formulation of a 1536-cocktail crystallization screen for membrane proteins. The experimentally derived phase boundary data and the 1536 membrane screen are available through the high-throughput crystallization facility located at the Hauptman-Woodward Institute.

Details

http://www.hwi.buffalo.edu/faculty_research/crystallization/membrane_protein.html


DisMeta: a meta server for construct design and optimization

Northeast Structural Genomics Consortium

The NESG typically designs 4 - 5 constructs for each protein target. Targets are evaluated with DisMeta, the NESG consensus disorder predictor. DisMeta polls a number of disorder prediction servers and returns a consensus plot of predicted disorder.

Details

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


Docking and scoring with ICM: the benchmarking results and strategies for improvement

GPCR Network

ICM was benchmarked for self-docking accuracy and virtual ligand screening using three test sets. The benchmarking results, calculation details, current developments, and future prospects for further improving performance are presented.

Details

http://gpcr.scripps.edu/