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Topics - xiangjun

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1
Site announcements / Highlights of recent developments of 3DNA/DSSR
« on: November 20, 2016, 07:13:58 pm »
Dear 3DNA Forum subscribers,

Here are some highlights of recent developments of 3DNA/DSSR:

Note: If you've difficulty in accessing the 3DNA homepage, possibly the case from mainland China (as I know it), please visit its duplicate at http://home.x3dna.org. This newsletter is written in Markdown, with a translated HTML version posted on the 3DNA homepage.

3DNA v2.3
  • The C source code is now available. Since the programs are written in strict ANSI C, 3DNA can be compiled (as is) on any computers/operating systems with a C (or C++) compiler. For user convenience, three binary distributions (with source code under the src/ subdirectory) are provided for Windows, Linux, and Mac OS X. The distributed Windows version works in native Windows (7 and up, via the cmd command-line interface, or ConEMU), MinGW/Msys (Msys2), and Cygwin, in either 32 or 64-bit.
  • A new set of 'simple' base-pair and step parameters was introduced to give 'intuitive' numerical values for non-Watson-Crick base pairs and associated steps. See the short communication titled Characterization of base pair geometry in the January 2016 issue of Computational Crystallography Newsletter (CCN).
  • The fiber program includes a new option, --pauling, for easy generation of Pauling & Corey triplex models of DNA/RNA with arbitrary base sequence. See my blogpost titled Pauling's triplex model of nucleic acids is available in 3DNA.
  • Thomas Holder (PyMOL Principal Developer at Schrödinger, Inc.) has built a PyMOL wrapper to 3DNA fiber models. Now generating standard, regular DNA/RNA models in PyMOL is straightforward -- thanks, Thomas!

DSSR (Dissecting the Spatial Structure of RNA)
  • Selected features of DSSR have been incorporated into Jmol (in collaboration with Robert Hanson, Jmol Principal Developer), and PyMOL (in collaboration with Thomas Holder). In Jmol application (via the Console window), one can now, for example, load =1ehz/dssr and then select hairpins; color red to see where the three hairpin loops are in 3D. The Jmol-DSSR web interface makes DSSR-enhanced visualization of nucleic acid structures in Jmol readily accessible to a broad user base, and has been employed in classes for educational purpose. A sample image of DSSR-derived cartoon-block representation via PyMOL is available for PDB entry 5dww, which has a G-quadruplex-duplex interface.
  • Since the publication of the Nucleic Acids Research paper in 2015, DSSR has been continuously refined and expanded, with a total of 36 new releases (from v1.2.8 to v1.6.4) as of this writing. Notably, the --json option provides DSSR-derived parameters in the simple, structured, and standard JSON format that can be easily parsed. This JSON output format is the (preferred) way for the outside world to interface with DSSR, and the Jmol-DSSR integration is built upon it. The --nmr option allows for batch processing of MODEL/ENDMDL-delineated NMR ensembles or trajectories of molecular dynamics (MD) simulations. Did you know that scripts and data files for reproducing the reported results are available in the DSSR-NAR paper section on the 3DNA Forum?
  • The User Manual is now 88-page long, covering nevertheless only the most common use cases of what DSSR has to offer. Miss a feature that you would like to have? Maybe it is already there or can be easily implemented in DSSR. Simply ask (on the 3DNA Forum), and I'll try my best to help.

SNAP (Structures of Nucleic Acid-Protein complexes)
  • SNAP aims to consolidate, refine, and significantly extend commonly used functionalities for DNA/RNA-protein structural analysis in one easy-to-use program. Currently in beta testing, SNAP is already fully functional, with features for characterizing the protein-nucleic acid interface and identifying amino acid-base pairing and stacking interactions.

A note for 3DNA/DSSR users in mainland China: It's a pleasure to see the ~100 registrations on the 3DNA Forum with emails ending in .cn, 163.com, or qq.com etc., mostly from recent years. I'm planning a trip to China in 2017, and I'd be happy to meet some of you for academic exchanges and possible collaborations (学术交流、合作). If you're interested, let's get in touch!

