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Author Topic: What other software is available?  (Read 6201 times)

Offline tanoramb

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What other software is available?
« on: May 06, 2008, 06:01:41 pm »
Hello everyone. I would like to know what other software besides 3DNA you know is available so as to build models of 3D DNA from sequence. I have read many papers and almost all of them describe software before 3DNA. Model.it, for instance, is a software currently available on-line but is very simple compared to 3DNA.

Thank you in advance for your replies.

Regards

Offline xiangjun

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Re: What other software is available?
« Reply #1 on: May 06, 2008, 11:02:29 pm »
Thank for posting a 3DNA-related question in the forum. I am hoping more people would share their experiences to questions like this one.

Depending what you want to do, you might check NAB from David Case's group.

HTH,

Xiang-Jun

PS: It helps to provide a link when referring to a resource, e.g. model.it.
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline Simonsig

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Re: What other software is available?
« Reply #2 on: January 30, 2011, 05:12:35 pm »
I have heard of ChemGraft and Facio, even though the last mentioned is not be too cool for visualization.
As far as the calculation scripts are used, they seem to be quite good and maybe some implementations and thoughts can be used.

Offline mickr

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Re: What other software is available?
« Reply #3 on: February 24, 2011, 11:48:25 pm »
@simonsig I think you mean ChemCraft? Which has been around since before 2004 and fairly well maintained, it also lets you create animated pictures of molecules, but it is limited in some features compared to 3DNA. One good thing about ChemCraft is that it is native in Linux as well, whereas 3DNA is only for Windows (correct me if i'm wrong?), although this is less of an issue nowadays thanks to virtual machine emulation.
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Offline mickr

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Re: What other software is available?
« Reply #4 on: February 24, 2011, 11:56:45 pm »
To answer my own question, 3DNA can be compiled on most platforms as detailed here:http://http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=3&t=122

I see Ben Eisenbraun has created a Mac OS X (Intel) version, has anyone used this?
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Offline antonivc

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Re: What other software is available?
« Reply #5 on: November 29, 2011, 01:43:01 pm »
Maybe some of these resources can help:

http://molbiol-tools.ca/molecular_biology_freeware.htm

Offline febos

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Re: What other software is available?
« Reply #6 on: February 04, 2014, 09:24:03 am »
Good Afternoon Dr. Lu.

Do you know any tools or programs which are similar to DSSR? (Especially for determining base-pairs from pdb-file).
DSSR is great for me but I need to know that it's the best and so far I could not find other programs.

Best regards,
Eugene

Offline xiangjun

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Re: What other software is available?
« Reply #7 on: February 04, 2014, 09:51:11 am »
Try the BGSU RNA Structural Bioinformatics resources by the Leontis-Zirbel Co-lab.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline febos

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Re: What other software is available?
« Reply #8 on: February 05, 2014, 01:21:46 am »
Thanks, Dr. Lu

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.