Improved protein contact predictions with the MetaPSICOV2 server in CASP12

被引：38

作者：

Buchan, Daniel W. A. ^{[1
]}

Jones, David T. ^{[1
]}

机构：

[1] UCL, Dept Comp Sci, London, England

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2018年 / 86卷

基金：

英国生物技术与生命科学研究理事会;

关键词：

contact prediction; machine learning; meta-prediction; bioinformatics; ASSISTED PREDICTIONS;

D O I：

10.1002/prot.25379

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

In this paper, we present the results for the MetaPSICOV2 contact prediction server in the CASP12 community experiment (). Over the 35 assessed Free Modelling target domains the MetaPSICOV2 server achieved a mean precision of 43.27%, a substantial increase relative to the server's performance in the CASP11 experiment. In the following paper, we discuss improvements to the MetaPSICOV2 server, covering both changes to the neural network and attempts to integrate contact predictions on a domain basis into the prediction pipeline. We also discuss some limitations in the CASP12 assessment which may have overestimated the performance of our method.

引用

页码：78 / 83

页数：6

共 14 条

[1] Eigen THREADER: analogous protein fold recognition by efficient contact map threading
Buchan, Daniel W. A.
Jones, David T.
[J]. BIOINFORMATICS, 2017, 33 (17) : 2684 - 2690
[2] Profile hidden Markov models
Eddy, SR
[J]. BIOINFORMATICS, 1998, 14 (09) : 755 - 763
[3] MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
Jones, David T.
Singh, Tanya
Kosciolek, Tomasz
Tetchner, Stuart
[J]. BIOINFORMATICS, 2015, 31 (07) : 999 - 1006
[4] PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
Jones, David T.
Buchan, Daniel W. A.
Cozzetto, Domenico
Pontil, Massimiliano
[J]. BIOINFORMATICS, 2012, 28 (02) : 184 - 190
[5] FreeContact: fast and free software for protein contact prediction from residue co-evolution
Kajan, Laszlo
Hopf, Thomas A.
Kalas, Matus
Marks, Debora S.
Rost, Burkhard
[J]. BMC BIOINFORMATICS, 2014, 15
[6] Assessment of CASP11 contact-assisted predictions
Kinch, Lisa N.
Li, Wenlin
Monastyrskyy, Bohdan
Kryshtafovych, Andriy
Grishin, Nick V.
[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016, 84 : 164 - 180
[7] Accurate contact predictions using covariation techniques and machine learning
Kosciolek, Tomasz
Jones, David T.
[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016, 84 : 145 - 151
[8] MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
Ma, Jianzhu
Wang, Sheng
Wang, Zhiyong
Xu, Jinbo
[J]. PLOS COMPUTATIONAL BIOLOGY, 2014, 10 (03)
[9] Protein 3D Structure Computed from Evolutionary Sequence Variation
Marks, Debora S.
Colwell, Lucy J.
Sheridan, Robert
Hopf, Thomas A.
Pagnani, Andrea
Zecchina, Riccardo
Sander, Chris
[J]. PLOS ONE, 2011, 6 (12):
[10] Direct-coupling analysis of residue coevolution captures native contacts across many protein families
Morcos, Faruck
Pagnani, Andrea
Lunt, Bryan
Bertolino, Arianna
Marks, Debora S.
Sander, Chris
Zecchina, Riccardo
Onuchic, Jose N.
Hwa, Terence
Weigt, Martin
[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (49) : E1293 - E1301

← 1 2 →