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.



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.


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


ignite Bay Area protein Dynamics

If you’re interested in protein dynamics and happen to be around the bay area you might want to attend iBAD or “ignite Bay Area protein Dynamics”. Featuring four 5 minute talks by:

  • Vijay Pande (Stanford)
  • Susan Marqusee (Berkeley)
  • Jacob Corn (Genentech)
  • Gira Bhabha (UCSF)

When: Nov. 5th 7pm (refreshments available before)

Where: UCSF mission bay campus – Byers Hall 212

See you there.

p.s. this event is sponsored by the protein society and hosted by the Fraser Lab.


Written by Nir London in: Events | Tags:

CAPRI 5th evaluation meeting

The CAPRI 5th evaluation meeting has just finished last week.

Unfortunately I couldn’t attend this year.

Fortunately, you can get the spirit of the meeting from this series of 3 blog posts over at Grid-Cast:

Combining and conquering at the CAPRI 5th evaluation meeting

Proteins by design – expanding on nature

Wrapping up at CAPRI – beers, bikes and brainstorming

The current CAPRI round is all about peptide docking! Exciting!

If anyone came back from the meeting please share your impressions.

Written by Nir London in: Events | Tags: , ,

CASP10 conference

Critical Assessment of Protein Structure Prediction *CASP10* (an EMBO conference)
9-12 December 2012 | Gaeta, Italy

Every two years since 1994 CASP has conducted a community wide experiment to assess the state of the art in protein structure modeling.
The 2012 conference will report the results of 10th experiment and celebrate progress over almost 20 years of monitoring the field.



Algorythms In Structural Bioinformatics – winter school

We are pleased to announce a one-week school on Algorithms in Structural Bioinformatics. The aim is to introduce advanced methods in this domain, giving special attention to interdisciplinary approaches. The main focus will be on methodological developments meant to analyze and predict macromolecular assemblies, as well as on the corresponding software.


Written by admin in: Events |

3DSIG and AFP-CAFA 2012

Two interesting and successful special interest group meetings will take place along side ISMB 2012 in Long Beach, CA


July 13-14, 2012: 3DSIG 2012


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.


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

Written by admin in: Events | Tags: , , , ,

Stanford-Sweden multiresolution molecular modeling workshop

We are excited to announce our Stanford-Sweden summer modeling workshop, to be held in Uppsala 20-22 June. This workshop 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. We will discuss structure prediction, dynamics, sampling, assembly, and aggregation from both a computational and experimental perspective. We will also give tutorials on simulation software, such as SimTK Simbody, DOCK_Blaster, and MMB/RNABuilder. Please post the attached flyer on your departmental email list, on physical bulletin boards, or otherwise circulate widely. Details on the program will be posted on our event page as they become available: http://xray.bmc.uu.se/flores/Stanford-Sweden-workshop-2011

Thanks, and hope you can make it!

Samuel Flores, Johan Åqvist, Erik Lindahl, and Michael Levitt

About the author: Samuel Flores (samuelfloresc AT gmail.com): I write easy to use multiresolution modeling software which helps predict how large biological molecules form and move. I and my collaborators have applied it to lots of problems, such as group I and group II intron structure, ribosome hybridization, and telomerase elongation. I’m also working on antibody design and other viral applications. Currently I’m extending my software, MMB, to handle huge complexes even more efficiently. A new feature called “physics where you want it” will let you apply a physics-based force field to a restricted region of your complex, e.g. an active site or interface, while treating the rest with coarser forces and kinematics. MMB will also start reading electron densities and other experimental data, expanding the types of constraints that can be used for modeling.

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