Jul
09
2015
0

Support computational protein design by voting Arzeda for the Sofinnova Start-Up Award!

Support computational protein design for green chemistry by voting for Arzeda before 10 July 2015 – 4:00pm CET at: bit.ly/renchem

Arzeda has been nominated for the Sofinnova Renewable Chemistry Start-up Award, as an innovative green chemistry company and the only computational protein design company ever selected. The competition is now entering the second phase where 5 out of 40 candidates will be selected by popular vote online, before final selection by a professional jury.

May
20
2015
0

New CABS-dock method enables protein-peptide docking without prior knowledge of the binding site

By Sebastian Kmiecik, Researcher at the Laboratory of Theory of Biopolymers, University of Warsaw

Researchers from the Laboratory of Theory of Biopolymers at the University of Warsaw have developed CABS-dock, a new computational method (available as a web server) which allows predicting the structure of protein-peptide complexes and uses no knowledge about the peptide binding site nor the peptide conformation. The method utilizes highly efficient simulation approach for molecular docking of peptides to proteins.

Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms (like Rosetta FlexPepDock or HADDOCK) require pre-defined localization of the binding site, CABS-dock doesn’t require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound dataset cases, high or medium accuracy models were obtained (sufficient for practical applications). The performance summary is presented in the Figure below.

image001

 

 

Figure caption. CABS-dock performance summary for 103 bound and 68 unbound benchmark cases. The percentages of high-, medium- or low-accuracy models (high accuracy: rmsd<3 Å; medium accuracy: 3 Å ≤ rmsd ≤ 5.5 Å; low accuracy: rmsd > 5.5 Å) are reported for the best quality models found in the sets of 10 000 models (all) and in the sets of 10 final models (top 10). Figure is taken from the CABS-dock paper [Nucleic Acids Res, 2015, doi: 10.1093/nar/gkv456]. Entire benchmark results are available in the online CABS-dock materials at http://biocomp.chem.uw.edu.pl/CABSdock/benchmark

Additionally, as optional features, CABS-dock enables to exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at http://biocomp.chem.uw.edu.pl/CABSdock

Article: Mateusz Kurcinski, Michal Jamroz, Maciej Blaszczyk, Andrzej Kolinski, Sebastian Kmiecik, CABS-dock web server for flexible docking of peptides to proteins without prior knowledge of the binding site, Nucleic Acids Research, 2015. doi: 10.1093/nar/gkv456

Supplementary video: http://www.youtube.com/watch?v=EOqRF-JOTFg

CABS-dock

Video description: An example simulation of protein-peptide molecular docking using CABS-dock web server. In the movie, the assembly of major histocompatibility complex (MHC)-peptide structure is simulated. Experimental peptide structure is shown in green, while the simulated peptide in red. The movie shows 1 of 10 trajectories generated in a standard CABS-dock simulation run. The predicted peptide structure, shown at the simulation end, differs from the experimental structure by 1.8 Ångstroms.

Apr
08
2015
0

Request an invitation to RosettaCON2015

Requests are now being accepted through the RosettaCON website for invitations for the limited openings for RosettaCON2015 for members of the pharmaceutical, biotech, and related industries.

RosettaCon is an invitation-only conference at the Sleeping Lady Mountain Retreat in Washington’s Cascade Mountains, where Rosetta Commons member laboratories share the latest experimental and computational research breakthroughs in protein and macromolecular engineering and structure prediction. The Commons grew out of David Baker’s laboratory at the University of Washington and is now a consortium of twenty-four international laboratories. Justin Siegel of the University of California at Davis and Frank DiMaio of the University of Washington organize this year’s conference. We are delighted to have Bill DeGrado of the University of California at San Francisco, Roberto Chica of the University of Ottowa, Lillian Chong of the University of Pittsburgh, and Gaël McGill of Digizyme and Harvard Medical School as confirmed invited guest speakers.

In addition to showcasing cutting edge research, there will be an industry-focused session for fostering collaborations and exploring the exchange of ideas, people and resources. We invite you to participate in this session through presentations, flip charts, and breakout discussions. We hope to expand on the growing number of industry-Rosetta Commons collaborations, such as:

  • Jeffrey Gray lab – AxioMx collaboration deciphering the specificity of antibodies binding phosporylated peptides
  • Jens Meiler lab – Eli Lilly collaboration developing methods for drug design
  • Tanja Kortemme lab –DSM collaboration developing ROSETTA applications to re-design enzyme substrate specificity

Hands-on Rosetta tutorial sessions may be offered for industry attendees interested in learning to use ROSETTA.

