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Questions and answers => General discussions (Q&As) => Topic started by: xiangjun on March 24, 2008, 10:23:21 pm

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Title: What users (objectively) have to say about 3DNA
Post by: xiangjun on March 24, 2008, 10:23:21 pm
Occasionally, just out of curiosity, I check the log of visitors to the 3DNA website. By following the links, I found some nice comments on 3DNA. As a humble person, I feel gratified to read them. I believe these comments reflect more objectively users' real experience and feelings about 3DNA.

Additionally,  over the years, I have received many compliments regarding 3DNA through e-mails.  I understand from experience, however, that people are more generous when they say kind words privately,  especially when asking for help  ;), than in public.

On the other hand, if you find any negative comments/notes on 3DNA on the internet, please add them here as well: I am always interested in improving 3DNA in ways that make sense to me.

Listed below is a sample of the nice comments about 3DNA that I happened to find on the internet (follow the link at the top of each item to see its original source).

[added: October 1, 2009] Re: [ccp4bb]: protein topology diagram, references for DNA and sugar conformation (http://www.hhmi.swmed.edu/Lists/ccp4-users/6877.html) (Michael Sierk http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html (http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html))

[added: April 8, 2008] Re: [ccp4bb] DNA building program (http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg07191.html) (Mensur Dlakic; Tue, 12 Aug 2008 15:50:41 -0700)
Quote
Depends for what you need the program. If you want rigorously built DNA molecule, I suggest 3DNA:

http://rutchem.rutgers.edu/~xiangjun/3DNA/ (http://rutchem.rutgers.edu/~xiangjun/3DNA/)

I have a program that may be better for visualizing built DNA molecules, but is not as rigorous when it comes to reconstructing DNA bases from parameters. Here are few screenshots:

http://www.homepage.montana.edu/~mdlakic/software.html (http://www.homepage.montana.edu/~mdlakic/software.html)

Excerpt from [ccp4bb]: Stretching Modelled B-DNA - Programs (http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01142.html) (Balvinder Dhaliwal; Tue, 10 Apr 2007 20:14:50 -0700)
Quote
Thank you for the prompt replies. I was able to generate B-DNA models of
varying pitch.
Two of the more versatile tools for manipulating nucleic acid structures
are:-

i)      NAMOT (suggested by William Scott, UCSC); download at
http://namot.lanl.gov/ (http://namot.lanl.gov/)<https://exchweb.bcm.tmc.edu/exchweb/bin/redir.asp?URL=http://namot.lanl.gov/>

ii)     3DNA (suggested by Nicola Abrescia, Strubi, Oxford); download at
http://rutchem.rutgers.edu/~xiangjun/3DNA/ (http://rutchem.rutgers.edu/~xiangjun/3DNA/)<https://exchweb.bcm.tmc.edu/exchweb/bin/redir.asp?URL=http://rutchem.rutgers.edu/%7Exiangjun/3DNA/>

                                                     Balvinder Dhaliwal.
(Baylor College of Medicine, Houston, Tx.)
From Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, University of Utah: "Re: AMBER: internal coordinates " (http://amber.ch.ic.ac.uk/archive/200605/0004.html)
Quote
my recommendation is to use another program
to build the helices.

3DNA - http://rutchem.rutgers.edu/~xiangjun/3DNA/ (http://rutchem.rutgers.edu/~xiangjun/3DNA/)

  A nice program by Xiang-Jun Lu that not only can analyze
  nucleic acid structure well, but generate models with
  fiber or user supplied parameters for arbitrary twist or
  alteration of helicoidals...

NAB - nucleic acid builder "language" by Dave Case's group, ...

Learning either one (or both) of these will be significantly more general and
useful than trying to reverse engineer nucgen...
From John E. Kerrigan, Ph.D. (Robert Wood Johnson Medical School, UMDNJ): " [gmx-users] pdb files of DNA" (http://www.gromacs.org/pipermail/gmx-users/2003-September/007241.html)
Quote
Hmmm...

