MODPROPEP Programs ****************** There should only be one of these per page and this will also -- when converting to pdf -- be used for the chapters. MODPROPEP_score.pl ================== :: __ __ ____ _____ _____ _____ ____ _____ ______ _____ | \/ |/ __ \| __ \| __ \| __ \ / __ \| __ \| ____| __ \ | \ / | | | | | | | |__) | |__) | | | | |__) | |__ | |__) | | |\/| | | | | | | | ___/| _ /| | | | ___/| __| | ___/ | | | | |__| | |__| | | | | \ \| |__| | | | |____| | |_| |_|\____/|_____/|_| |_| \_\\____/|_| |______|_| ___ ___ ___ _ __ ___ / __|/ __/ _ \| .__/ _ \ \__ \ (_| (_) | | | __/ |___/\___\___/|_| \___| 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 :ref:`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 =================== :: __ __ ____ _____ _____ _____ ____ _____ ______ _____ | \/ |/ __ \| __ \| __ \| __ \ / __ \| __ \| ____| __ \ | \ / | | | | | | | |__) | |__) | | | | |__) | |__ | |__) | | |\/| | | | | | | | ___/| _ /| | | | ___/| __| | ___/ | | | | |__| | |__| | | | | \ \| |__| | | | |____| | |_| |_|\____/|_____/|_| |_| \_\\____/|_| |______|_| _ _ _ | | (_) |__ __ _ ___ _ __ | | | | |_ \ / _` |/ _ \ |_ \ | |___| | |_) | (_| | __/ | | | |_____|_|_.__/ \__, |\___|_| |_| |___/ 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