MODPROPEP Programs¶

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MODPROPEP_score.pl¶

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| \  / | |  | | |  | | |__) | |__) | |  | | |__) | |__  | |__) |
| |\/| | |  | | |  | |  ___/|  _  /| |  | |  ___/|  __| |  ___/
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                                        / __|/ __/ _ \| .__/ _ \
                                        \__ \ (_| (_) | | |  __/
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Usage¶

MODPROPEP_score.pl < -p PDBFILE -r RECEPTORCHAIN -l LIGANDCHAIN -m SCORINGMATRIX -o outfile > [Options]

Options¶

-h, --help Print this help

-p, --pdbfile Pdb file containing coordinates of protein (receptor) and ligand(peptide) (required)

-r, --rchain Receptor chain identifier letter in pdb coordinate file (required)

-l, --lchain Ligand chain identifier letter in pdb coordinate file (required)

-s, --sequence File name of protein sequence in fasta format to be scanned (required)

-o, --outfile Name of the outputfile (required)

-m, --matrixfile

Scoring matrix file properly formated (required)

-d, --distance Distance for considering two atoms to be in contact in angstroms ( default 4.5)

-a, --atomtype Which atom types should be considered for contact between receptor and ligand (default “any”) Options: any=any atoms between receptor and ligand cb=c-beta; only C-beta to C-beta distances between receptor and ligand will be considered

-e, --excludebb

Exclude backbone (sugar-phosphate atoms in DNA; N,C,CA,O atoms in Peptide/proteins) (default F) Options: T (true), F (false)

Examples¶

$ perl MODPROPEP_score.pl --pdbfile complex.pdb -rchain A -lchain L \\
      -matrixfile MJ.mat -distance 6 -atomtype CB -o outfile

$ perl MODPROPEP_score.pl -p complex.pdb -r A -l L -m MJ.mat -d 6 -a CB

Details¶

MODPROPEP_score.pl is the main program in the MODPROPEP suite. It calculates a numerical score for the interactions between two chains in a protein-protein or a protein-peptide complex given in PDB format. The program calculates the residues that are in contact with each other at the interface of two chains. The criteria for the contacts is chosen by the user. For example two residues could be said to be in contact if any two atoms (one atom from each of them) from them are within a distance of 4 angstroms. This criteria is too rigid and dependent on the side chain conformation of the residues. For this reason the user may choose another criteria wherein the residues are said to be in contact if their C-beta atoms are within a certain distance range. The program uses list of contact to score a contact potential which is the sum of contact potential of all the residue-residue contact types at the interface of the complex. The contact potential is residue-residue contact is taken from the residue-residue pair potential matrix. The results are stored in the output file specified.

-h, –help

Prints the help

-p, –pdbfile

PDB file containing the coordinates of protein-protein or protein-peptide complex. All the chains in the complex should have a distinct identifier. (Required)

-r, –rchain

Receptor chain identifier ( e.g. “A” ) in the PDB file. (Required)

-l, –lchain

Ligand chain identifier ( e.g. “C” ) in the PDB file. (Required)

-s, –sequence

File name of protein sequence in fasta format to be scanned. (Required). The sequence in this file will be broken down into all possible peptides of length equal to that of the ligand in the PDB file. A score will be calculated for all of these peptides which will reflect the binding affiny of them in complex the receptor in PDB file.

-o, –outfile

Name of the outputfile. (Required)

-m, –matrixfile

Scoring matrix file properly formated. (Required). See Pair-Potential Matrix

-d, –distance

User defined distance for considering two atoms to be in contact with each other (Default 10 angstroms)

-a, –atomtype

Which atom types should be considered for defining contact between amino acids of receptor and ligand (default “any”)

Options:

any=any atoms between receptor and ligand

cb=c-beta; only C-beta to C-beta distances between receptor and ligand will be considered

-e, –excludebb

Do not consider the backbone atoms for calculating contacts between amino acids. (Default F)

Options: F=False, T=True

MODPROPEP_libgen.pl¶

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|  \/  |/ __ \|  __ \|  __ \|  __ \ / __ \|  __ \|  ____|  __ \
| \  / | |  | | |  | | |__) | |__) | |  | | |__) | |__  | |__) |
| |\/| | |  | | |  | |  ___/|  _  /| |  | |  ___/|  __| |  ___/
| |  | | |__| | |__| | |    | | \ \| |__| | |    | |____| |
|_|  |_|\____/|_____/|_|    |_|  \_\\____/|_|    |______|_|
                                 _     _ _
                                | |   (_) |__   __ _  ___ _ __
                                | |   | | |_ \ / _` |/ _ \ |_ \
                                | |___| | |_) | (_| |  __/ | | |
                                |_____|_|_.__/ \__, |\___|_| |_|
                                               |___/

Usage¶

MODPROPEP_libgen.pl -l library_name -t direcory_of_templates

MODPROPEP_libgen.pl -info

Options¶

-h, --help Print this help

-l, --lib Name of the library to be created.

-t, --temp Name of the directory containing the templates. The templates should be copied to this directory after necessary formatting

-i, --info Prints library information. (Default F) Options P=Prints a list of libraries installed. “library_name”=Prints information of “library_name” if installed

Examples¶

$ perl MODPROPEP_libgen.pl -l kinases -t /data/naren/kinase/templates

$ perl MODPROPEP_libgen.pl --info

Details¶

Although some programs in libgen can be used as standalone, you will need a library of templates to work with MODPROPEP. MODPROPEP_libgen.pl is the utility to create, maintain and update MODPROPEP library. More than one libraries can be maintained at the same time.

Requirements

TEMPLATE SOURCE: You will need to create a directory <TEMPLATE SOURCE> and copy all the templates as “xxxx.pdb” files. The template files should only contain the polypeptide chains that are required to be mutated. All the templates must contain same number of chains and chain identifiers whould be exactly the same in all the templates.

templates.list: <TEMPLATES SOURCE> directory should have a file “templates.list” containing a list of all the templates in the following format

@chain A:PROTEIN_KINASE
@chain C:Peptide
@index=A
1APM.pdb       AC
2PHK.pdb       AC
1JBP.pdb       AC
The lines starting with @chain store the name of the chain in the pdb template file. There should be one line each for each chain in the templates. The line starting with @index stores the chains name that are marked for indexing. The protein sequences of the chains marked for indexing are extracted and copied in <chain_name>_<chain_id>.fasta file in the index folder of the library. These sequence files could be indexed using the blast suite. These index files could be searched for detecting the best matching chain for an unknown sequence, which could be used to build its 3D model.

Rest of the lines in the templates.list file are the list of templates in the directory. Each file contain the pdb file names follwed by a <tab> followed by the chain names (without space).

-h, –help

Prints the help.

-l, –lib

The name of the library to be build. A library will be created with this name. If the library name provided already exists then new templates will be added to it.

-t, –temp

The directory containing the source templates. This directory must contain “templates.list” file in the proper format (see above). PDB templates in this directory will be copied to the library specified with -l flag.

-i, –info

Prints the information about the installed libraries.

Options

P = Prints a list of installed libraries.

Library_name = Prints information of library “Library_name” if it exists.