Macromolecular Modeling Blog ™

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)

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

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.

Rosetta Workshop

An Introductory Workshop to the Rosetta Protein Modeling Suite.

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Where: Grand Hotel San Michele, Centraro, Italy

When: 14-16/06/2010

Abstract submission deadline: 21/05/2010

This meeting, which corresponds to the biennial conference organized by the President of the International Society of Quantum Biology and Pharmacology, aims at bringing together specialists from around the world, and from all areas of biomolecular simulation to look at recent progress and to identify the most important challenges facing the field in the coming years in terms of methodology and practical applications.

For details: ISQBP 2010

This is the fifth and last post in the CAPRI series, summarizing the presentations of Xiaoqin Zou and Ora Schueler-Furman (Saving the best for last..), as provided by the speakers. I hope the CAPRI series was able to give a snapshot of the state of computational protein-protein docking and its community. I want to thank again to everyone that took part in the meeting and helped me with this series.

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As in previous years, we would like to invite representatives of the pharma and biotech industry to participate in RosettaCon 2010. Take part in the workshops, seminars, and have an opportunity to meet the Rosetta Commons researchers. Get to know Rosetta from the inside. RosettaCon will take place during August 3-6 at the beautiful Sleeping Lady Mountain Retreat in Leavenworth, Washington, about 2.5 hours outside Seattle, in a dramatic mountain scenery – the only fitting environment for a scientific discussion really.

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This is the fourth post in the CAPRI series, summarizing the presentations of Paul Bates, Martin Zacharias, and Carlos Camacho, as provided by the speakers. More to appear in the continuation of the series.

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This is the third post in the CAPRI series, summarizing the presentations of Jeffrey Gray, Zhiping Weng, and Miriam Eisenstein, as provided by the speakers. More to appear in the continuation of the series.
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A meeting for everyone that liked this post (17 Protein disorder prediction servers):

Dates: 4-6 October, 2010

Venue: Institut d’Estudis Catalans, Barcelona, Spain.

Registration deadline: July 15, 2010.

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