Try using 3DNA, a program developed by Wilma Olson's group at Rutgers for
analyzing and cleaning up PDB files of DNA/RNA structures.  See
http://rutchem.rutgers.edu/~xiangjun/3DNA/ (http://rutchem.rutgers.edu/~xiangjun/3DNA/) for more info and download.

3DNA is to nucleic acids what procheck is to proteins for analysis.  Very
handy.

Enjoy 3DNA!

John

-----------------------------------------
John E. Kerrigan, Ph.D.
Robert Wood Johnson Medical School, UMDNJ
675 Hoes Lane
Piscataway, NJ 08854  USA
-----------------------------------------
From Ho-Leung Ng (UC Berkeley)  "[ccp4bb]: programs for DNA conformation analysis" (http://www.ysbl.york.ac.uk/ccp4bb/2002/msg00595.html)
Quote
Curves: http://www.ibpc.fr/UPR9080/Curindex.html (http://www.ibpc.fr/UPR9080/Curindex.html)

Freehelix: http://ndbserver.rutgers.edu/NDB/ftp/ND ... eehelix98/ (http://ndbserver.rutgers.edu/NDB/ftp/NDB/programs/freehelix98/)

3DNA:http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html (http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html)


   I recommend 3DNA. Cheers!


Ho-Leung Ng
UC Berkeley
3DNA has been selected as an "Essential and helpful software" by [url=http://www.biomedscience.co.uk/]http://www.biomedscience.co.uk/ (http://www.biomedscience.co.uk/kitslinks/pages/Essential_and_helpful_software/)[/url].

Recommended by Michael Banck for DNA molecular building at CCL mailing list (http://www.ccl.net/chemistry/resources/messages/2002/10/07.002-dir/index.html)
Quote
Re: CCL:dna molecular building

    * From: Michael Banck <banck \at// donjuan.stud.chemie.tu-muenchen.de>
    * Subject: Re: CCL:dna molecular building
    * Date: Mon, 7 Oct 2002 13:23:18 +0200

Hi,
 > I would like to know if there is any dna molecular building free
 > program that, providing the nucleotide sequence, it outputs
 > a first approximation to dna molecular moldel, in PDB format,
 > if possible.
 have a look at
 http://rutchem.rutgers.edu/~xiangjun/software.html (http://rutchem.rutgers.edu/~xiangjun/software.html)
 or
 http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html (http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html)
 hope that helps,
 Michael
 
Recommended by Jeffrey Nauss (Ph.D., Lead Training Scientist,  Accelrys) for DNA structural analysis at CCL mailing list (http://www.ccl.net/chemistry/resources/messages/2007/01/27.001-dir/index.html)
Quote
CCL: Windows-based software for the analysis of the DNA structure

    * From: Jeff Nauss <jnauss*|*accelrys.com>
    * Subject: CCL: Windows-based software for the analysis of the DNA structure
    * Date: Fri, 26 Jan 2007 05:18:54 -0800

 Sent to CCL by: Jeff Nauss [jnauss__accelrys.com]
 owner-chemistry]~[ccl.net wrote on 01/26/2007 12:42:24 AM:
 > Sent to CCL by: "Patrick  Pang" [skpang::ctimail.com]
 > Dear all,
 >
 > Would you suggest software for the analysis of the DNA structure (e.
 > g. major groove, minor groove, bent angle (like cisplatin binding to
 > DNA), twist angle ...) under Windows?
 You may want to check out 3DNA at URL
 http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html (http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html).
 Jeff
 --
 Jeffrey L. Nauss, Ph.D.
 Lead Training Scientist
 Accelrys
 10188 Telesis Court, Suite 100
 San Diego, CA 92121-4779
 Phone: +1-858-799-5555
 Fax: +1-858-799-5100
 http://www.accelrys.com/services/training/ (http://www.accelrys.com/services/training/)
 

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University