PepSurf
PepSurf is a program for mapping a set of peptides, affinity selected against a probe molecule, onto a three dimensional structure of a target protein.

Download the program (for WINDOWS):
Current version is from 10.2.2007.
For support and questions please email me: itaymay@post.tau.ac.il
pepSurf.exe

You can try the program by typing pepSurf.exe -I 17b.pep -P 1g9m.pdb -C G

1g9m.pdb (PDB file format).
17b.pep (peptides file format).

Prior to running PepSurf, the surface accessibility of each residue should be calculated using the Surface Racer program (Tsodikov et al. 2002. J Comput Chem, 23, 600-9). The surface accessibility file (the output of Surface Racer) should be given as an additional input to PepSurf using the -S option.

When running Surface Racer choose these options:
Van del Waals radii sets: Chothia (option 2)
Probe radius in angstrom: 1.4
Calculation mode: Accessible and molecular surface areas (option 2)
Surface Racer downloads: [Windows] [Linux]

Source code and copyrights:
Source code (C++) is available for download here: [pepSurf.3.0.source.zip].
To compile in Unix / Linux, unzip all files to one directory, and use the Makefile command.
Alternatively, type: g++ -o pepSurf.exe -O3 *.cpp.

If there are problems with the compilations (occasionally, with old versions of g++) - please email me and I'll try to help. To modify the code, or use parts of it for other purposes, permission is requested. Please contact Tal Pupko at talp@post.tau.ac.il

When using the PepSurf program you agree upon these terms and conditions.

Overview for the stand alone program:
A phage-display library of random peptides is a combinatorial experimental technique that can be utilized to study antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that bind the antibody with high affinity. This set of peptides can then be used to infer the antibody's corresponding epitope. The rationale behind this technique is that the peptides that bind the antibody mimic the genuine epitope of its interacting antigen.
PepSurf is an algorithm for mapping a set of affinity-selected peptides onto the solved structure of the antigen. The problem of epitope mapping is converted into a task of aligning a set of query peptides to a graph representing the surface of the antigen. This is achieved by searching for the best alignment of each peptide against virtually all possible paths in the graph. Following a clustering step, which combines the significant hits, a predicted epitope is inferred. PepSurf can further be used to infer the interface between any two interacting proteins, for which one of the proteins was subjected to a phage-display experiment, and the other has a three-dimensional structure.

Methodology:
The program uses as input the precomputed surface accessibility of the target protein to create a surface graph representing the exposed residues of the target protein. It then aligns each peptide to this surface graph. The output is one (or more) predicted patches of residues on the surface of the antigen that correspond to putative epitope sites.

In citing the PepSurf program please refer to:

Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T. 2007. A graph-based algorithm for epitope mapping using combinatorial phage-display libraries. Nucleic Acid Research. 35(1): 69-78

Usage


Inputs:
The obligatory inputs are a peptides file, a pdb file of the target protein, a chain identifier, and a surface accessibility file. This peptides file should contain the list of peptides to be aligned to the PDB structure. An example of the peptides file format can be found here. Each peptide sequence should be preceded by a line starting with >. Optionally, a number can follow the > mark. This number specifies the number of times the peptide was isolated in the biopanning experiment. The list of peptides should be proceeded by a #PEPTIDES_START line, and end with a #PEPTIDES_END line.

quick help:

Flag Description Default
-I [peptides file] The input sequence file name.
Obligatory
-P [PDB file] The input pdb file name Obligatory
-S [Surface accessibility file] The surface accessibility file as computed using the Surface Racer program Obligatory
-O [output file] The results output file pepSurf.res
-C [chain identifier] The chain id of the target protein in the input pdb file Obligatory
-G [gap penalty] Penalty for opening a gap -0.5
-M [Substitution similarity matrix] Substitution matrix type:
-80 = BLOSUM80
-62 = BLOSUM62
-30 = BLOSUM30
-62
-V [probability] Probability for obtaining the best path 0.95
-h help


Out files:

The output files of PepSurf are given under the RESULTS directory. The output files include:
pepSurf.res:
This file includes the predicted clusters sorted according to their score. For each cluster the amino acids comprising it are given. In addition, each cluster contains the list of peptides that have corresponding paths in it. This list is given under "Peptide Contribution".
rasmol.scr:
A rasmol script file for visualizing the predicted clusters with the RASMOL or RASTOP programs.
Folder sigPathsAln:
Files in this folder contain the list of alignments for each peptide.


Mapitope

Current version is from 10.2.2007.
For support and questions please email me: itaymay@post.tau.ac.il



Source code and copyrights:
Source code (C++) is available for download here: [Mapitope.source.zip].
To compile in Unix / Linux, unzip all files to one directory, and use the Makefile command.


If there are problems with the compilations (occasionally, with old versions of g++) - please email me and I'll try to help. To modify the code, or use parts of it for other purposes, permission is requested. Please contact Tal Pupko at talp@post.tau.ac.il

When using the PepSurf program you agree upon these terms and conditions.

In citing the Mapitope program please refer to:

Bublil EM, Freund NT, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein ND, Pupko T, Gershoni JM. 2007. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins. 68(1):294-304

Usage


Inputs:
The obligatory inputs are a peptides file, a pdb file of the target protein, a chain identifier, and a surface accessibility file. This peptides file should contain the list of peptides to be aligned to the PDB structure. An example of the peptides file format can be found here. Each peptide sequence should be preceded by a line starting with >. Optionally, a number can follow the > mark. This number specifies the number of times the peptide was isolated in the biopanning experiment. The list of peptides should be proceeded by a #PEPTIDES_START line, and end with a #PEPTIDES_END line.


Prior to running Mapitope, the surface accessibility of each residue should be calculated using the Surface Racer program (Tsodikov et al. 2002. J Comput Chem, 23, 600-9). The surface accessibility file (the output of Surface Racer) should be given as an additional input to Mapitope using the -S option.

When running Surface Racer choose these options:
Van del Waals radii sets: Chothia (option 2)
Probe radius in angstrom: 1.4
Calculation mode: Accessible and molecular surface areas (option 2)
Surface Racer downloads: [Windows] [Linux]


You can try the mapitope by typing: mapitope -A -P 1g9m.pdb -S surfracer_output -I 17b.pep -C G -D 9.0 -V 3.0 -F 3 -Y

1g9m.pdb (PDB file format).
17b.pep (peptides file format).


quick help:

Flag Description Default
-I [peptides file] The input sequence file name.
Obligatory
-P [PDB file] The input pdb file name Obligatory
-S [Surface accessibility file] The surface accessibility file as computed using the Surface Racer program Obligatory
-O [output file] The results output file epitomap.res
-C [chain identifier] The chain id of the target protein in the input pdb file Obligatory
-A Distance calculation method: If this option is set then calculates the c-alpha vs. c-alpha distance all-atoms vs. all-atoms
-F [Fill-in range] 0 (do not fill in)
-h help