buildModel.pl

Usage

usage:   buildModel.pl [options] [fastaFile]
options:               [-models value]
                       [-maxloop value]
                       [-verbose]
                       [-nocenter]
                       [-stats file]
                       [-pdbdir name]

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Description

This script is used for template-based structure prediction. It takes an alignment file in FASTA file as input, finds the PDB template, builds a homology model and adds missing (loop) residues via Modeller.

A typical input file is expected to look as follows:

>TARGET 
RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP   
>1IHG_A ::4e-96::61::Chain A, Bovine Cyclophilin 40, Monoclinic Form
NPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVAKILENVEVK-GEKPAKLCVIAECGEL..

Note the PDB code and chain ID in the third line. A properly formatted file can be generated with the psiblast.pl tool from PSI-Blast output.

For this tool to work, it is necessary to have a local copy of the PDB (or at least a directory where the structures for the needed templates are present) either at the location pointed to by the environment variable PDBDIR or given through the option -pdbdir.

Furthermore, Modeller needs to be installed and available. The script will try to guess the location of the Modeller executable, but it is better to provide the location through the environment variable MODELLEREXEC

Options

-help 

usage information