Model Submission Guide

This is a brief documentation of steps required for successful submission of the models (predicted protein structures). In case the form is not submitting, please verify the entries shown in pink boxes once again. Please contact vips.bioinfo@gmail.com for further queries.

A. Following files are required to be uploaded :-

1. 3D coordinate file -
Atomic coordinates are to be provided in PDB format. This file can be downloaded or viewed in the model description page generated after The file should have .pdb extension.

2.Query Sequence file -
The query sequence is to be given in FASTA format. The file should also have .fasta extension. This sequence will be used in the generation of Structure Coverage Map of the corresponding virus. 

3. Query Template Alignment file -
This file contains the target template alignment data. The file should have .aln or .txt extension.

4. PROCHECK Analysis file -
The Ramachandran plot for the structure should be uploaded as PROCHECK analysis file in pdf format only.

5. ProSA-web analysis file -
The energy graph of the structure is uploaded  as ProSA-web analysis file in pdf format only.

B. Source Virus Information Section-

Please submit the complete name of source virus and the virus family. The NCBI taxonomy ID for the virus is also needed. (e.g. source virus -Dengue Virus 1, family - Flaviviridae, NCBI taxon ID  - 11053). The host entry is optional.

C. Model Building Information Section-

1. Number of chains/ chain id - Number of chains in the atomic coordinates file is required. If the chain ids are not assigned please specify any alphabet or 'X'.
2. Query id code - Please specify the GenPept or UniProt protein ID(e.g. GenPept / NP_733807).
3. Sequence status/ Fragment - If the sequence modelled is partial then specify the length of fragment or start-stop positions.
4. Template PDB ids - Please specify the pdb id of the template.
5. %identity - between the template and query seuence.
6. Modellling software used - Please give the details for the modelling software or the method used for predicting structure(e.g. Homolgy modeling/ InSight II).

D. Submitter Information Section-

1. Please provide your name, company's name, location and its url.
2. The institutional email id will be used for communication. You will receive auto-generated mails about model submission on this id only.

E. After Successful Submission -

If the form is submitted successfully you will get a message indicating the successful submission and the files uploaded by you. An email stating the same will be sent at your institutional email-id.
After the entries are verified and processed for deposition in the ViPs database, a unique model-id will be assigned to it and another email will be sent stating the model-id and the link for webpage where you can view the details about your model including the structure coverage map generated for it. You will probably receive this email in about a week's time.

Thanks for using ViPs database!