Best regards,

Xiang-Jun

2
Site announcements / Pauling's triplex model of DNA and RNA
« on: November 17, 2016, 11:26:31 am »
As of v2.3-2016nov16, the 3DNA fiber program has added the --pauling option. This new feature is intended for easy generation of DNA/RNA triplex models based on the historical paper of Pauling and Corey in 1953, titled "A proposed structure for the nucleic acids". Combined with the existing --sequence option, 3DNA users can now construct a Pauling triplex model with arbitrary base sequence.

The basic usage is very straightforward, as illustrated in the following list of examples. There are also other variants as well, which may be useful for advanced users.

Code: [Select]
fiber -pauling triplex-C10C10C10.pdb        # default: 10 Cs per strand
fiber -pauling -seq=AAA triplex-A3A3A3.pdb  # 3 As per strand
fiber -pauling -seq=AAAA:CCCC:GGGG Pauling-triplex-A4C4G4.pdb
fiber -pauling -seq=ACGGUU,UUGGAC,GGAACC  Pauling-triplex-mixed.pdb
fiber --pauling-dna -seq=ACGGTT,TTGGAC,GGAACC  Pauling-triplex-DNA.pdb

A sample 3D image for the mixed sequence (last one in the above list, Pauling-triplex-DNA.pdb) is shown below:



See my blogpost titled "Pauling's triplex model of nucleic acids is available in 3DNA" for further information.

3
Site announcements / The number registrations has reached 3000
« on: October 15, 2016, 11:51:55 am »
As of October 15, 2016, the number of registrations on the 3DNA Forum has reached over 3,000! It takes slightly longer (15 days) than I predicted in my previous post "Summary of registrations" dated April 26, 2016, where I said:

Quote
If the current trend continues, the number of 3DNA Forum registered users will reach 3,000 by the end of September 2016.

In the past fews months, the number of new registrations has been in the 40s, slightly lower than the 50s averaged over previous years/months.

With 3,000 registrations from users all overall the world, yet no spams, the Forum is certainly functioning better than I could originally imagine. It serves well as a virtual platform that I can interact effectively with the ever-increasing 3DNA/DSSR user community. It is worth noting that the Forum has recently received contributions from Dr. Steve Harvey, a well-known computational structural biologist.

I'll write another announcement post when the number of registration reaches 5,000.

5
MD simulations / MOVED: Concatenated Helices
« on: August 29, 2016, 12:19:08 pm »

8
Site announcements / Summary of registrations
« on: April 26, 2016, 03:25:27 pm »
Since the current 3DNA Forum (using SMF in place of the initial phpBB) was started in early 2012, it has attracted 2,750+ registrants as of today (April 26, 2016). Over the past four years, there are around 50 new registrations per month, or ~600 per year, as shown below:

Code: [Select]
2012 -- 601
2013 -- 667
2014 -- 696
2015 -- 598

If the current trend continues, the number of 3DNA Forum registered users will reach 3,000 by the end of September 2016. Overall, the Forum has fulfilled its intended goals on "Q&As related to 3DNA" and serving as "an online community for DNA/RNA structural bioinformatics."

A large number of the registrants use their work email addresses (e.g., .edu), in line with the trust the community has gradually put on the 3DNA Forum. For example, over half of this month's 62 registrations (as of this writing, 2016-04-26) are filled with clearly identifiable job-related emails. Of course, personal emails (e.g., gmail, yahoo mail, qq.com or 163.com from China) are perfectly fine for registration with this Forum. Whatever the case, users information is kept confidential. Over the past four years, I remember having only sent two DSSR-related newsletters to all members.

Throughout the time, I've committed to a zero-tolenance policy on spams of various types. As a result, the Forum has remained spam free. Most legitimate registrations are activated automatically, and new users can gain immediate access to the download page. Occasionally, however, the anti-spam software blocks suspicious registrations even with .edu email accounts. In such rare cases, I am quick to verify/activate them manually, and notify the effected users by email. Of course, this process may take hours, depending on your time zone.

