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Help on format of file Sample custom potential file
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Job Parameters

 
 
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Parameters with help content are in bold face.
JOBNAME
The jobname is chosen by the user for the job. Jobname is useful when the user wants to distinguish between the different submitted job(s).
EMAIL

If the user provide an email address then an email notification will be sent to inform the user about the job completion or unexpected termination of the job.

It is advised that a valid and active email address must be provided to receive notifications about the job status.

PDB Structure

The PDB structure is the primary input to the server. The PDB structure can be specified in the following ways:

1. By writing the four letter valid PDB complex code
2. By uploading a valid PDB file.

Caution: If a wrong PDB code is entered or if the uploaded file is not a valid PDB file then the job will be rejected by the server and the user will be informed of the respective error.

Mutational Analysis

Amino acid residues on the interface are mutated in-silico and the interfaces rescored to estimate the contribution of individual residues towards the interface. The user is presented with three options in this regard.

Option Requirement
Interface Alanine Scanning This option will mutate all the interface residues to alanine.
Interface Saturated Mutagenesis This will do a saturated mutagenesis for all the interface residues.
Manual mutation specification: This option allow to manually specify the residues to be mutated. Further, user can mutate specific interface residue to other residue(s), to alanine or do a saturated mutagenesis for the selected residue.

A a sample mutagenesis file is also provided to illustrate how different type of mutations can be specified by the user. Each line of the file has two tab separated fields.
Mutation Type Field 1 Field 2
Mutating the residue to Alanine
(mutate the residue number 177 (valine) in chain 'B' to Alanine)
177:VAL:B ALA
Mutating a residue to every other residue
(mutate the residue number 20 (histidine) in chain 'A' to all the other residues, Saturated mutagenesis)
20:HIS:A *
Mutating the residue to specific residue
(mutate residue number 27 (gultamate) in chian 'A' to lysine)
27:GLU:A LYS
Mutating the residue to a list of residue
(mutate residue number 27 (gultamate) in chian 'A' to lysine and valine)
27:GLU:A LYS,VAL
Distance Threshold

Two amino acid residues are defined as interacting if any relevant atom of residue A was within any relevant atom of residue B. The user can specify different distance thresholds for defining interface residue contacts and choose between 4 Å, 6 Å and 8 Å.

Note: A smaller distance threshold will provide a more stringent definition of the interface whereas a larger threshold might be helpful in the case of a loosely binding complex.

Custom Potential
Using this option, the user can upload their own potentials for scoring interfaces. There are two types of potentials:

1. Residue pairing preferences (Scoring Matrix)
2. Atomic Propensity

Users can upload up to three scoring matrices and three atomic propensity matrices, one for each interaction type. It is not compulsory to upload all 6 matrices. In case, where a user uploads fewer matrices, PIZSA will use the default matrices for rest of the potentials.
All custom potential files are required to be comma separated files (CSV). The format for Scoring Matrix and Atomic Propensity files are different and are described below:

Scoring Matrix file format:
[Res1],[Res2],[Score]
Res1 - Residue 1
Res2 - Residue 2
Score - Residue pairing score (Real Number)

Example:
GLU,HIS,0.864
ILE,SER,-2.307
ASP,MET,-1.247
MET,TRP,1.112
ALA,PRO,-2.529
GLN,TRP,0.866
GLY,PRO,-4.183
GLN,PRO,-0.570
ASP,ASP,-0.201
GLY,LYS,-4.183

Symmetric scores
Input: Interpreted Scores
ASP, MET, -1.247 ASP-MET = -1.247
MET-ASP = -1.247
Asymmetric scores
Input: Interpreted Scores
ASP, MET, -1.247
MET, ASP, 2.021
ASP-MET = -1.247
MET-ASP = 2.021

Atomic Propensity file format
[Res1],[Res2],[AtomCount],[Score]
Res1 - Residue 1
Res2 - Residue 2
AtomCount - Number of contact atoms (Integer)
Score - Residue pairing score (Real Number)

Example:
ARG,GLU,2,0.46
ARG,GLU,3,0.42
ARG,GLU,4,0.93
ARG,GLU,5,1.10
ARG,GLU,6,3.00
ARG,GLU,7,3.00
ARG,GLU,8,4.00
ARG,GLU,9,4.00
ARG,GLU,10,1.00
ARG,GLU,11,0.00

Symmetric scores
Input: Interpreted Scores
ARG, GLU, 7, 3.00 ARG-GLU[7] = 3.00
GLU-ARG[7] = 3.00
Asymmetric scores
Input: Interpreted Scores
ARG,GLU,7,3.00
GLU,ARG,7,1.50
ARG-GLU[7] = 3.00
GLU-ARG[7] = 1.50
Note:
1) Files should have 1 to 400 lines (rows).
2) Matrix Scoring files should have 3 comma(,) separated fields (columns) and Atomic Propensity files should have 4 comma(,) separated fields (columns).
3) Reverse residue pairs have the same score as the original residue pair, unless user specifies a different score.
4) Unspecified residue pairs are automatically assigned a score of 0.
5) AtomCount can have integer values from 2 to 28.
6) Scores can have real number values greater than or equal to 0.
Specific Interface
By default, all the interfaces in a multimeric query structure are scored. To generate predictions about a particular interface only, the user can specify the interface using this parameter. Specifying the interface of interest can significantly speed up computation times.

For example, user can specify only chain A (as interface 1) and chain B (as interface 2) and look at the residue interactions on these interfaces.

Processing your request.