Literature DB >> 34595772

Assessing the accuracy of contact and distance predictions in CASP14.

Victoria Ruiz-Serra1, Camila Pontes1, Edoardo Milanetti2,3, Andriy Kryshtafovych4, Rosalba Lepore1, Alfonso Valencia1,5.   

Abstract

We present the results of the assessment of the intramolecular residue-residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction methods was evaluated with the measures used in previous CASPs, while distance predictions were assessed based on a new protocol, which considers individual distance pairs as well as the whole predicted distance matrix, using a graph-based framework. The results of the evaluation indicate that predictions by the tFold framework, TripletRes and DeepPotential were the most accurate in both categories. With regards to progress in method performance, the results of the assessment in contact prediction did not reveal any discernible difference when compared to CASP13. Arguably, this could be due to CASP14 FM targets being more challenging than ever before.
© 2021 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.

Entities:  

Keywords:  CASP14; benchmarkin; community-wide experiment; numerical evaluation measures; prediction of residue-residue contact and distance

Mesh:

Substances:

Year:  2021        PMID: 34595772      PMCID: PMC8616839          DOI: 10.1002/prot.26248

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


  31 in total

1.  Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction.

Authors:  C A Orengo; J E Bray; T Hubbard; L LoConte; I Sillitoe
Journal:  Proteins       Date:  1999

Review 2.  The architecture of complex weighted networks.

Authors:  A Barrat; M Barthélemy; R Pastor-Satorras; A Vespignani
Journal:  Proc Natl Acad Sci U S A       Date:  2004-03-08       Impact factor: 11.205

3.  Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

Authors:  Iakes Ezkurdia; Osvaldo Graña; José M G Izarzugaza; Michael L Tress
Journal:  Proteins       Date:  2009

4.  Improving contact predictions by the combination of correlated mutations and other sources of sequence information.

Authors:  O Olmea; A Valencia
Journal:  Fold Des       Date:  1997

5.  Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin.

Authors:  A T Brünger; G M Clore; A M Gronenborn; M Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  1986-06       Impact factor: 11.205

6.  Improved protein structure prediction using potentials from deep learning.

Authors:  Andrew W Senior; Richard Evans; John Jumper; James Kirkpatrick; Laurent Sifre; Tim Green; Chongli Qin; Augustin Žídek; Alexander W R Nelson; Alex Bridgland; Hugo Penedones; Stig Petersen; Karen Simonyan; Steve Crossan; Pushmeet Kohli; David T Jones; David Silver; Koray Kavukcuoglu; Demis Hassabis
Journal:  Nature       Date:  2020-01-15       Impact factor: 49.962

7.  Analysis of distance-based protein structure prediction by deep learning in CASP13.

Authors:  Jinbo Xu; Sheng Wang
Journal:  Proteins       Date:  2019-09-13

8.  Evaluation of residue-residue contact predictions in CASP9.

Authors:  Bohdan Monastyrskyy; Krzysztof Fidelis; Anna Tramontano; Andriy Kryshtafovych
Journal:  Proteins       Date:  2011-09-17

9.  Evaluation of residue-residue contact prediction in CASP10.

Authors:  Bohdan Monastyrskyy; Daniel D'Andrea; Krzysztof Fidelis; Anna Tramontano; Andriy Kryshtafovych
Journal:  Proteins       Date:  2013-08-31

10.  Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age.

Authors:  Joerg Schaarschmidt; Bohdan Monastyrskyy; Andriy Kryshtafovych; Alexandre M J J Bonvin
Journal:  Proteins       Date:  2017-11-07
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  1 in total

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

Authors:  Andriy Kryshtafovych; Torsten Schwede; Maya Topf; Krzysztof Fidelis; John Moult
Journal:  Proteins       Date:  2021-10-07
  1 in total

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