Weekly literature review
A selection of this week’s interesting papers, brought to you via the Furman Lab
Apr
26
2012
26
2012
Apr
16
2012
16
2012
Weekly literature review
A selection of this week’s interesting papers, brought to you via the Furman Lab
Apr
12
2012
12
2012
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.
Apr
05
2012
05
2012
Mobile apps for structural biology and protein design
Hi folks, with all of these smartphones and touch tablets showing up, it’s very possible you could be carrying one around in a lab, at a conference, or at even some agonizing situation where you are bored and away from a real computer. In that case your structural needs can now be satisfied by mobile apps! I’ve personally made a demo to show just how easy this can be: https://play.google.com/store/search?q=andmol
Expect to see the development of more fully-featured mobile apps that allow you to consume and perform science from anywhere at your fingertips. You may even end up developing your own mobile Rosetta plugins soon. In the meantime, your general structural needs can be satisfied by the fully-featured JMol Android port: https://play.google.com/store/search?q=jmol The JMol folks were able to port the mature JMol Java suite to Android. Way to go! I consider that a success story for Android’s choice of platform.
By Justin Ashworth
About Justin: Justin is a postdoctoral fellow at the Institute for Systems Biology in Seattle, WA. He earned his PhD with David Baker at the University of Washington. He has been involved in the development and application of the Rosetta software suite for macromolecular design.
Apr
05
2012
05
2012
Weekly literature review
A selection of this week’s interesting papers, brought to you via the Furman Lab
Apr
03
2012
03
2012
Protein–protein interaction inhibitors get into the groove
In a recent ‘News and Analysis’ piece on Nature Reviews Drug Discovery, Asher Mullard, heralds the advancement in drug discovery efforts against Protein-protein interactions – “the unmined biology gold reserve”.
Apr
03
2012
03
2012
From protein modeling to the world of small molecules
Keen observers and avid followers of this blog must have noticed the dwindle if not complete lack of posts in the past 3-4 months. The main reason for this drought was my personal and professional transition. I have completed my Ph.D. studies (on peptide-protein interactions) at the Furman Lab (The Hebrew University, Jerusalem, Israel) and took a position as a post-doctoral fellow at the Schoichet Lab (University of California, San Francisco) in the field of structure based virtual screening of small molecules with a touch of Chemoinformatics.
The move, the acclimation to California and to a new research area, have left little to no time for writing, but now as the dust settles, I hope to find time now and then to share interesting papers, opinions and news. I imagine this change in research area will reflect in future content, and am sure you’ll find it as fascinating as I do.
Looking forwards to see what the future holds…
Mar
31
2012
31
2012
3DSIG and AFP-CAFA 2012
Two interesting and successful special interest group meetings will take place along side ISMB 2012 in Long Beach, CA
3D SIG 2012 – STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS
July 13-14, 2012: 3DSIG 2012
(http://bcb.med.usherbrooke.ca/3dsig12/)
We are happy to announce the eighth 3Dsig meeting. Two very full days with a balance of invited talks, short oral presentations, two laptop/poster sessions, and critical, topic-focused discussions. A truly unique event bringing together in one place the structural computational biology community.
3DSIG 2012 will present the third “Warren DeLano Structural Bioinformatics and Computational Biophysics Award” in honor of Warren DeLano and the contributions he made to our community. The award sum of $1000 will be given for the best presentation on behalf of the DeLano foundation. Further prizes also available for best posters.
Relevant topics include:
Application of structure to systems biology / Structure-based drug discovery including polypharmacology and network pharmacology / Structure representation, classification and predication / Macromolecular assembles / Structural genomics / 3D databases and data mining / Molecular visualization / Relevant methods of structure determination, particularly hybrid methods / Structure-based function prediction / Evolution studied through structures / Docking, analysis, prediction and simulation of biomolecular interactions such as protein-protein, protein-ligand and protein-nucleic-acid / Prediction and analysis of protein domains / Membrane protein structure analysis and prediction / Protein dynamics and disorder / The structural basis of immunology.
Important dates:
March 19, 2012: Registration opens for 3DSIG and ISMB
March 16, 2012: Deadline to submit a poster for ISMB – a necessary requirement to be eligible for an ISMB travel fellowship.
April 6, 2012: ISMB poster acceptance notification
April 13, 2012: Deadline for submitting an abstract to 3DSIG to be considered for oral presentation.
Deadline for travel fellowship application for the main ISMB meeting by invitation only
May 11, 2012: Late 3DSIG poster abstract submission deadline. Late submissions will not be considered for oral presentation (see april 13).
May 25, 2012: ISMB Travel Fellowship acceptance notification.
June 1st, 2012: Early registration deadline to the main ISMB conference. Note: you may register only for 3DSIG.
THE AUTOMATED FUNCTION PREDICTION MEETING (a.k.a. AFP-CAFA)
July 14, 2012, Long Beach, California, USA
(http://BioFunctionPrediction.org ; afpcafa2012 AT gmail.com)
The deluge of genomic information has led to the following fundamental question: what do all these genes do? Many genes are not annotated, and many more are partially or erroneously annotated. Given a genomic stretch which is partially annotated at best, how do we fill in the blanks? Moreover, with structural genomics information starting to pour in, we are faced with the novel problem of predicting function from structure, a problem which did not exist until recently. For all these reasons and many more, automated function prediction is rapidly gaining attention in
computational biology.
Computational biologists have been attacking the problem of automated function prediction from several angles, based on needs and scientific interest. Among the methods are functional inferences based on genomic context; metabolic or signaling pathway context; distant homolog searches; phylogenetic profiling; and combinations of methods using several sources of information and employing data mining and machine learning algorithms.
Important dates:
• April 18, 2012: Deadline for submitting extended abstracts.
• May 9, 2012: Notifications for accepted abstracts e-mailed to corresponding authors.
• May 16, 2012: Deadline for presenters to confirm acceptance of invitation to speak
Mar
14
2012
14
2012
Tezcan-RDG supramolecular design collab in the news
Stu Borman wrote a nice piece in Chemical & Engineering News (CEN) highlighting a recent paper in Nature Chemistry that presents the work of a collaboration between the Tezcan Lab at UCSD and the Rosetta Design Group. In this work, a monomeric protein was redesigned to become capable of forming metal and pH tunable nano- to micro- scale sheets, tubes, and other assemblies.
Mr. McGuire: I just want to say one word to you. Just one word.
Benjamin: Yes, sir.
Mr. McGuire: Are you listening?
Benjamin: Yes, I am.
Mr. McGuire: Plastics. Proteins.
Benjamin: Exactly how do you mean?
Dec
14
2011
14
2011
New opening at Intrexon
Check out the Jobs Board for a new opening from Intrexon and others: http://rosettadesigngroup.com/blog/molecular-modeling-jobs/
