Basic question re: nucleotide sequence
Hello, I am trying to use Chimera to predict the structure of a nucleotide sequence that does not have a PDB ID. This is an unstudied protein, and I’m hoping to get some structure information and to visualize it using the software. I tried using the tutorials, but the best I can tell it appears to work off of already available PDB IDs. Is there a way I can enter the nucleotide sequences as a starting point? If so I’d really appreciate a few step/steps on how to do this. Best, Chad _______________________________________ Chad V. Pecot, M.D. Assistant Professor UNC Lineberger Comprehensive Cancer Center Thoracic Medical Oncology 450 West Drive, Office 32.048 Chapel Hill, NC 27599 Office: 919-966-4779 Cell: 615-305-3955 Fax: (919) 966-6735 pecot@email.unc.edu
Hello Chad, Chimera does not translate nucleic acid sequence into amino acid sequence, nor does it do “de novo” (without a template 3D structure) modeling, sorry. There are a lot of translation tools online… googling finds these and several more: <https://web.expasy.org/translate/> <http://www.bioinformatics.org/sms2/translate.html> <http://insilico.ehu.es/translate/> Comparative modeling requires a related 3D structure, which might even have relatively low sequence identity with your structure of interest. In general, the reliability of the sequence alignment between the two and of the resulting 3D model will be lower for lesser sequence identity. You could try using the Modeller approach available in Chimera if you can find known structures that might be sufficiently related. Usually this is done with BLAST search for similar sequences in the PDB, or threading your sequence of interest through known 3D structures. Chimera can do BLAST vs. PDB either in the Blast Protein tool (menu: Tools… Sequence.. Blast Protein) or “mda” command to find template(s), followed by use of Modeller comparative modeling with known template(s) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/blast.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mda.html> For example, if I use “mda” on Uniprot Q6F9H7 it finds me 4 templates with 43-47% sequence identity with the query (as does Blast Protein, but then it takes more steps to see the % identity). … but for threading, or completely de novo modeling, you would need to use some other software outside of Chimera. You could also see if there’s already models for your sequence in ModBase, but these are also comparative models (based on alignments with known structures) built with Modeller. <https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 24, 2018, at 4:57 PM, Pecot, Chad V. <pecot@email.unc.edu> wrote:
Hello, I am trying to use Chimera to predict the structure of a nucleotide sequence that does not have a PDB ID. This is an unstudied protein, and I’m hoping to get some structure information and to visualize it using the software.
I tried using the tutorials, but the best I can tell it appears to work off of already available PDB IDs.
Is there a way I can enter the nucleotide sequences as a starting point? If so I’d really appreciate a few step/steps on how to do this. Best, Chad
Hi Elaine, thanks for all of the great info! I'm used to dealing with RNA so I mistakenly wrote nucleic acids instead of amino acids I'll take a look at some of the modeling approaches you mentioned. Thanks again, Chad ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, November 26, 2018 1:35:36 PM To: Pecot, Chad V. Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Basic question re: nucleotide sequence Hello Chad, Chimera does not translate nucleic acid sequence into amino acid sequence, nor does it do “de novo” (without a template 3D structure) modeling, sorry. There are a lot of translation tools online… googling finds these and several more: <https://web.expasy.org/translate/> <http://www.bioinformatics.org/sms2/translate.html> <http://insilico.ehu.es/translate/> Comparative modeling requires a related 3D structure, which might even have relatively low sequence identity with your structure of interest. In general, the reliability of the sequence alignment between the two and of the resulting 3D model will be lower for lesser sequence identity. You could try using the Modeller approach available in Chimera if you can find known structures that might be sufficiently related. Usually this is done with BLAST search for similar sequences in the PDB, or threading your sequence of interest through known 3D structures. Chimera can do BLAST vs. PDB either in the Blast Protein tool (menu: Tools… Sequence.. Blast Protein) or “mda” command to find template(s), followed by use of Modeller comparative modeling with known template(s) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/blast.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mda.html> For example, if I use “mda” on Uniprot Q6F9H7 it finds me 4 templates with 43-47% sequence identity with the query (as does Blast Protein, but then it takes more steps to see the % identity). … but for threading, or completely de novo modeling, you would need to use some other software outside of Chimera. You could also see if there’s already models for your sequence in ModBase, but these are also comparative models (based on alignments with known structures) built with Modeller. <https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 24, 2018, at 4:57 PM, Pecot, Chad V. <pecot@email.unc.edu> wrote:
Hello, I am trying to use Chimera to predict the structure of a nucleotide sequence that does not have a PDB ID. This is an unstudied protein, and I’m hoping to get some structure information and to visualize it using the software.
I tried using the tutorials, but the best I can tell it appears to work off of already available PDB IDs.
Is there a way I can enter the nucleotide sequences as a starting point? If so I’d really appreciate a few step/steps on how to do this. Best, Chad
participants (2)
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Elaine Meng -
Pecot, Chad V.