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to determine protein structures using only the sequence of amino acids of newly experimentally determined but as yet unpublished structures.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
David Kim, Sergey Ovchinnikov
Baker Lab
University of Washington
USA
Rosetta decoys, GREMLIN contact predictions
Chen Keasar, Tomer Sidi
Ben Gurion University
Israel
Model ranking tools, model refinement,
datasets for training and testing scoring functions
Chris Kieslich, Melis Onel, Jason Souvaliotis, Utkarsh Shah
Floudas Lab
Texas A&M University
USA
TIGRESS will be used to refine Keasar's top 10-20 server models.
Secondary structure predictions
Contact predictions
Beta-sheet topology predictions
Domain splitting
Yi He, Yanping Yin, Pawel Krupa,
Magdalena Mozolewska

Scheraga Lab
Cornell University
USA
Sampling. Will use coarse-grained UNRES force field with the multiplexed replica exchange method
Adam Liwo, Cezary (Czarek) Czaplewski, Adam Sieradzan, Agnieszka Lipska, Agnieszka Karczyńska, Robert Ganzynkowicz, Michał Głuski, Artur Giełdoń, Magdalena Ślusarz, Rafał Ślusarz, Krzysztof Bojarski, Marcel Thiel, Maciej Baranowski, Stanislaw Ołdziej, Łukasz Golon, Emilia Lubecka, Mariusz Makowski
Gdansk Lab
University of Gdansk
Poland
Sampling. Will use coarse-grained UNRES force field with the multiplexed replica exchange method
Jie Hou, Badri
Cheng Lab,
University of Missouri, Columbia
USA
Model ranking tools/data, model refinement tools/data, and server models
Chaok Seok, Lim Heo,
Gyu Rie Lee and Minkyung Baek

Seok Lab
Seoul National University
South Korea
GalaxyRefine and other methods
Björn Wallner
Wallner Lab
Linköping University, Sweden
Scoring methods
Ahmad Naqib Shuid, Ali Hassan A. Maghrabi, Rob Kempster & Liam McGuffin
McGuffin Lab
University of Reading,
UK
Model quality assessment
Sambit Ghosh and Soma Ghosh
Vishveshwara Lab
Indian Institute of Science, India
Refinement, selection
Eshel Faraggi and Andrzej Kloczkowski
Kloczkowski Lab
Nationwide Children's Hospital
USA
Model assessment
Yasser Ruiz-Blanco
Unit of Computer-Aided Molecular Discovery and Bioinformatic Research
Facultad de Química y Farmacia
Universidad Central "Marta Abreu" de Las Villas
Cuba
Sampling. Will provide decoys/solutions generated with a metaheuristic search of the conformational space of proteins. Such conformational space will be defined by all values of the phi and psi angles of the backbone of the protein.
Solutions/decoys will be obtained by optimizing a coarse-grained physic-based potential developed in our group. Some articles related to our energetic approach are:
1) Ruiz-Blanco et al. 2014. A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL. Chemical Physics Letters 610–611, 135-140
2) Ruiz-Blanco et al. 2013. Global Stability of Protein Folding from an Empirical Free Energy Function. Journal of Theoretical Biology 321, 44-53
3) Ruiz-Blanco et al. 2015. A Hooke׳s law-based approach to protein folding rate. Journal of Theoretical Biology 364, 407-417,
Silvia Crivelli, Shokoufeh Mirzaei
LBNL
Scoring
Silvia Crivelli, Kai Petarsky 
LBNL/NERSC
USA
Gateway