Macromolecular Modeling Blog ™

New opening at Intrexon

Xavier Ambroggio — Wed, 14 Dec 2011 15:07:04 +0000

Check out the Jobs Board for a new opening from Intrexon and others: http://rosettadesigngroup.com/blog/molecular-modeling-jobs/ Random Posts

Protein design: breaks gluten, wins iGEM2011

Nir London — Wed, 09 Nov 2011 14:47:02 +0000

An undergraduate group of students from the University of Washington, managed to redesign an enzyme to efficiently break down a model peptide for Gluten, achieving an increase in activity of hundreds fold over the only current clinically tested treatment for Gluten intolerance - Winning iGEM2011. All this, over the summer. Oh, and they also managed to produce Diesel in E. Coli.

A twitter roundup

admin — Sat, 05 Nov 2011 15:25:28 +0000

For those not yet following us (@molmodelblog) on twitter, a roundup of interesting links from the weekend: MIT Research: New Protein Folding Model Helps With Genetic Data Deluge http://bit.ly/rwsl0u Postdoctoral Position in Protein Engineering and Chemical Biology, The Eindhoven University of Technology, Netherlandshttp://bit.ly/rPbWIT Tau proteins in nerve cells interact strongly with neg. lipids on the membrane [...]

Molecular Modeling Software

Nir London — Fri, 04 Nov 2011 09:38:10 +0000

@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.

Olympic Crystal Packing

Nir London — Fri, 04 Nov 2011 06:39:50 +0000

In the spirit of the 2012 Olympic games. Found at the webpage of the group of Prof. Heinz Neumann, Department for Molecular Structural Biology, Georg-August-University Göttingen. Anyone knows what protein is it? HT to ravehb for the finding. Related postsThe Europeans are cleaning up the PDB, woohoo!!!Short Course: Crystallography for Modelers

One Sided De-Novo Computational Design of a Protein-Protein Interaction

Nir London — Wed, 08 Jun 2011 16:09:46 +0000

In a recent Science paper, Sarel Fleishman et al. report the de-novo computational design of a protein interface to specifically target and tightly bind a surface patch of the flu hemaglutinin protein. We interview Sarel to get the insights from behind the scenes and the outlook for this exciting approach.

A PLoS ONE Rosetta Collection

Nir London — Thu, 26 May 2011 18:07:57 +0000

Three articles recently published in PLoS ONE are the harbinger of a RosettaCon 2010 PLoS one collection. How do you design a new enzyme from scratch? How do you model peptide binding with almost no prior information? And what puzzles CAN'T Rosetta solve?

A more dynamic literature review

Nir London — Thu, 19 May 2011 17:39:53 +0000

Though I like posting them, and some of the readers like sifting through, the literature reviews always struck me as too static, I wanted to have a more nimble system that can allow readers to comment on a specific paper, to 'like' specific papers, and to be able to sort the list this way or another. Following the recent post on Annotator, it came to mind that Disqus might indeed be the answer for a few of these problems.

Annotatr and The MD Club

Nir London — Fri, 06 May 2011 12:02:37 +0000

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.

Stanford-Sweden multiresolution molecular modeling workshop

Gauthor — Wed, 20 Apr 2011 18:12:30 +0000

The Stanford-Sweden summer modeling workshop, to be held in Uppsala 20-22 June, brings together scientists from the Bay Area, Sweden, and the wider world to discuss late-breaking research on simulation of macromolecules and complexes, spanning levels of resolution from coarse to fine.