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
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: , , ,
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.

Jun
25
2012
1
Apr
05
2012
1

Mobile apps for structural biology and protein design

AndMol

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.

Written by Xavier Ambroggio in: Uncategorized | Tags: , , , , ,
Jul
15
2010
1

2010 Cryo-EM Modeling challenge

Cryo-EM single particle analysis is a method for determining structures of large molecules and macromolecular assemblies at resolutions ranging from 3.5- 30 A. Interpreting the density maps produced by this technique represents an ongoing challenge, for which molecular modeling techniques offer some unique solutions.

Over the last five years, cryo-EM single particle analysis has begun producing structures at resolutions better than 5 A, with subnanometer resolutions becoming common. At resolutions between 5 and 9 A it becomes possible to move beyond simple rigid-body docking and alter atomistic models to reposition helices and sheets, to better fit the cryo-EM based density maps. At 3-5 A resolution de-novo C-alpha traces and in some cases full atomistic models can be constructed directly from the cyro-EM density without invoking x-ray crystallography.

We call this a challenge rather than a contest because, unlike CASP, there is no hidden answer to be revealed. In this project, we provide publicly available cryo-EM densities for a selected set of structures at different resolutions, and challenge those in the modeling community to apply their tools to extract as much information as they can from each. At the end, the results will be evaluated by comparing the results of different groups, and validating against any other existing knowledge about each target. We hope this will yield new insights into these published structures, and at the very least, it will establish the capabilities of current modeling methods, and give the cryo-EM community some guidance as to how to proceed with maps in various resolution ranges. For modelers it provides a new area in which to apply/develop their techniques, and demonstrating your tools’ capabilities may lead to new opportunities for collaboration.

Please see the challenge website for more details.

Written by Nir London in: Uncategorized | Tags: , , , ,
Apr
14
2010
0

8th International NCCR Symposium on New Trends in Structural Biology

Dates: 2-3 September, 2010

Venue: ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland

Confirmed plenary lecturer: James U. Bowie, Kathryn M. Ferguson, John Kuriyan, Jonathon Howard, Jan Löwe, Krzystof Palcezski, Bob Stround.

This symposium series provides a yearly update on current structural biology themes and newest developments in the field. Renowned structural biology scientists from all over the world exchange their knowledge and current research ideas in an interactive way. The format of the symposium includes plenary lectures by invited guest scientists, discussions and poster presentations by NCCR scientists.

More details on the meeting website

Written by admin in: Uncategorized | Tags: , ,
Nov
09
2009
0

PyRosetta

PyRosetta Book

PyRosetta Book

The Gray Lab at Johns Hopkins University has just released PyRosetta, a Python-based interactive platform for accessing the objects and algorithms within the Rosetta protein structure prediction suite.

In addition to the code, the Gray Lab has put together a book that leads the reader through basics of protein structure and energetics to applications in folding, refinement, docking and design. The focus is on enabling users to write custom scripts, so it includes material on Rosetta fundamentals and the appendices have a list of PyRosetta commands and a breakdown of the input files. The book was beta-tested by students during a course at JHU. The course is a series of workshops that teach how to measure and manipulate protein conformations, calculate energies in low- and high-resolution representations, fold proteins from sequence, model variable regions of proteins (loops), dock proteins or small molecules, design protein sequences, and build custom protocols for operations tailored to particular biomolecular applications

The book can be purchased through Lulu:

http://www.lulu.com/content/paperback-book/the-pyrosetta-interactive-platform-for-protein-structure-prediciton-and-design-a-set-of-educational-modules/7187010

or downloaded for free as pdf chapters from http://www.pyrosetta.org under the Tutorial link.

Nov
06
2009
1

Warren DeLano has passed away, a terrible tragedy.

We recently saw these posts reporting that Warren DeLano passed away on Tuesday:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;19EK9w;20091105105413-0800

http://www.macresearch.org/memoriam-warren-l-delano

This is a terrible tragedy and our hearts go out to his family and friends. He was a truly incredible person whose work with PyMOL changed the face of molecular modeling. He also had a huge personal impact on our community. He was dedicated to science and dedicated to making the world a better place through his example and by the personal way he interacted with everyone.

When I was considering starting the Rosetta Design Group a few years back, I asked Warren for some advice by email. He promptly called and we talked for a few hours. After our conversation I reflected on how much his call and advice meant to me, and hoped that I would act as he did in the same situation.

May his example, memory, and code live on forever.

Sep
24
2009
3

We’ve got Aspergers.

My jaw dropped when I saw this. Hilarious. Scary. So true.

Molecular Modelers have Aspergers

Molecular Modelers have Aspergers

Its from: http://en.wikipedia.org/wiki/Asperger_syndrome

Written by Xavier Ambroggio in: Uncategorized |

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