Apr
12
2012
0

Rosetta 3.4 released

Just a short note to let you know that Rosetta 3.4 was released a couple of weeks ago. This release contains new applications and features like Noncanonical amino acid utilities, Point mutations scan, New RNA applications and many more.

The word on the street in the Rosetta developers community is that releases are about to become much more frequent, so there is a lot to look forward to.

Written by admin in: News,Resources | Tags: , ,
Nov
05
2011
0

A twitter roundup

For those not yet following us (@molmodelblog) on twitter, a roundup of interesting links from the weekend:

Written by admin in: Resources,Title Madness | Tags: ,
Nov
04
2011
9

Molecular Modeling Software

@biosoftcn avidly tweets and curates bioinformatics and modeling software (collected at http://www.mybiosoftware.com). We selected some links relevant to you molecular modelers. Feel free to add software not found here through the comments.
Written by Nir London in: Resources | Tags: ,
May
06
2011
3

Annotatr and The MD Club

Some months ago, Bosco Ho, Molecular Dynamics (MD) boy wonder and HTML5 wiz, contacted a group of scientists, myself included, to start a world wide Journal Club (JC). The subject: Molecular Dynamics, the venue? Annotatr – a mashup of CiteULike and Disqus. The motivation behind Annotatr was to get scientists to comment on articles (lower the energy barrier if you prefer).

Since then the MD JC had several prolific sessions, discussing some great MD papers on which I’ll discuss briefly below, as well as recently, a completely unrelated theoretical evolutionary paper just to broaden our horizons.

(more…)

Feb
05
2011
0

Rosetta 3.2 Released

Rosetta 3.2 is the first rosetta release in over a year and is chock-full of new features. Get your (free for academia) copy at: www.rosettacommons.org/software and find the new and improved documentation at: www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide

What’s new in Rosetta 3.2 ?

“Automatic” Comparative Modeling: build structural models of proteins using one or more known structures as templates for modeling.

Flexible Peptide Docking: create high-resolution models of complexes between flexible peptides and globular proteins, starting from approximate, coarse-grain models.

Symmetric Docking: predict the structure of symmetric homooligomeric protein assemblies starting from the structure of a single subunit. The relative subunit orientation and conformations of side-chains are simultaneously optimized for a symmetric protein assembly.

RosettaMatch Application: search through a protein backbone (“scaffold”) to find positions where a binding site for a desired small molecule (or biomolecule, in the more general case) target can be introduced.

Molecular Replacement: solve difficult molecular replacement problems. It will generally be used alongside the molecular replacement software Phaser.

Sequence Tolerance: perform specificity prediction and library design (i.e. for phage display, yeast display, or other selection techniques).

Written by admin in: News,Resources | Tags: , ,
Dec
17
2010
2

Rosetta Web Servers

The Rosetta macromolecular modeling suite has a very wide range of applications, and although installing and running Rosetta, becomes increasingly easier over the years, some non-experts would still prefer to run it over a comfortable to use web-server. We have assembled here the list of Rosetta applications for which such a web-server exists. Bookmark for future modeling tasks.

(more…)

Jul
14
2010
0

Jobs Wanted

We launched a new Jobs page.

If you’re looking to hire – fill in the form at the top of the page. If you’re looking for a molecular modeling job – search the jobs (posted in reverse chronological date)

Molecular Modeling Jobs

Molecular Modeling Jobs

We hope this resource would help both employers and modelers.

Written by admin in: Jobs,Resources | Tags: ,
Jul
03
2010
1

PDB mode for Emacs

Are you tired of manually editing PDB files ?

Checkout this PDB mode for Emacs that helps you do most of the usual modeler editing tasks in a press of a button.

Via @leninwtigger

Written by Nir London in: Resources | Tags: ,
Apr
17
2010
1

Practically useful: what the Rosetta protein modeling suite can do for you

In a recent review published in Biochemistry, Kaufmann, Lemmon and DeLuca et al. from the Meiler Lab, cover the Rosetta modeling suite capabilities. More importantly, as supplementary information they provide tutorials to demonstrate 6 basic use cases of Rosetta.

(more…)

Written by Nir London in: Literature Reviews,Resources | Tags: , , ,
Jan
04
2010
2

NAR 2010 DB issue – What’s in it for us?

NAR just published the new special “Database” issue for 2010. We collected 23 papers that might be of interest to structural biologists, modelers and other protein people.

(more…)

Written by Nir London in: Literature Reviews,Resources,Title Madness | Tags: ,

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