CE and FATCAT are methods for calculating pairwise structure alignments. They align two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. This site provide access to the Java implementation of these algorithms, called jCE and jFATCAT, as part of the Protein Comparison Tool.
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RCSB PDB - jCE/jFATCAT Structure Alignment Server V. 2.11 - All vs All Protein Structure Comparison and Alignment | source.rcsb.org Reviews
https://source.rcsb.org
CE and FATCAT are methods for calculating pairwise structure alignments. They align two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. This site provide access to the Java implementation of these algorithms, called jCE and jFATCAT, as part of the Protein Comparison Tool.
source.rcsb.org
Combinatorial Extension (CE) - A method for comparing and aligning protein structures
http://source.rcsb.org/jfatcatserver/ceHome.jsp
A method for comparing and aligning protein structures. A method for comparing and aligning protein structures. This page is intended as a pointer to get you to the most recent information on CE and to enable you to perform the calculations you need. CE is now an integral part of the RCSB Protein Data Bank. PDB) and continues to be developed in the Bourne laboratory. Access to CE from the RCSB PDB http:/ www.rcsb.org/pdb/workbench/workbench.do. CE - web site. CE used to map existing protein fold space [2].
jCE/jFatCat Help - Explanation of frequently used terms.
http://source.rcsb.org/jfatcatserver/help.jsp
Explanation of frequently used terms. CE is a method for calculating pairwise structure alignments. JCE is a re-implementation of the original CE source code in the Java programming language. While the algorithm is principle exactly the same as in the original implementation, jCE provides several improvements over the original code:. New internal data model:. The internal representation of jCE is now based on the BioJava protein structure module. It supports both PDB file and mmCif files as input. The or...
Download jCE/jFatCat - Get a copy of jCE for running locally
http://source.rcsb.org/jfatcatserver/download.jsp
Get a copy of jCE for running locally. Get the latest structure comparison tool bundle. Download the code for running locally. Release date: 2016 Mar 24. Precalculated Protein Structure Alignments at the RCSB PDB website. Andreas Prlic; Spencer Bliven; Peter W Rose; Wolfgang F. Bluhm; Chris Bizon; Adam Godzik; Philip E. Bourne. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq572. Please see footer of this page for additional relevant references. Of the available command line arguments is available.
Documentation jCE/jFATCAT - Available command line arguments
http://source.rcsb.org/jfatcatserver/docu.jsp
Available command line arguments. Documentation Command Line Arguments. Documentation of jCE and jFATCAT command line options. Show help on command line. Displays the menu that allows to run alignments through a user interface. Click for Large Image. Specifies two files to be aligned. Uses the full content of the files for alignment. For alignment. See Naming convention below for supported names. Specifies a path in the local file system which contains a local copy of PDB files. Range (',' range)? Exampl...
RCSB PDB - jCE/jFATCAT Structure Alignment Server V. 2.11 - All vs All Protein Structure Comparison and Alignment
http://source.rcsb.org/jfatcatserver/index.jsp
RCSB PDB - jCE/jFATCAT Structure Alignment Server V. 2.11. All vs All Protein Structure Comparison and Alignment. The source.rcsb.org server gives you access to the developmental version of jCE and jFATCAT. You can launch a pairwise alignment of the latest development code from below. Launch Protein Comparison Tool. Specify what PDB chains to be aligned from here:. JCE algorithm - Java Web Start. JFatCat - Java Web Start (rigid). JFatCat - Java Web Start (flexible). 3D alignment based on Smith Waterman.
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This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. 2014) Nucleic Acids Research. URL: www.rcsb.org. The RCSB PDB...
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RCSB PDB - jCE/jFATCAT Structure Alignment Server V. 2.11 - All vs All Protein Structure Comparison and Alignment
RCSB PDB - jCE/jFATCAT Structure Alignment Server V. 2.11. All vs All Protein Structure Comparison and Alignment. The source.rcsb.org server gives you access to the developmental version of jCE and jFATCAT. You can launch a pairwise alignment of the latest development code from below. Launch Protein Comparison Tool. Specify what PDB chains to be aligned from here:. JCE algorithm - Java Web Start. JFatCat - Java Web Start (rigid). JFatCat - Java Web Start (flexible). 3D alignment based on Smith Waterman.
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