9
Howtos / Install 3DNA on Windows via MinGW/MSYS
« on: March 06, 2016, 08:46:19 pm »
Again, thanks for your persistence. In the end, you may find the learning experience well worth it!

3DNA should work if you have installed MinGW/MSYS properly. Given the difficult you experienced with installing Cygwin, let's focus on MinGW/MSYS. To get you up and running ASAP, please answer the following questions:

  • Which version of Windows are you using?
  • Where have you put the 3DNA v2.3 download (i.e. file x3dna-v2.3-mingw-win.tar.gz)?
  • Have you extracted the tarball file into its folder x3dna-v2.3?
  • In your MinGW/MSYS shell, what do you get with the command: "tar"?

Xiang-Jun

10
Howtos / MOVED: Analysis of Amber .mdcrd File
« on: February 19, 2016, 01:01:44 pm »

11
Site announcements / CCN short communication on base-pair geometry
« on: February 06, 2016, 10:57:25 am »
The 2016 January issue of the Computational Crystallography Newsletter (CCN) contains a short communication titled "Characterization of base pair geometry" (p.5-8) by Dr. Wilma Olson and me. This essay had been mostly motivated by two publications in the 2015 July issue of CCN by Dr. Jane Richardson: an article titled "A context-sensitive guide to RNA & DNA base pair & base-stack geometry," and an 'Expert advice' of 'Fitting Tip #10' titled "How do your base pairs touch and twist?" In both pieces, Richardson emphasized the importance of base-pair (bp) non-planarity introduced by Buckle and Propeller (see Figure below) for improved fit of DNA/RNA models to X-ray electron density maps. I derived a complete set of six simple bp parameters for a complete qualitative description of bp geometry. The term 'simple' is used because the parameters are more intuitive for non-canonical pairs, and to differentiate them from the existing local bp parameters in 3DNA.


In the CCN short communication, we also highlighted the DSSR-introduced cartoon-block representations of DNA and RNA structures that combine PyMOL cartoon schematics with color-coded rectangular base blocks (See Figure below). The simple, informative cartoon-block representations facilitate understanding of the base interactions in small to mid-sized nucleic acid structures where the base identity, pairing geometry, and stacking interactions are immediately obvious.


A blogpost with the same title "Characterization of base-pair geometry" contains details for reproducing the cartoon-block images in the figure above. See also links therein for further information.

Xiang-Jun

12
Site announcements / Alternative 3DNA homepage at URL home.x3dna.org
« on: October 11, 2015, 01:37:43 pm »
In addition to the well-known 3DNA homepage at URL http://x3dna.org, I've recently duplicated its contents to an alternative site at http://home.x3dna.org. Hosted at Columbia University, the alternative homepage is accessible from countries like mainland China.

Over the years, I've heard of many times from potential 3DNA users in China who cannot visit http://x3dna.org which is on a shared host. Now http://home.x3dna.org, the 3DNA Forum (http://forum.x3dna.org), and a few other 3DNA/DSSR-related web services are all hosted on dedicated servers under my desk. They should be universally reachable.

Web-based technologies (on both the server and client sides) are now matured enough to make writing web applications enjoyable. The infrastructure in place makes it feasible to add more web-based functionality. Moreover, existing web services will be consolidated and refined to ensure sustainability and wide accessibility of 3DNA.

Xiang-Jun

13
Bug reports / MOVED: NUPARM vs 3DNA
« on: October 09, 2015, 12:45:24 pm »

14
Site announcements / The Forum was down due to a power failure
« on: October 05, 2015, 11:49:39 am »
While at a meeting during the week (Oct. 2-4, 2015), I noticed that the Forum was suddenly out of service. Further explorations showed that several other websites and the DSSR manual were all not accessible. I suspected a power failure that had brought down the two servers (named x3dna and dssr) under my desk.

When I came to office this morning, I immediately found that both of my machines were off. Simply switching them on, and everything is back to normal. This is the first power failure experience after the x3dna and dssr servers have been put into service. Yet, it does remind me to have a backup plan.

Sorry for the inconvenience the shutdown may have caused.

Xiang-Jun

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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.