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.


BLU-ICE: beamline control GUI

Joint Center for Structural Genomics

JCSG contributed to the ongoing development of the BLU-ICE data collection software at SSRL, in close collaboration with the Structural Molecular Biology group at SSRL. In addition to the new crystal screening capabilities, BLU-ICE also supports completely automated execution of MAD data collection.

Details

http://smb.slac.stanford.edu/public/facilities/software/blu-ice/


Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries

A formal Bayesian framework has been developed for estimating the posterior probability of essentiality for each gene identified by analyzing transposon insertion libraries using next-generation sequencing.

Details

http://www.sacclab.com/


BlastProfiler - an automatic sequence profile generator program

New York Structural Genomics Research Consortium

As a first step in establishing an automated annotation pipeline, Fajardo, Madrid, Zhai and Fiser coded BlastProfiler, an automatic sequence profile generator program.

Details

http://www.fiserlab.org/servers_table.htm


C-ME: A 3D community-based, real-time collaboration tool for scientific research and training

Accelerated Technologies Center for Gene to 3D Structure

C-ME is a collaborative web-enabled community-based database software application for 3D protein structure annotation.

Details

http://c-me.scripps.edu/default.aspx


CMMR: A web server for comparative modeling for molecular replacement in x-ray crystallography

New York Structural Genomics Research Consortium

CMMR is an interactive web-server that combines comparative protein structure modeling with protein structure determination by molecular replacement.

Details

https://modbase.compbio.ucsf.edu/scgi//display.cgi?type=help&server=server#account


Chemical shift and structure validation

Northeast Structural Genomics Consortium

Web-based tools have been developed at Rutgers for validation of chemical shift and atomic coordinate data generated across the NESG Consortium.

Details

http://www.nesg.org/web_tools.html


ConCavity: Predicting protein ligand binding sites

Midwest Center for Structural Genomics

ConCavity is a small molecule binding site prediction algorithm that integrates evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities.

Details

http://compbio.cs.princeton.edu/concavity/