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Record W2112130467 · doi:10.1016/j.jmb.2011.09.031

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

2011· article· en· W2112130467 on OpenAlexafffund
Sarel J. Fleishman, Timothy A. Whitehead, Eva‐Maria Strauch, Jacob E. Corn, Sanbo Qin, Huan‐Xiang Zhou, Julie C. Mitchell, Omar Demerdash, Mayuko Takeda‐Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun-su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jérôme Azé, Seren Soner, Şefik Kerem Ovalı, Pemra Özbek, Nir Ben‐Tal, Türkan Haliloǧlu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Pérez‐Cano, Carles Pons, Juan Fernández‐Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H. Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Da‐Chuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Barnett‐Itzhaki, Ora Schueler‐Furman, Yuval Inbar, Vladimir Potapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita, Camden Driggers, Robert G. Hall, Jessica L. Morgan, Victor L. Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Weiyi Zhang, Carlos J. Camacho, Krishna Praneeth Kilambi, Aroop Sircar, Jeffrey J. Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen J. Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel‐Rodríguez, Daisuke Kihara, P. Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng-You Huang, Xiaoqin Zou, Shoshana J. Wodak, Joël Janin, David Baker

Bibliographic record

VenueJournal of Molecular Biology · 2011
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicProtein Structure and Dynamics
Canadian institutionsUniversity of Toronto
FundersNational Center for Research ResourcesNational Institute of General Medical SciencesAdvanced Research Projects AgencyCancer Research UKNational Institutes of HealthHuman Frontier Science ProgramCanadian Institutes of Health ResearchDefense Threat Reduction AgencyDefense Advanced Research Projects AgencyHoward Hughes Medical Institute
KeywordsCASPSolvationComputer scienceDocking (animal)ElectrostaticsProtein designProtein structureProtein structure predictionChemistry

Abstract

fetched live from OpenAlex
No abstract in any covered source. Its absence is recorded, not treated as a negative.

No abstract. This is not a gap in this database; OpenAlex has none either. 23.3% of the frame is in this state, and the screen finds HALF as much metaresearch here, so the absence is a measured bias rather than a missing field.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.023
metaresearch head score (Gemma)0.042
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch
Consensus categoriesnone
DomainCandidate signal: Methods · Consensus signal: none
Study designCandidate signal: Observational · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.977
Threshold uncertainty score0.122

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0230.042
Meta-epidemiology (narrow)0.0010.000
Meta-epidemiology (broad)0.0020.002
Bibliometrics0.0010.001
Science and technology studies0.0020.000
Scholarly communication0.0020.003
Open science0.0040.002
Research integrity0.0020.001
Insufficient payload (model declined to judge)0.0040.001

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.067
GPT teacher head0.362
Teacher spread0.294 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designObservational
DomainMethods
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations136
Published2011
Admission routes2
Has abstractno

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