ASSP
A Program for assigning Secondary Structures in proteins

Instructions for offline users of ASSP:

ASSP is available for both Linux/ Unix and Windows operating system. One can download it from the Download section or by clicking on the respective operating system name.

Requirements:

• ASSP

The ASSP executable, along with the input coordinate file should be kept in the same folder.

Input Files:

• File with three dimensional coordinates: The three dimensional coordinates in PDB file format. The extension must be .pdb

The Command-Line Options:

• -i           Input file with 3D atomic coordinates in PDB file format
• -tor       [Y/N] Whether to generate file containing φ-ψ of each residues. Default type is N
• -img     [Y/N] Whether to generate pictorial representations of ASSP assignments. Default              type is N
• -h         Help for ASSP
• -v         Version of the program in use

Except options -v and -h, the others can be combined in any order and used to get desired results.

Command line usage:
Sample usage of options for running ASSP

• ./assp -i input file
  This command prompts the program to generate the results in the text format.

• ./assp -i input file -tor Y or N
  This command prompts the program to generate the results in the text format along with the file containing φ-ψ of each residues.

• ./assp -i input file -img Y or N
  This command prompts the program to generate the results in the text format along with the file containing the pictorial representation of the assignments done by ASSP.

A successful run of ASSP (with default options) will give four nonempty files named:

• *_nh.out
• *_diff.out
• *_cont.out
• *_assp.out

Along with ASSP, two more programs are provided namely 'ASSP_tor' and 'ASSP_img'.

• ASSP_tor: will give the φ-ψ for each residues. File will be named as '*_tor.out'.
• ASSP_img: will generate pictorial representation of the assignments done by ASSP. File will be named as '*_assp.png'.

Detailed description about each file can be found at the output file section.

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Instructions for online users of ASSP:

User has got two options for using the web-server:

• PDB identifier
  • Single input PDBID
  • Multiple input PDBID seperated by commas(,)
  • Uploading a file containing PDBIDS one per line (Example file)
• Uploading the PDB formatted file

if the length of the uploaded PDB file name is more than 11 (including the extension), last 11 characters from the name will be considered and input file will be renamed. If the uploaded file name contains a hyphen (-) or underscore (_), the special character will be removed. A corresponding message will be displayed on the result page.

Successful run will take the user to the page containing links to the text and graphical representation of the assignment done by ASSP. user will be given an option for running HELANAL-Plus for the ASSP assigned helices with length more than 8 residues. In case of the multiple input PDB files, options for each files will be given in a seperate row. User can download output files corresponding to one or all input files at a time by clicking proper Download button.

Information about the graphical representation page:

Link to the corresponding text representation page displaying various plots will be given. A pictorial representation of the assignment is inspired by PDBsum/ STRIDE web server. The input protein will be displayed in a JmolApplet in ribbon representation and residues will be colored according to the color assigned to each secondary structure as mentioned in the top of the page. pictorial representations are made interactive and reveal the information about the residue. Assignments done by ASSP can be compared with that of done by DSSP or STRIDE. after selecting the program, corresponding assignment will be displayed in graphical form, just below the assignment done by the ASSP for each residue. Same protein will be displayed in second JmolApplet in the ribbon representation and residues will be colored according to the secondary structure assigned by the selected program (DSSP/ STRIDE). If PDB identifier is provided as an input, links to various popular databases like PDB, SCOP, CATH, PDBsum and PDBe will be provided.

Ramachandran plot and rise per residue vs Twist for the protein structure can be found here. At the same time user can compare the same with that of DSSP or STRIDE. By default the first chain will be displayed, but other chains can also be selected by means of selecting any chain from the drop down menu given in the right hand side. Residues in the Ramachandran plot or the (twist, Height) of repeating unit belonging to a particular secondary structure will be colored according to the color code given on the top of the page.

Information about the text representation page:

Link to the corresponding graphical representation will be given. If PDB identifier is provided as an input, information aboout the input file will be displayed, which will be directly taken from the PDB file, with no modification. Assignment done by ASSP will be printed in the text format. The format is PDB HELIX format. If PDB identifier is provided as an input, links to various popular databases like PDB, SCOP, CATH, PDBsum and PDBe will be provided.

Helical Wheel:

A helical wheel is a plot of a helix, when it is visualized from top. In short it is the 2D representation of a helix. We use the twist per repeating unit to generate the helical wheel, giving the real time orientation of two consecutive amino acids when they are seen down the axis. Users will have three options namely

• Any ASSP assigned helices can be selected from the drop down menu. The background of each option is colored according to the helix type. User has to select the number of residues displayed at a time.
• One can select the option of displaying helical wheel for the full helix.
• User can specify the residue start, end and Chain identifier for generating the corresponding helical wheel.

Color code for the helices and spheres representing the residues can be found by letting the cursor hover over 'Color Code [?]'.