RDC - PROSPECT

				 	Feb 18, 2004

				 	version  1.65



INTRODUCTION:

RDC-PROSPECT is a computer program for protein structure prediction based on a structural homolog 
or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the 
15N-1H RDC data of the protein recorded in a single ordering medium. It uses only RDC data and 
predicted secondary structure information. Threading is performed against SCOP 40 structure 
database (currently v1.65, release of Dec, 2003). The alignment and Z-score for the top 20 ranked
templates are reported in the output file. 

Please note only those templates that have the sequence length of between 50% to 200% of the 
test protein sequence length are considered. For protein domains, templates fall outside this 
sequence length range are not likely to belong to the same family or superfamily with the test 
protein and thus not considered. 

The template rotations are now made around Z, Y', Z'' axes. This is different from the original 
X, Y, Z rotations as used in our NAR paper. This is because it appears the Z, Y', Z'' rotations
are more widely used in other programs. So we just follow the tradition.

RDC-PROSPECT is written in C and has only been tested under LINUX. 

The current version 1.65 can only use N-H RDC data in one aligning medium. Use of multiple types 
of RDC and RDC in multiple media will be added in the next version.


AUTHORS:

Youxing Qu, Jun-tao Guo, Victor Olman, Ying Xu

Computational Systems Biology Lab
Life Sciences Building A110
Dept of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
U.S.A.
Phone: 706-542-9762
Fax: 706-542-9751
Web: http://csbl.bmb.uga.edu


REFERENCES:

Qu Y, Guo JT, Olman V, Xu Y. (2004) Protein structure prediction using sparse dipolar coupling data.
Nucleic Acids Res.,32, 551-561. 

Y. Qu, J.-T. Guo, V. Olman, and Y. Xu, Protein Fold Recognition Through Application of Residual 
Dipolar Coupling Data, Pacific Symposium on Biocomputing, 2004, 459-470.


PROBLEMS AND SUGGESTIONS:

Please contact    Dr. Youxing Qu  
E-mail: youxing@csbl.bmb.uga.edu        

or  Dr. Ying Xu
E-mail: xyn@bmb.uga.edu

Thank you for using RDC-PROSPECT and any comment is appreciated !


UPDATE

Please send us an email after you download the RDC-PROSPECT program. We will send you information 
on update or new versions when they become available.



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PROGRAM PACKAGE:

The package includes 2 directories:

program     - all executable codes, compiled under redhat9.0 LINUX. The program must be run in this
directory! It will try to find template files in the "../template" directory.

templates   - all the templates files (5,674 domains from SCOP 40 v1.65) for threading. Please note these 
files are NOT PDB files!


INPUT:

The input file contains protein sequence (sequence, secondary structure) and RDC data information 
(Da, Dr, N-H RDC). Please see the provided example.inp file for detail instructuions.


OUTPUT:

The output file contains the alignment information and Z-scores for the top 20 ranked templates. 
Please see the provided example.out file for details.

RANK_#     - ranking of the templates is based on alignment raw score (SCORE)
SEQIDEN_%  - sequence identity between the test protein and the template protein
S          - RDC order parameter
Q          - RDC Q value
R          - RDC R factor
TEMP_#     - template index number
TEMPLATE   - template name (SCOP domain name)
FAMILY     - SCOP family
LENGTH     - the sequence length of the template protein
QUERY      - the sequence length of the test (query) protein
SCORE      - alignment raw score
Z          - Z-score of the alignment
ANG_Z      - Euler angle for clockwise rotation around Z axis
ANG_Y'     - Euler angle for clockwise rotation around Y' axis
ANG_Z''    - Euler angle for clockwise rotation around Z'' axis

query      - test protein
t          - template

The detailed alignment is given under "Structure_Alignment:" for each template.


RUN RDC-PROSPECT:

rdc.exe   test.inp  >  test.out  &

if not working, please try

./rdc.exe   test.inp  >  test.out  &


STATUS CHECK:

A temporary tmp.out file is created to report the threading scores (no Z-score) of the templates 
that have been checked. The tmp.out will remain in the directory after the program finishes, and it
will be overwritten next time when RDC-PROSPECT is run. Other temporary files (file name ending with 
_tmp) will be removed when the program finishes.

An example_tmp.out file is provided for reference.

START      - start residue number of the template
END        - end residue number of the template
NOUSE      - this column is not used in this version of PROSPECT. It is prepared for future use.

**note: -888 and -999 in the output files indicate the template is not used.

To check the status of the program running, use

more tmp.out                  or

tail -f tmp.out


IMPORTANT !

Only run one job each time under a directory ! Otherwise you will get bizzare results. However, 
the program can be run simultaneously under different directories, provided both the "program" and 
the "templates" folders are present under each directory.


COMPUTER TIME:

RDC-PROSPECT takes <3 hours (computer time, not CPU time) to run for a 100-residue test protein on a 
P4/2.4GHz/1GB PC under LINUX.