Programs

Note that to get the list of options for ematchsite, simply execute the program command with no arguments. Below is the full description of available options.

ematchsite

ematchsite performs a local, sequence order-independent structure alignment of ligand binding sites in two proteins.

Input options:

-i input_file, where input_file is a single text file that provides the locations of all data files required by eMatchSite. Each line should contain only one keyword followed by a space and the location of input file. Lines starting with # are ignored

Keywords (A - first protein, B - second protein):

  • structureA, structureB: target structure in PDB format
  • profilesA, profilesB: sequence profiles
  • secstrA, secstrB: secondary structure profiles
  • pocketsA, pocketsB: eFindSite pockets
  • numberA, numberB: eFindSite pocket number (default 1)
  • alignmentsA, alignmentsB: eFindSite alignments
  • ligandsA, ligandsB: eFindSite ligands

Alternatively, you can specify the locations of individual data files from command line using the following options:

-structureA first_pdb where first_pdb is the first protein in PDB format

-structureB second_pdb where second_pdb is the second protein in PDB format

-profilesA first_prf where first_prf is a sequence profile for the first protein

-profilesB second_prf where second_prf is a sequence profile for the second protein

-secstrA first_sec where first_sec is a secondary structure profile for the first protein

-secstrB second_sec where second_sec is a secondary structure profile for the second protein

-pocketsA first_pkt where first_pkt is a pocket file constructed for the first protein by eFindSite

-pocketsB second_pkt where second_pkt is a pocket file constructed for the second protein by eFindSite

-numberA first_num where first_num is a pocket number in the first protein

-numberB second_num where second_num is a pocket number in the second protein

-alignmentsA first_ali where first_ali is an alignment file constructed for the first protein by eFindSite

-alignmentsB second_ali where second_ali is an alignment file constructed for the second protein by eFindSite

-ligandsA first_lig where first_lig is a ligand file constructed for the first protein by eFindSite

-ligandsB second_lig where second_lig is a ligand file constructed for the second protein by eFindSite

Output options:

-o output_name, where output_name is a PDB file that contains all results from eMatchSite

Virtual screening options:

-m score_func, where score_func lets you choose the scoring method; these are currently implemented functions (default sum):

  • single scoring functions:
    • tst - classical Tanimoto coefficient for Daylight
    • tsa - average Tanimoto coefficient for Daylight
    • tsc - continuous Tanimoto coefficient for Daylight
    • tmt - classical Tanimoto coefficient for MACCS
    • tma - average Tanimoto coefficient for MACCS
    • tmc - continuous Tanimoto coefficient for MACCS
  •  combined scoring functions:
    • sum - data fusion using sum rule
    • max - data fusion using max rule
    • min - data fusion using min rule
    • svm - machine learning using Support Vector Machines (SVM)

Output files:

A single file that contains numerical scores for the constructed alignment of binding sites, aligned residue pairs and the corresponding Cα-Cα distances, transformation matrices to superpose the second protein onto the first one, and the coordinates of the second protein upon the optimal binding site superposition.

 

© Michal Brylinski
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