After the conference, hikes, climbs, and backing trips are organized by conference attendees on the most scenic trails and stellar climbs in all of Washington State.

 

Apr
02
2015
1

CALL FOR IMAGE SUBMISSIONS FROM CEREBELLA DESIGN

Are you a scientist with a passion for sharing your research with the world through art & design? 

We invite scientists around the globe to participate in our design process by submitting science images to “Cerebella Submit: Where Scientists are Artists” and inspire our next spring/summer textile collection. 

Photomicrographs are the most common images submitted, however we encourage scientists who utilize molecular graphics and modeling to participate and share their work!

—–

ABOUT: Cerebella Design was founded in 2013 in Vermont, USA. We specialize in designing unique textiles inspired by the natural world. Our patterns are applied in fashion, architectural, and industrial domains and have been featured in the New York Times, Wired, Cool Hunting, and more. Our mission is to share science in style. 

Written by Gauthor in: Competitions,Uncategorized | Tags: , , ,
Mar
04
2015
0

Announcement and call for abstracts: Structural Bioinformatics microsymposium at ECM29, August 23-28, Rovinj, Croatia

The 29th European Crystallographic Meeting (ECM29), to be held on August 23-28 in Rovinj, Croatia, will feature a Structural Bioinformatics microsymposium (http://ecm29.ecanews.org/programme/microsymposia/#ms10). All structural bioinformatics topics with relevance to macromolecular crystallography are welcome. Abstract submission (for oral or poster presentation) is available at http://ecm29.ecanews.org/participate/abstract-submission/, with deadline March 23. The final program will encompass two 30-min talks from invited speakers, three 20-min talks chosen from the submitted abstracts, and poster presentations. For questions or additional information please Email guido.capitani@psi.ch.

May
15
2014
0

Two spots remaining for RosettaCon2014!

There are two spots remaining for RosettaCon2014 this summer, July 30th – August 2nd! RosettaCon is the annual meeting of members of the Rosetta Commons and scientists using Rosetta in the pharmaceutical and biotechnology sectors. There will be workshops, seminars, and a special industry collaboration session. The conference will take place at the beautiful Sleeping Lady Mountain Retreat in Leavenworth, Washington, about 2.5 hours outside Seattle in the dramatic Cascade mountain range. Kick back, have a beer, fold a protein, re-design a protein, and go for a hike.

Please email info@rosettadesigngroup.com for more information and registration details.

May
08
2014
0

Webinar: AMBER 14 & GPUs – Creating the World’s Fastest MD Package

Please join us on May 13th for a webinar presented by Professor Ross Walker of UC San Diego, Professor Adrian Roitberg of University of Florida and Scott Le Grand of Amazon Web Services. This webinar will provide an overview of the AMBER Molecular Dynamics Software package with focus on new GPU accelerated features in the recently released version 14. This includes details of peer-to-peer support and optimizations, which have resulted in version 14 being the fastest MD software package on NVIDIA GPUs. Other GPU features include support for multi-dimensional replica exchange MD, hydrogen mass repartitioning, and support-as-a-service on Amazon Web Services. Benchmarks will be provided, along with recommended hardware choices. This webinar is planned for May 13th 2014 at 9.00 AM Pacific Time. Register at: http://bit.ly/AMBER14

by guest author: Perri Needham, UCSD

Mar
21
2014
1

Poly-publications on the polypharmacology of kinase/bromodomains dual inhibitors

When you consider how vast the chemical space is and how restricted the topology and chemical environment of a specific pocket in a protein is, it’s quite surprising we can find molecules that the protein was not evolved to bind that can nonetheless bind and inhibit it potently. It is therefore even more surprising when a single molecule can potently hit two completely unrelated (by sequence, by structure and by function) proteins. Thus, when two independent groups publish such dual kinase/bromodomain inhibitors a week a part from each other, the mind reels.

(more…)

Feb
20
2014
0
Nov
02
2013
0

Molecular Dynamics, believe it or not

Anthony Nicholls (of OpenEye scientific software, Cambridge, MA) recently gave a critical talk on the usage and reporting of Molecular Dynamics simulations. Luckily Ash from The Curious Wavefunction was there to beautifully summarize the main points. I urge you to head over and read the full summary. Below are the main headlines.

  • MD is not a useless technique but it’s not held up to the same standards as other techniques, and therefore its true utility is at best unknown
  • MD can accomplish in days what other techniques can achieve in seconds or hours
  • MD can look and feel “real” and seductive
  • Using jargon, movies and the illusion of reality, MD oversells itself to the public and to journals
Written by admin in: Weird science | Tags: ,

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