CASP Coopetition Forum

Welcome to the CASP Coopetition Forum.

This forum is similar to the other WeFold experiments. Its participants contribute different components of the protein structure prediction pipeline and create hybrid pipelines that will be tested in CASP12. Some participants also contribute the models generated by their own pipelines. The combination of all models (i.e. those generated by individual groups and WeFold groups) may be further refined and/or ranked by WeFold participants, and submitted to CASP12 as a WeFold group. Every single contribution can be tracked in the forums and discussion groups and used as a proof of ownership.

We kindly ask our more senior participants to encourage their students and mentees to participate in this experiment. It is an exciting experience for all.

We kindly ask our young participants to not hesitate sharing their insights. This is a very supportive community and any and all ideas and suggestions are welcome.

List of participants and what they plan to contribute:

Participant/Group Contribution
David Kim & Sergey Ovchinnikov
Baker Lab
University of Washington,
USA
Rosetta decoys, 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 server models selected by Keasar.
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 Group
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 & Minkyung Baek
Seok Lab
Seoul National University
South Korea
GalaxyRefine and other methods
Bjorn 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
Eshel Faraggi & Andrzej Kloczkowski
Kloczkowski Lab
Nationwide Children's Hospital
USA
Model assessment
Sambit Ghosh & Soma Ghosh
Vishveshwara Lab
Indian Institute of Science, India
Refinement, selection
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,
Shokoufeh Mirzaei
Crivelli Lab
Lawrence Berkeley Lab
USA
Scoring
Kai Petarski and Shreyas Cholia
Crivelli Lab
LBNL/NERSC
USA
Gateway