/ 
SmotifTF-0.07
River stage zero No dependents
/ RankEnumeratedStructures

NAME

RankEnumeratedStructures

VERSION

Version 0.01

SYNOPSIS

This module ranks all the enumerated structures using a composite energy function that consists of four parameters: (1) Radius of Gyration (2) Solvation potential (3) Hydrogen bond potential (4) Statistical potential

use RankEnumeratedStructures;

rank_structures ($pdbcode,$stericlimit,@indices);

EXPORT rank_structures pre_rank_structures get_energy

pre_rank_structures

Subroutine to prepare for rank_structures

rank_structures

This subroutine ranks the structures generated by the full enumeration of the candidate smotif combinations. The ranking takes place in two parts: the full set is ranked using a 'coarse' scoring function, and the top 1000 structures are re-ranked using a 'refined' scoring function. Both functions use 4 scoring component values: radius of gyration, statistical pairwise contact potential, implicit solvation potential, and long range H bond potential.

INPUT ARGUMENTS 1) $pdbcode - the 4-character name of the folder to store input and output data 2) $sterlimit - number of allowable steric clashes (these clashes are calculated during the enumeration and are part of the input file - they are not calculated directly by this script) 3) @st - list of 4 numbers corresponding to the indices of the scoring function components in the tab-delimited output file from the full enumeration. Index numbering starts from 0 (not 1). See "INPUT FILES" for further details.

REQUIRED FILES (all to be found in the <pdbcode> directory) <pdbcode>.out - file containing a list of start and end points of smotifs in the query protein, as well as secondary structure and loop lengths. This is one of the standard output files of the generate_shift_files.pl script. <pdbcode>_motifs_best.csv - file containing a list of candidates for each putative smotif. This is one of the standard output files of the findranks.pl script.

INPUT FILES In the <pdbcode> directory, a set of files indicating the results of the full enumeration. These are the standard output files from the all_enum.pl script, and have the following format:

Sample line for a structure with 4 smotifs 1.437 0.740 1.867 8.377 224162 148918 54194 127698 1.7483 0.9973 0.9616 1.2306 8.8294 58.8240 12 0 0 0 0

Explanation: 1.437 0.740 1.867 8.377 : RMSDs of the 4 smotif components individually 224162 148918 54194 127698 : Nids of the 4 smotif components 1.7483 : Per-residue radius of gyration z-score 0.9973 : Per-residue pairwise contact potential z-score 0.9616 : Per-residue solvation potential z-score 1.2306 : Long-range H-bond potential z-score 8.8294 : Overall structure RMSD (from solved structure) 58.8250 : Overall structure GDT_TS score 12 0 0 0: List of indices of smotifs, as found in the <pdbcode>_motifs_best.csv file 0 : Number of steric clashes

In this case, the indices for the scoring function components are 8,9,10, and 11. In general, the indices will be from 2*n through 2*n+3 inclusive, where n is the number of smotifs

OUTPUT FILES In the <pdbcode> directory: 1) <pdbcode>_ranked_coarse.csv : Top 5000 structures as ranked by the coarse scoring function. The format of each line is the same as in the enumeration output files (see INPUT FILES, above), with an additional final entry representing the scoring function output for each line. 2) <pdbcode>_ranked_refined.csv : Same as 1), but for the top structures re-ranked using the refined scoring function.

rank_energies

Subroutine to calculate energy and rank structures, given a list of energy function component scores and weights

AUTHORS

Fiserlab Members , <andras at fiserlab.org>

BUGS

Please report any bugs or feature requests to bug-. at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=..

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc RankEnumeratedStructures

LICENSE AND COPYRIGHT

Copyright 2015 Fiserlab Members .

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

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