MoDPepInt Server
MetaServer - Help
BIF
IFF

Introduction

The Meta-server has been implemented for the non-expert users. The output comprises predictions for all available domains for SH2, SH3 and PDZ. It reports only the 5 most confident predictions for each domain. The users are not required to set any parameters in this mode. By default all the parameters are on except pY filter (for SH2PepInt) and Cellular localization filters (for all three tools) since they need UniProt IDs of the query proteins. However, the user can easily select one of the dedicated tools for the same input to access the full prediction results and have a finer control over its parametric setting.

When using MetaServer please cite :

Results are computed with MetaServer version 1.0.0

Overview

The following parameters are used to control the execution of MetaServer

Furthermore, additional information is available

Input Parameters

?  Protein/Peptide FASTA

PDZPepInt accepts input in form of a multiple FASTA file. An example looks like this:
	
>EbbB1
MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV
VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA

>ErbB2
MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNL	
ELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNG

>ErbB3
MRANDALQVLGLLFSLARGSEVGNSQAVCPGTLNGLSVTGDAENQYQTLYKLYERCEVVM
GNLEIVLTGHNADLSFLQWIREVTGYVLVAMNEFSTLPLPNLRVVRGTQVYDGKFAIFVM

>ErbB4
MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQYRALRKYYENCEVVM
GNLEITSIEHNRDLSFLRSVREVTGYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIF

Input can be given either as direct text input or uploading a file.
Note: Input size is limited to restrict computation time and memory requirements.
The parameter constraints are: The input has to be in valid FASTA format. The number of sequences has to be at least 0 and at most 500. Sequence lengths have to be in the range 1-5000. The allowed sequence alphabet is 'GPAVLIMCFYWHKRQNEDST'. Either FASTA input or a UniProt ID list have to be provided. In case an enabled filter requires UniProt IDs: Each FASTA sequence header/name has to be just a valid UniProt ID or a valid UniProt FASTA header.

?  Protein UniProt IDs

Instead of feeding directly protein sequences, you can provide UniProt IDs of the targeted proteins as an input. In this case, the protein sequence will be automatically downloaded from the UniProt database. Multi UniProt IDs separated by below mentioned separators are also accepted. An example looks like this:
 P00533, P04626, P21860
The parameter constraints are: Has to be a list of 0-500 UniProt IDs that are separated by ([,\.;: \t\n]|\r\n). Access to the UniProt database is needed. The value has to match against the regular expression '^[^;'"]*$'.

Output Description

The output tables summarize all predicted protein-domain interactions.

Detailed descriptions:
  • 1. Input sequence id
  • 2. Binding region in the protein
  • 3. Binding sequence
  • 4. Binding domain/s with the protein
Within the SH2 result table: Y indicates binding Tyrosine residue while pY indicates binding Tyrosine residue whose phosphorylation has been validated and reported in PhosphoSitePlus database.
Note: predictions cover all domains available independent of the organism of interest. In order to select for a specific organism, please relate to the according dedicated tool.

Input Examples

?  general example

This is an example for the interaction prediction of human SH2, SH3 and PDZ domains with two sample target proteins.
The example's result can be directly accessed here

List of Changes