Literature DB >> 26857434

CASP11 statistics and the prediction center evaluation system.

Andriy Kryshtafovych1, Bohdan Monastyrskyy1, Krzysztof Fidelis2.   

Abstract

We outline the role of the Protein Structure Prediction Center (predictioncenter.org) in conducting the CASP11 and CASP ROLL experiments, discuss the experiment statistics, and provide an overview of the present CASP infrastructure. The biggest changes compared to the previous CASPs are the implementation of the evaluation system incorporating practically all evaluation measures, statistical tests, and visualization tools historically used by the CASP assessors, the expansion of the infrastructure to incorporate new categories of contact-assisted and multimeric predictions, and the redesign of the assessors' web-workspace enabling assessments based on multiple measures for different group categories and target sets. Proteins 2016; 84(Suppl 1):15-19.
© 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Entities:  

Keywords:  CASP; protein structure modeling; protein structure prediction

Mesh:

Substances:

Year:  2016        PMID: 26857434      PMCID: PMC5479680          DOI: 10.1002/prot.25005

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  24 in total

1.  A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment.

Authors:  A Zemla; C Venclovas; K Fidelis; B Rost
Journal:  Proteins       Date:  1999-02-01

2.  Improving the performance of DomainParser for structural domain partition using neural network.

Authors:  Jun-tao Guo; Dong Xu; Dongsup Kim; Ying Xu
Journal:  Nucleic Acids Res       Date:  2003-02-01       Impact factor: 16.971

3.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.

Authors:  Michael Remmert; Andreas Biegert; Andreas Hauser; Johannes Söding
Journal:  Nat Methods       Date:  2011-12-25       Impact factor: 28.547

4.  New encouraging developments in contact prediction: Assessment of the CASP11 results.

Authors:  Bohdan Monastyrskyy; Daniel D'Andrea; Krzysztof Fidelis; Anna Tramontano; Andriy Kryshtafovych
Journal:  Proteins       Date:  2015-11-17

5.  Assessment of template-based protein structure predictions in CASP10.

Authors:  Yuanpeng J Huang; Binchen Mao; James M Aramini; Gaetano T Montelione
Journal:  Proteins       Date:  2014-02

6.  CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Krzysztof Fidelis
Journal:  Proteins       Date:  2013-10-18

7.  Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11.

Authors:  Andriy Kryshtafovych; Alessandro Barbato; Bohdan Monastyrskyy; Krzysztof Fidelis; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2015-09-28

8.  Protein structure prediction center in CASP8.

Authors:  Andriy Kryshtafovych; Oleh Krysko; Pawel Daniluk; Zinovii Dmytriv; Krzysztof Fidelis
Journal:  Proteins       Date:  2009

9.  MolProbity: all-atom structure validation for macromolecular crystallography.

Authors:  Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21

10.  New tools and expanded data analysis capabilities at the Protein Structure Prediction Center.

Authors:  Andriy Kryshtafovych; Andreas Prlic; Zinoviy Dmytriv; Pawel Daniluk; Maciej Milostan; Volker Eyrich; Tim Hubbard; Krzysztof Fidelis
Journal:  Proteins       Date:  2007
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  21 in total

1.  Critical assessment of methods of protein structure prediction (CASP)-Round XII.

Authors:  John Moult; Krzysztof Fidelis; Andriy Kryshtafovych; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2017-12-15

2.  CoinFold: a web server for protein contact prediction and contact-assisted protein folding.

Authors:  Sheng Wang; Wei Li; Renyu Zhang; Shiwang Liu; Jinbo Xu
Journal:  Nucleic Acids Res       Date:  2016-04-25       Impact factor: 16.971

3.  Protein structure prediction assisted with sparse NMR data in CASP13.

Authors:  Davide Sala; Yuanpeng Janet Huang; Casey A Cole; David A Snyder; Gaohua Liu; Yojiro Ishida; G V T Swapna; Kelly P Brock; Chris Sander; Krzysztof Fidelis; Andriy Kryshtafovych; Masayori Inouye; Roberto Tejero; Homayoun Valafar; Antonio Rosato; Gaetano T Montelione
Journal:  Proteins       Date:  2019-12

4.  Assessment of model accuracy estimations in CASP12.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Krzysztof Fidelis; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2017-09-08

5.  End-to-End Differentiable Learning of Protein Structure.

Authors:  Mohammed AlQuraishi
Journal:  Cell Syst       Date:  2019-04-17       Impact factor: 10.304

6.  Evaluation of the template-based modeling in CASP12.

Authors:  Andriy Kryshtafovych; Bohdan Monastyrskyy; Krzysztof Fidelis; John Moult; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2017-12-04

7.  Assessment of protein assembly prediction in CASP12.

Authors:  Aleix Lafita; Spencer Bliven; Andriy Kryshtafovych; Martino Bertoni; Bohdan Monastyrskyy; Jose M Duarte; Torsten Schwede; Guido Capitani
Journal:  Proteins       Date:  2017-11-08

8.  Evaluation system and web infrastructure for the second cryo-EM model challenge.

Authors:  Andriy Kryshtafovych; Paul D Adams; Catherine L Lawson; Wah Chiu
Journal:  J Struct Biol       Date:  2018-07-12       Impact factor: 2.867

9.  SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data.

Authors:  Jie Hou; Badri Adhikari; John J Tanner; Jianlin Cheng
Journal:  Proteins       Date:  2019-12-27

10.  CASP13 target classification into tertiary structure prediction categories.

Authors:  Lisa N Kinch; Andriy Kryshtafovych; Bohdan Monastyrskyy; Nick V Grishin
Journal:  Proteins       Date:  2019-07-24
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