nodalpoint.org - Protein structure - Comments

simulaid

bosco — Thu, 16 Aug 2007 13:23:16 -0400

I downloaded it but couldn't get it to work properly for NAMD to AMBER.

Simulaid

Animesh — Thu, 16 Aug 2007 10:46:02 -0400

I have no idea about converting trajectories, but people talk about using Simulaid [ http://inka.mssm.edu/~mezei/simulaid/ ] for similar stuff, did you check it?

Looks familiar

Neil — Wed, 15 Aug 2007 09:52:19 -0400

Good to see that file format conversion is a full-time preoccupation in structural biology as well as for people working with sequences. Nice how-to.

Just a wild guess, but I'm

Greg — Tue, 14 Aug 2007 14:11:00 -0400

Just a wild guess, but I'm thinking this particular piece will not have the same broad impact of "Notes to a young computational biologist". Nonetheless, I am thinking that maybe your posts on these topics have brought a few more structural biologists into the world of blogging :)

Nightmares

mndoci — Tue, 14 Aug 2007 14:09:44 -0400

And I shudder at the memories of trajectory formats.

We should start a movement for MD standards, as in Force Field standards, trajectories, etc etc.

very mini

Neil — Mon, 25 Sep 2006 05:45:43 -0400

I'll keep an eye out for you. I'll probably be wearing black and lurking in a corner, I'm not keen on crowds :)

meetup ?

pansapiens — Fri, 22 Sep 2006 23:37:36 -0400

I'm dropping in for the last day of ComBio ... could there be, by chance, any other nodalpointers going ? It might be a good opportunity for a mini nodalpoint meetup !?

announcement vs. advertisement

yogibear — Thu, 27 Apr 2006 18:09:34 -0400

I have enquired in the irc #nodalpoint channel before posting, and Neil Saunders was kind enough to get back to me and enourage me to post. Announcements, by definition, are made by the people who have developed the product, aren't they? So yes, announcements are a special form of advertisement, and yes, I am from Biomatters. However, in this case the advertisement is for a freeware product.

I have never claimed that Geneious is open source. It is freeware, but closed source. We control the platform only in so far as we are the only ones who can make new platform releases. We can not take the existing platform, which we have provided for free, back from the community.

So the community will always be free to use that platform, and to develop plugins that extend the existing freeware version of the platform. I think it should be obvious that the community benefits from this possibility. What if the Eclipse platform was freeware closed source? People could still use Eclipse productively, and develop as many plugins as they feel like.

I personally think you should really reserve your aggressions for people who try to get your money, not for people who have just given you free stuff.

Please post announcements in

Greg — Thu, 27 Apr 2006 10:03:06 -0400

Please post announcements in the forums. Also if you are from Biomatters then this is not just an announcement it is advertising, in which case please let us know. For the moment I'll give this post published status, however not to the front page.

Also, I'm curious about Biomatter's claims regarding open source. The product itself is not open source, it only provides a plug-in API ? So that means you control the platform, in which case how does the benefit the community ?

I think this should be

Greg — Thu, 02 Mar 2006 04:24:40 -0500

I think this should be re-posted in the Announcements forum.

Structure vs function

chris — Sun, 18 Sep 2005 22:23:59 -0400

Like the perl folks say, there's more than one way to do it. You've asked a highly context-dependent question: the answers are likely to be different for each protein.

Two uses I can think of for the extra amino acids : (i) responsible for some other function/interaction; (ii) loop material, allowing the polypeptide to bend into its active conformation more easily.

You have asked an

Greg — Thu, 15 Sep 2005 12:07:14 -0400

You have asked an interesting question. However if you want this posted to the front page I would suggest adding some links to papers or articles that discuss this question. Or maybe you could give a brief introduction with some real examples ?

See the posting guide for more suggestions and only your hard work can make you knowledgeable about science :)

emacsen

chris — Tue, 26 Oct 2004 20:10:46 -0400

I am using Latex and Bibtex, and Emacs becomes then quite a powerfull[sic] tool to manage even large databases using flat files.

I must admit I find it hard to get excited about latex through emacs. Yes, emacs is powerful, yes it can be incredibly useful (I use it for Sweave document preparation and R/ess sessions) but unless you speak elisp, it's hard to do cool stuff. And elisp is a little too esoteric for me.

I use Kile for latex, which allows customisable compiles, multiple-file projects, bib compiles, etc. Not perfect by any means, but very good for a minimal user investment.

Have you tried Jabref?

Anonymous — Tue, 26 Oct 2004 15:22:21 -0400

Well it all depends if your are using a WYSIWYG editor, like word or openoffice or if you are using Latex. If you are using word, the easiest is porbably Endnote, but neither word nor endnote are free.

I am using Latex and Bibtex, and Emacs becomes then quite a powerfull tool to manage even large databases using flat files. I have nevertheless tried some of the freewares available and the simpliest and most useful one I have found is Jabref. It is java based, has a nice GUI, is free, works on any plateform, and is easy to install. It is also very straightforward to use, and has an import option from Web of Knowledge or Medline.

Perl and Eutils

Neil — Mon, 25 Oct 2004 23:35:01 -0400

I also recommend Perl (of course!) and the NCBI EUtils services. This is exactly how I generate the "weekly publications" list over at ArchaeaWeb. Perl script runs as a cron job each Friday to access esearch/efetch using LWP and get the last 7 days publications in XML format. Then the Bioperl Bio::Biblio module is employed to reformat the XML to HTML and the HTML is uploaded to the website. You could also use an XML parser, or just regex for the tags, use RefDB to convert to RIS and import to MySQL...the possibilities are almost endless. So you need to spend some time deciding exactly what you want to do and designing the system accordingly.