QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: GJK on January 9, 2014, 05:09

Title: Requirement of structures of cell lines or gene sequences
Post by: GJK on January 9, 2014, 05:09

Dear all.

Like Drug Bank,which provides  drugs in .mol format ,do we have any database which can provide cell lines or gene sequences of normal human cells and cancerous cells???

If then kindly tell me the procedure for download and conversion.

For the kind information i tried in NCBI but to my knowledge it has no .mol or any downloadable format.

Janani.K

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: GJK on January 16, 2014, 02:13

Dear all,

I need your help for downloading the gene sequence.

I can download the complete sequence from gene bank but how to reduce the number of sequences

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: Nordland on January 16, 2014, 09:16

I dont know much about gene sequence apart from the things that my wife tells me know and then :)

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: GJK on January 16, 2014, 11:28

Thank you for your outspoken reply.

But since I am working with biosensor towards anticancer activity I posted.Sorry if I have committed any error by posting this question.

One more doubt Mr. Nordland we have Nucleotide structures in the database of our ATK-VNL.
Just confirm me whether they are the basic structures of human nucleotides. The confirmation will enable me to speed up my research.

Also tell me in a  ATK-VNL license what is the maximum number of atoms we can optimize.
According to my research with VNL it is (150 atoms).Am I right?(I doesn't mean a cluster pack here)

Thanks in advance.

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: Nordland on January 16, 2014, 12:58

There is no limit on the number of atoms in regards to the license you have.

Depending on the system size and the method used it will use a vary amount of memory, but 150 atoms does not sound like a lot. I can do many thousands atoms on my personal laptop.

The nucleotides in our database (Nucleobasis) are the 5 most common building blocks of nucleic acids, so I guess it safe to say that they are the basic structure of human genome.

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: GJK on January 16, 2014, 14:52

Dear Mr.Nordland,

Thank you for all your valuable suggestions.

Kindly clarify my problem in the attachment

Edit: I added your content of the doc so it was searchable other as well.

Quote

If you say that "I can do many thousands atoms on my personal laptop",
If we can perform calculations for more than 1000 atoms kindly suggest the memory requirement. Because when I did some calculations with Graphene Nanoribbon ZGNR (6,0) of 10 unit cells and molecules like anthracene, porphyrin etc. the simulation terminated half way through when the number of atoms exceeded 150 done by varying the concentration of the moleules.Kindly clarify!

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: Nordland on January 16, 2014, 15:21

With standard default parameters a graphene nanotube like you describe would at maximum take 1 GB of memory.

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: GJK on January 16, 2014, 16:18

Thank you Mr. Nordland.Will post  regarding this issue after verifying the problem exceeding 150 atoms.In the mean time if I get any error when exceeding 150 atoms I will post the error message for clarification.

Title: Re: Requirement of structures of cell lines or gene sequences
Post by: techenthusiast on May 21, 2025, 11:11

Good morning , Hope you are doing well. How to extract celllines or protien or DNA or RNA or Aptamer as a biomarker for FET based Sensor?
For Example -    https://pubchem.ncbi.nlm.nih.gov/cell/CVCL_0031

Keratin and some other smaller molecules are not able to deal with Pubchem CID.
As per my experience -Pubchem CID was there for only molecules.

Thank You.