ArticleScientific reports2018
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.
Abstract readComparative Study
In one paragraph
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10citing papers in PubMed
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Who cites it
10 citing papers in PubMed.
- Protein folding: Funnel model revised.Computational and structural biotechnology journal · 2024Article
- Role of environmental specificity in CASP results.BMC bioinformatics · 2023Article
- The Possible Mechanism of Amyloid Transformation Based on the Geometrical Parameters of Early-Stage Intermediate in Silico Model for Protein Folding.International journal of molecular sciences · 2022Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.Journal of chemical information and modeling · 2020Article
- Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning.Proteins · 2019Article
- GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure.Nucleic acids research · 2019Article
- A Nonlinear Support Vector Machine-Based Feature Selection Approach for Fault Detection and Diagnosis: Application to the Tennessee Eastman Process.AIChE journal. American Institute of Chemical Engineers · 2019Article
- Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization.PloS one · 2019Article
- Analysis validation has been neglected in the Age of Reproducibility.PLoS biology · 2018Article
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Authors and funding
74 authors.
Chen KeasarDepartment of Computer Science, Ben Gurion University of the Negev, Be'er sheva, Israel.
Liam J McGuffinBiomedical Sciences Division, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK.
Björn WallnerDivision of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden.
Gaurav ChopraDepartment of Chemistry, College of Science, Purdue University, West Lafayette, IN, USA.
Badri AdhikariDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
Debswapna BhattacharyaDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
Lauren BlakeLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Leandro Oliveira BortotLaboratory of Biological Physics, Faculty of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, São Paulo, Brazil.
Renzhi CaoDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
B K DhanasekaranMolecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India.
Itzhel DimasLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Rodrigo Antonio FaccioliInstitute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil.
Eshel FaraggiResearch and Information Systems, LLC, Carmel, IN, USA.
Robert GanzynkowiczFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Sambit GhoshMolecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India.
Soma GhoshMolecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India.ORCID 0000-0002-6729-4838
Artur GiełdońFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Lukasz GolonFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Yi HeSchool of Engineering, University of California, Merced, CA, USA.
Lim HeoDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.ORCID 0000-0002-3153-2363
Jie HouDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
Main KhanDepartment of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA.
Firas KhatibDepartment of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA.
George A KhouryDepartment of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
Chris KieslichTexas A&M Energy Institute, Texas A&M University, College Station, TX, USA.
David E KimDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Pawel KrupaFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Gyu Rie LeeDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Hongbo LiDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
Jilong LiDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
Agnieszka LipskaFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Adam LiwoFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Ali Hassan A MaghrabiBiomedical Sciences Division, School of Biological Sciences, University of Reading, Reading, RG6 6AS, UK.
Milot MirditaMax Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Shokoufeh MirzaeiLawrence Berkeley National Laboratory, Berkeley, CA, USA.
Magdalena A MozolewskaFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Melis OnelArtie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
Sergey OvchinnikovDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Anand ShahDepartment of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA.
Utkarsh ShahArtie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.ORCID 0000-0002-7357-5660
Tomer SidiDepartment of Computer Science, Ben Gurion University of the Negev, Be'er sheva, Israel.
Adam K SieradzanFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Magdalena ŚlusarzFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Rafal ŚlusarzFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.ORCID 0000-0003-3335-9047
James SmadbeckDepartment of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
Phanourios TamamisTexas A&M Energy Institute, Texas A&M University, College Station, TX, USA.
Nicholas TrieberDepartment of Computer and Information Science, University of Massachusetts Dartmouth, MA, USA.
Tomasz WireckiFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Yanping YinBaker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
Yang ZhangDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
Jaume BacarditInterdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing, Newcastle University, Newcastle-upon-Tyne, UK.
Maciej BaranowskiIntercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.
Nicholas ChapmanCenter for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
Seth CooperCollege of Computer and Information Science, Northeastern University, Boston, MA, USA.
Alexandre DefelicibusInstitute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil.
Jeff FlattenCenter for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
Brian KoepnickDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Zoran PopovićCenter for Game Science, Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
Bartlomiej ZaborowskiFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Jianlin ChengDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.
Cezary CzaplewskiFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Alexandre Cláudio Botazzo DelbemInstitute of Mathematical and Computer Sciences, University of São Paulo, São Paulo, Brazil.ORCID 0000-0003-1810-1742
Christodoulos FloudasTexas A&M Energy Institute, Texas A&M University, College Station, TX, USA.
Andrzej KloczkowskiFaculty of Chemistry, University of Gdansk, Gdańsk, Poland.
Stanislaw OłdziejIntercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.ORCID 0000-0002-4583-3941
Michael LevittDepartment of Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA.
Harold ScheragaBaker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
Chaok SeokDepartment of Chemistry, Seoul National University, Seoul, Republic of Korea.
Johannes SödingMax Planck Institute for Biophysical Chemistry, Göttingen, Germany.ORCID 0000-0001-9642-8244
Saraswathi VishveshwaraMolecular Biophysics Unit and IISC Mathematics Initiative, Indian Institute of Science, Bangalore, India.
Dong XuDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA.ORCID 0000-0002-4809-0514
Foldit Players consortium
Silvia N CrivelliLawrence Berkeley National Laboratory, Berkeley, CA, USA. SNCrivelli@lbl.gov.
Funding
TRAINING IN MOLECULAR AND CELLULAR BIOLOGYT32GM007270 · NIGMS · UNIVERSITY OF WASHINGTON · PI RAIBLE, DAVID W · 1985 to 2020
$21.0MINTERNAL BONDIN IN PROTEINSR01GM014312 · NIGMS · CORNELL UNIVERSITY ITHACA · PI MAISURADZE, GIA, RACKOVSKY, SHALOM R · 1985 to 2021
$9.4MEmergent Properties of Complex Systems: From Atoms to Macromolecules; from Humans to SocietiesR35GM122543 · NIGMS · STANFORD UNIVERSITY · PI MICHAEL LEVITT · 2017 to 2026
$5.1MIntegrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8MI-TASSER based atomic-level protein structure predictionR01GM083107 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ZHANG, YANG · 2008 to 2019
$3.5MSTRUCTURE PREDICTION OF PEPTIDES VIA GLOBAL OPTIMIZATIONR01GM052032 · NIGMS · PRINCETON UNIVERSITY · PI FLOUDAS, CHRISTODOULOS ACHILLEUS · 1996 to 2011
$1.9MTemplate-based docking refinement approach to protein-protein structure modelingR01GM116960 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ZHANG, YANG · 2016 to 2019
$1.4MDevelopment of MUFOLD for Building High-Accuracy Protein Structure ModelsR01GM100701 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI XU, DONG · 2012 to 2016
$1.4MNIGMS NIH HHS R01 GM014312NIGMS NIH HHS R01 GM052032NIGMS NIH HHS R01 GM083107NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM100701NIGMS NIH HHS R01 GM116960NIGMS NIH HHS R35 GM122543NIGMS NIH HHS T32 GM007270
Abstract
Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.
Indexed as
Models, MolecularSoftwareCaspase 12CaspasesComputational BiologyHumansProtein ConformationCASP12 protein, humancaspase 11, humanCaspase 12Caspases
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