cns-mac-linux - http:/cns-online.org/v1.21/ Structure...

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http://cns-online.org/v1.21/ Structure Calculation using CNS DO THE FOLLOWING, IF YOU HAVE NOT ALREADY DONE SO: First, look in your home directory to see if there is a subdirectory named “cns”: [your-user-name@localhost ~]$ pwd /home/your-user-name [your-user-name@localhost ~]$ ls -F Desktop / example / Molecules / cns / [your-user-name@localhost ~]$ The “cns” subdirectory should contain a file called “anneal.inp” and two subdirectories, “reference” and “restraints”: [your-user-name@localhost ~]$ cd cns [your-user-name@localhost ~]$ pwd /home/your-user-name/cns [your-user-name@localhost ~]$ ls -F anneal.inp reference / restraints / [your-user-name@localhost ~]$ If you do not have the “cns” subdirectory, or its contents do not appear to be correct, you will have to create the directory, download the contents from the course website (as a “tar” file), and extract the “tar” file in your home directory. You may need assistance from the course instructors to do this. You should now be ready to begin.
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Introduction In this exercise, we will use available NMR-derived restraint information (NOE-based distance restraints, hydrogen bond restraints and dihedral angle restraints) to calculate the structure of a protein/peptide complex using simulated annealing/restrained molecular dynamics as implemented in the program CNS (C rystallography and N MR S ystem). The complex is a mixed disulfide between a human thioredoxin mutant (C35A, C62A, C69A, C73A) and a 13 residue peptide comprising its target site in human Ref-1 (residues 59-71 of the P50 subunit of Nfkb). We will then use the program PyMol to visualize the resulting calculated structure. CNS is a “newer version” of the program X-PLOR. Details about the programs can be found at the web sites (below). Also, the X-PLOR manual (“X-PLOR: Version 3.1, A System for X-ray Crystallography and NMR, by Axel T. Brünger, Yale Press) is an extremely good reference, and probably essential for those of you interested. It is also available online (below). A version of X-PLOR maintained by the NIH (X-PLOR-NIH) is also available (below): CNS: http://cns-online.org/v1.21/ X-PLOR-NIH: http://nmr.cit.nih.gov/xplor-nih/ X-PLOR manual online: http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/htmlman.html Using a web browser (Internet Explorer, Safari, Mozilla) you can go to http://cns-online.org/v1.21/ and poke around a bit if you like before you begin the tutorial. However, we will be going to this web site at the end of the tutorial and using some of the tools there.
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Exercise 1: Calculating the structure of a thioredoxin-peptide complex Getting started CNS can be run in an interactive mode, or in a non-interactive mode. -
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cns-mac-linux - http:/cns-online.org/v1.21/ Structure...

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