Programs

The eFindSitePPI software distribution includes the following main programs: efindsiteppi and efindsiteppi_map. To get the list of available options for each program, simply execute the program command with no arguments. Below is the full description of the programs.

efindsiteppi

efindsiteppi predicts interfacial sites and residue interactions for a given protein structure using threading data.

Mandatory arguments:

-s input_file, where input_file is the target protein structure in PDB format; you can use either experimental structure or protein model

-t target_ethread, where target_ethread is the output file from eThread

-e seq_prf, where seq_prf is the target sequence profile; it can be generated e.g. by SP3 or SPARKS.

-o output_name, where output_name is used to save two output files with different extensions that store interface prediction results, see below

Optional arguments:

-b seq_cut, where seq_cut is a sequence identity threshold of the target protein to templates. Note that this argument should be used only for benchmarks. The default value of 1.0, which means that all identified templates will be used to predict binding sites

-m tm_score, where tm_score is a TM-score threshold. The default value is 0.4, which means that only these template structures whose TM-score to native is ≥ 0.4 will be used

-x template_max, where template_max is the maximum number of templates, default 1000

Output files:

output_name.sites.dat: detailed information on the predicted interface residues and interactions, the list of templates, rotation matrices to align templates onto the target, the confidence of the prediction, etc

output_name.alignments.dat: structure alignments between the target and template proteins constructed by fr-TM-align

efindsiteppi_map

efindsiteppi_map prepares a mapping file that maps threading templates to protein dimer templates used by efindsiteppi.

Mandatory arguments:

-t thread_lib, where thread_lib is a complete threading library in FASTA format

-p efindsiteppi_lib, where efindsiteppi_lib is the eFindSitePPI library in FASTA format, look for pdb.fasta

-o output_file, where output_file is the mapping file linking threading and eFindSitePPI libraries

Optional arguments:

-a proc_num, where proc_num is the number of the processors to be used, default 1

Output files:

A mapping file required to run efindsiteppi

 

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