News

Working Group on Theoretical Structural Models Validation

The establishment of the "Working Group on Theoretical Structural Models Validation" was recommended at the community workshop on "Applications of Protein Models in Biomedical Research" The role of this working group is to address several open issues concerning structural models (Structure, 17, 151-159). One of the most urgent questions was validation of theoretical structural models.

It has been recommended that a community Working Group establishes guidelines for model validation and estimating model accuracy, with special emphasis on identifying criteria reflecting the suitability of models for specific biological applications. The Working Group is also expected to set policies for journal publication, to define minimum annotation and validation standards, and to establish the scope and requirements of public archiving of published structural models.

The "Working Group on Theoretical Structural Models Validation" will mainly work in electronic form (email, wiki) to develop these recommendations, which will then be presented to the modeling community for comments and feed-back. Once a year, a Working Group workshop will be organized to give the members of the team the opportunity for direct interaction and in-depth discussions.

If you are interested to partcipate in the "Working Group on Theoretical Structural Models Validation", please contact us by [email].

Workshop Report

The outcome of the workshop on "Applications of Protein Models in Biomedical Research" held at the University of California, San Francisco, July 11-12, 2008 has been published in the February issue of "Structure":


Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack Jr RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek Jr. SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, and Wilson IA.
Outcome of a Workshop on Applications of Protein Models in Biomedical Research. Structure (2009) 17: 151-159.



Events

Workshops

Summary of the 2013 Meeting of the Working Group on Theoretical Structural Models Validation
Oct 21st & 22nd 2014
Rutgers, NJ, USA

The first day of the workshop was dedicated to the development of standards for model data deposition (model archiving) and validation of models for peer-reviewed publications. After a short update on recent developments of the Model Portal and Model Archive, representatives from the experimental wwPDB task forces have described the current status of data deposition and validation in their respective fields.[1] In a session on state-of-the-art methods for validation and assessment of models, it was decided, that adequate measures and standards should be defined through the continuous assessment platform CAMEO (www.cameo3d.org) in close collaboration with CASP organizers. It was also discussed which information should be captured for models in general (e.g. comparative models, de novo predictions, protein-protein docking and virtual screening) in detail, focussing on minimal information standards and a standard model validation report.

The second day was concentrated on the PDBx/mmCIF data exchange format for structural biology (PDBx/mmCIF format), which the wwPDB has established as the new standard format for data exchange and archiving in structural biology. Existing software implementations in various areas have been presented along with first suggestions on extending this format to meet the requirements to represent modeling specific information. The latter was passed on to a small task force focussing on the actual implementation of this extension within mmCIF.

More information on the Meeting

References

[1] Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure (2013) 21(6):875-81.

2010 NIGMS Workshop: Enabling Technologies in Structure and Function
April 19, 2010 - March 21, 2010
Bethesda (Maryland), USA

The 2010 NIGMS Workshop: Enabling Technologies in Structure and Function continues a series of annual meetings held by National Institute of General Medical Sciences (NIGMS) Protein Structure Initiative participants, which were popularly designated Bottlenecks Workshops. The primary focus of this 2.5 day meeting will be the technical issues affecting the speed, cost, and success of protein structure determination and the combination of structure with other biophysical methods to enable functional characterization of macromolecules.

The 2010 meeting will address a wide range of topics applicable to all scales of effortfrom the individual bench scientist to high-throughput research centers. The workshop program will include oral platform and poster presentations as well as workshops emphasizing the combination of methods and technologies for protein structure determination and other biophysical methods applied to all classes of proteinsfrom uncharacterized hypothetical proteins to membrane proteins and protein-protein complexes.

For more information and registration, please visit the [Workshop Homepage]

2009 NIGMS Workshop - Enabling Technologies for Structural Biology
March 4, 2009 - March 6, 2009
Bethesda (Maryland), USA

The 2009 NIGMS Workshop: Enabling Technologies for Structural Biology continues a series of annual meetings held by NIGMS Protein Structure Initiative participants, which were popularly designated "Bottlenecks" Workshops. As in the past, the primary focus of this 2½ day meeting will be the technical issues affecting the speed, cost, and success of protein structure determination.
The 2009 meeting will address a wide range of topics applicable to all scales of effort, from the individual bench scientist to high-throughput research centers. The workshop program will include oral platform and poster presentations as well as pedagogical sessions emphasizing the methods and technologies for protein structure determination for all classes of proteins, from uncharacterized hypothetical proteins to membrane proteins and protein-protein complexes.

For more information, please visit: http://www.blsmeetings.net/2009workshop_enablingtechnologies/

Workshop on Applications of Protein Models in Biomedical Research
University of California, San Francisco
July 11&12, 2008


A workshop on "Applications of Protein Models in Biomedical Research" was held at the University of California, San Francisco, July 11-12, 2008. The purpose of this workshop was to explore, how protein structure models can be used in biomedical research projects, which requirements and limitations exist for the different applications today, and how the interaction between the experimental and computational research communities could be strengthened so that computational protein structure modeling can contribute effectively to our understanding of biological systems.

For more information, please visit: http://www.proteinmodelportal.org/workshop/