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.


2dx_merge – Data management and merging for 2D crystal images

Center for Structures of Membrane Proteins

We present here the program 2dx_merge, which assists the user in the management of a 2D crystal image-processing project, and facilitates the merging of the data from multiple images.

Details

http://2dx.org


3-D Protein Structure Comparison and Alignment

This website has databases and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) method.

Details

http://source.rcsb.org/jfatcatserver/ceHome.jsp


A modular perspective of protein structures: application to fragment-based loop modeling using ArchPred

New York Structural Genomics Research Consortium

"Smotifs" are composed of two secondary structures connected by a loop. These generically defined supersecondary structure elements were used to explore the evolution and current variety of structure building blocks. The Smotifs classifications were used in a loop conformation modeling algorithm, ArchPred.

Details

http://manaslu.aecom.yu.edu/loopred/


A tool for automated PCR primer generation

Joint Center for Structural Genomics

A tool has been created for the automatic generation of primers.

Details

http://www.jcsg.org/scripts/prod/primer/primer_input_form.cgi


Automated extraction and data analysis from the JCSG database

Joint Center for Structural Genomics

A number of automated reporting tools have been developed that greatly facilitate the work of JCSG researchers by extracting and summarizing large amounts of raw data from the JCSG database.

Details

http://www.jcsg.org


Automated protein structure annotation

New York Structural Genomics Research Consortium

Novel methods have been developed that automatically examine protein structures and extract structural functional information. Functional analysis of all PSI-1 and PSI-2 NYSGXRC structures, including tabulations of structure comparison and output from Dali, CE, and SURFNET, are available at http://www.nysgrc.org/nysgrc/result.html

Details

http://www.nysgrc.org/nysgrc/result.html


Automated structure report and manuscript preparation using AUTOPUBLISH

New York Structural Genomics Research Consortium

AUTOPUBLISH is a comprehensive web server that automatically annotates protein sequences and structures and prepares manuscript drafts in the style of a short structure reports like those published in Acta Crystallographica, Section F.

Details

http://ogre.aecom.yu.edu/autopublish-cgi/index.cgi