RE: [predictprotein-science:648] Problems and advices relatedproteinmodelling and Protein protein interaction

[Avijit Patra]

Good morning
Dr. Mahapatra,
Thanks for the compliment. My details contacts are given below,
Please.

Regards
A.Patra


AVIJIT PATRA
FISH MICROBIOLOGIST
FISH GENOMIC AND PROTEOMIC LAB.
DEPARTMENT OF AQUATIC ANIMAL HEALTH.
FACULTY OF FISHERY SCIENCE.
WEST BENGAL UNIVERSITY OF ANIMAL AND FISHERY SCIENCE.
CHAKGARIA-700094

Email-a...@gmail.com
avijit_c...@rediffmail.com
Mob-9681824890

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From: R A J Rajkishore
Sent: ‎01-‎05-‎2014 04:59 PM
To: predictprot...@googlegroups.com
Subject: Re: [predictprotein-science:648] Problems and advices relatedproteinmodelling and Protein protein interaction

Thanks Avijit for the response.

I have completed many more protocols.

Its time for bit discussion and analyzing the outputs.

Please share me your mail id or contact info.

With best regards,

Raj.

On Monday, April 21, 2014 7:59:41 PM UTC+5:30, avijit patra wrote:

Hello
Dr.Mahapatra
First you plot this protein sequences in RAM PAGE server, and see which are the residues coming  of the region,
You can use the yasara minimization software for minimize this residues and than open this in pdb file in discovary studio..

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From: R A J Rajkishore
Sent: ‎21-‎04-‎2014 19:01
To: predictprot...@googlegroups.com
Subject: [predictprotein-science:643] Problems and advices related proteinmodelling and Protein protein interaction

Hello Everyone , 

I have a protein named LOXL1 (Human). This protein has no so called structures in PDB,neither any other databases.It just contains a structure with less identity in ProteinModel DB.

I am modelling this protein. As far I have investigated this , this protein contains 57% of disordered region ,30% structural identity and query coverage of 10%.I have collected all the 

details of the protein and identified that it causes pseudoexfoliation disease with binding another protein named FIBULIN 5.This protein has also same affairs like LOXL1.Also I have 

check the mutation region of this two proteins which is around 50% with each other.

Now Please be kind to suggest me my doubts , 

1. Need I must refer for Protein protein Interaction between this two protein?

2. How can I model LOXL1 , I have generated the model in servers like I-tassar , Swiss Model , Phyre2 and Rosetta.

So from all this structures which is the best one .. how can I recommend and also I have the model structured by Modeller.

How can I do model of this protein ..??

Please suggest me .. !!

Regards , 

Raj Kishore Mohapatra

Lab of Computational Biology

Center For DNA Fingerprinting and Diagnostics (CDFD)

​ 

DBT Lab.​

Hyderabad - 500001

Mobile :  +91 9030912109

                 +91 9861233393

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