Jiang Lab, Institute of Biophysics, Chinese Academy of Sciences   中文版

CISRR

1. Description

   CISRR is a user friendly program for accurate prediction of protein side chains and effective elimination of their inner atomic clashes.

   Most of the state-of-the-art side-chain modeling methods are based on discrete rigid side-chain rotamers. The use of discrete rigid rotamers could inherently lead to atomic clashes and prevent the accurate modeling of protein side chains. To overcome this issue CISRR couples a novel clash-detection guided iterative search algorithm (CIS) with rotamer relaxation (RR), which removes atomic clashes effectively and achieves high accuracy (about 86% and 76% for Chi1 and Chi1&2, respectively, within 40 degree cutoff).

   CISRR could be a very useful tool for subsequent analysis and refinement of protein structures.

   CISRR is free for non-commercial users. Other users please contact us.

2. Please Cite

   Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation. Yang Cao, Lin Song, Zhichao Miao, Yun Hu, Liqing Tian, Taijiao Jiang. Bioinformatics, 2011 Mar 15;27(6):785-90

3. Install

   CISRR is a command-line application under Linux.

   Extract the CISRR.tar.gz and place the CISRR folder anywhere in your computer whithout modifying the subdirectories and files.

   Then you can run the software (<program path>/bin/CISRR).

4. Usage

   -i [Input PDB File]

   The protein whose side-chains will be packed. It should be a PDB file which contains backbone atom records (N, CA, C, O). Alternative atoms (e.g., alt_loc of "B") and OXT atoms are ignored.

   -o [Output PDB file with predicted side-chain information]

   Example:

   ~$ ../bin/CISRR -i 1AGIcln_main.pdb -o 1AGIcln_sp.pdb

   ***********************CISRR***********************

   Hello! CISRR is ready for your side-chain modeling.

   Institute of Biophysics, CAS

   Mon Oct 18 16:55:18 2010

   ***********************CY2010**********************

   Protein Atom: 1013 Res: 124

   Defective Residues 115

   Iteration Round 1 Score: 71.4013

   Iteration Round 2 Score: -157.9404

   Iteration Round 3 Score: -176.2625

   Iteration Round 4 Score: -176.7581

   Iteration Round 5 Score: -186.7023

   Iteration Round 6 Score: -191.0497

   Success! Final Score: -191.1450

   Run Time: 6.920 sec.
   

5. Options

   -l [ligand file (mol2 format)]: Ligand Restriction for side-chain modeling

   -H [add hydrogen atoms]: The hydrogen atoms will be added according to Charmm22 standard topologies.

   -h [help]: Help information;

   -m [mutation information]: The format after -m is [chain id] [sequence number] [orginal residue name (3 letter)] [new residue name (3 letter)]

   Multiple mutations are supported by adding more -m [mutation info]

   -F [Fast packing]: The program will bypass rotamer relaxation and is about 4~5 times faster. (1-2% less accurate)

    

6. Download

   CISRR_v1.01

    

7. Contact

   taijiao（AT）moon.ibp.ac.cn (Replace（AT）by @ )

Copyright © 2010 by Institute of Biophysics, Chinese Academy of Sciences