About WeFold

What is CASP?

CASP, Critical Assessment of techniques for protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. The experiment challenges computational scientists to determine protein structures using only the sequence of amino acids of newly experimentally determined but as yet unpublished structures.

What is WeFold?

This site, http://wefold.nersc.gov, is a science community gateway designed to bring together labs and individuals from all over the world for online discussion and collaboration during CASP. Started in April 2012, it has enabled the interaction among various groups that work on different components of the protein structure prediction pipeline thus making it possible to leverage expertise at a scale that has never been done before. If you have questions about WeFold or would like to participate please contact Silvia Crivelli.

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List of participants and what they plan to contribute:

Participant/Group/Institution Contribution
Firas Khatib & Foldit Players
Baker Lab, Khatib Lab
University of Washington,
University of Massachussetts-Dartmouth
USA
Protein structures generated by Foldit players
Chen Keasar
Ben Gurion University
Israel
Model ranking tools, model refinement,
datasets for training and testing scoring functions
George Khoury, James Smadbeck, Chris Kieslich, Phanourios Tamamis, and
Betul Uralcan

Floudas Lab
Princeton University
USA
Access to Princeton_TIGRESS Refinement (http://atlas.princeton.edu/refinement).
This will be restricted only to WeFold2 participants during CASP11. Additionally, Princeton_TIGRESS will be used to refine protein structure predictions/models generated by WeFold2 participating groups.
Secondary structure predictions
Contact predictions
Beta-sheet topology predictions
Domain splitting
Yi He
Scheraga Lab
Cornell University
USA
Sampling. Will use coarse-grained UNRES force field with the multiplexed replica exchange method
Adam Liwo, Adam Sieradzan, Pawel Krupa,
Magdalena Mozolewska, Tomasz Wirecki, Magdalena Slusarz, Rafal Slusarz,
Artur Gieldon, Robert Ganzynkowicz,
Agnieszka Lipska, and Bartlomiej Zaborowski

Liwo Lab
University of Gdansk
Poland
Sampling. Will use coarse-grained UNRES force field with the multiplexed replica exchange method
Debswapna Bhattacharya and Jilong Li
Cheng Lab,
University of Missouri, Columbia
USA
Model ranking tools/data, model refinement tools/data, and server models
Chaok Seok, Lim Heo, and
Gyu Rie Lee

Seok Lab
Seoul National University
South Korea
GalaxyRefine and other methods
Yang Zhang
Zhang Lab,
University of Michigan
USA
Contact predictions.
100+ decoys from I-TASSER server to be scored by another WeFold2 group
Rodrigo Faccioli, Leandro Bortot and Alexandre Delbem
Delbem Lab
University of Sao Paulo
Brazil
Multi-Objective Evolutionary Algorithms and Molecular Dynamics Simulations
Björn Wallner
Wallner Lab
Linköping University, Sweden
Scoring methods
Milot Mirdita
Soeding Lab
Max-Planck Institute for Biophysical
Chemistry
and Gene Center,
LMU Munich
Germany
HHPred models
Liam McGuffin
McGuffin Lab
University of Reading,
UK
Model quality assessment
Bertil Schmidt, Andreas Hildebrandt, and Anna-Katharina Hildebrandt
Johannes Gutenberg University of Mainz,
Germany
Clustering
Andrzej Kloczkowski, Eshel Faraggi, and Marcin Pawlowski
Kloczkowski Lab
Nationwide Children's Hospital
USA
Model assessment
Jaume Bacardit
Bacardit Lab
Newcastle University,
UK
ICOS (contact predictions). ML-related tasks
Gajendra Raghava
Institute of Microbial Technology
India
Protein structure prediction. Disordered residues.
Gaurav Chopra
Levitt Lab, Samudrala Lab
Diabetes Center, School of Medicine
University of California, San Francisco and
Stanford University
USA
KoBaMIN refinement (http://csb.stanford.edu/kobamin/),
structure prediction servers STRINGS and MATRIX,
QA server based on binding site information for model selection (BITS)
Silvia Crivelli, Nelson Max,
Nathan Lin, Kelvin Lu, Alexander Parella

Crivelli/Max group
University of California, Davis
USA
Rough models created by BuildBeta. Could use predictions of beta topologies and sampling techniques that use the rough models as starting points. (Will be ready in 2-3 weeks)
Silvia Crivelli, Nelson Max, Evan Racah, Cameron Massoudi, and Aubrey Gress
Crivelli/Max group
University of California, Davis
USA
Scoring (will be ready in June)
Silvia Crivelli, Stephanie Cabanela, and Shreyas Cholia
LBNL/NERSC
USA
Gateway