Estimation of model accuracy in CASP15 using the ModFOLDdock server

被引:12
作者
Edmunds, Nicholas S. [1 ]
Alharbi, Shuaa M. A. [1 ]
Genc, Ahmet G. [1 ]
Adiyaman, Recep [1 ]
McGuffin, Liam J. [1 ,2 ]
机构
[1] Univ Reading, Sch Biol Sci, Reading, England
[2] Univ Reading, Sch Biol Sci, Whiteknights, Reading RG6 6EX, England
基金
英国生物技术与生命科学研究理事会;
关键词
3D modeling; EMA; estimates of model accuracy; model quality assessment; protein structure prediction; QA; quaternary structure;
D O I
10.1002/prot.26532
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 CASP15, there was a greater emphasis on multimeric modeling than in previous experiments, with assembly structures nearly doubling in number (41 up from 22) since the previous round. CASP15 also included a new estimation of model accuracy (EMA) category in recognition of the importance of objective quality assessment (QA) for quaternary structure models. ModFOLDdock is a multimeric model QA server developed by the McGuffin group at the University of Reading, which brings together a range of single-model, clustering, and deep learning methods to form a consensus of approaches. For CASP15, three variants of ModFOLDdock were developed to optimize for the different facets of the quality estimation problem. The standard ModFOLDdock variant produced predicted scores optimized for positive linear correlations with the observed scores. The ModFOLDdockR variant produced predicted scores optimized for ranking, that is, the top-ranked models have the highest accuracy. In addition, the ModFOLDdockS variant used a quasi-single model approach to score each model on an individual basis. The scores from all three variants achieved strongly positive Pearson correlation coefficients with the CASP observed scores (oligo-lDDT) in excess of 0.70, which were maintained across both homomeric and heteromeric model populations. In addition, at least one of the ModFOLDdock variants was consistently ranked in the top two methods across all three EMA categories. Specifically, for overall global fold prediction accuracy, ModFOLDdock placed second and ModFOLDdockR placed third; for overall interface quality prediction accuracy, ModFOLDdockR, ModFOLDdock, and ModFOLDdockS were placed above all other predictor methods, and ModFOLDdockR and ModFOLDdockS were placed second and third respectively for individual residue confidence scores. The ModFOLDdock server is available at: . ModFOLDdock is also available as part of the MultiFOLD docker package: .
引用
收藏
页码:1871 / 1878
页数:8
相关论文
共 18 条
[1]   DockQ: A Quality Measure for Protein-Protein Docking Models [J].
Basu, Sankar ;
Wallner, Bjorn .
PLOS ONE, 2016, 11 (08)
[2]   Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology [J].
Bertoni, Martino ;
Kiefer, Florian ;
Biasini, Marco ;
Bordoli, Lorenza ;
Schwede, Torsten .
SCIENTIFIC REPORTS, 2017, 7
[3]   OpenStructure: an integrated software framework for computational structural biology [J].
Biasini, M. ;
Schmidt, T. ;
Bienert, S. ;
Mariani, V. ;
Studer, G. ;
Haas, J. ;
Johner, N. ;
Schenk, A. D. ;
Philippsen, A. ;
Schwede, T. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2013, 69 :701-709
[4]   DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning [J].
Guo, Sai-Sai ;
Liu, Jun ;
Zhou, Xiao-Gen ;
Zhang, Gui-Jun .
BIOINFORMATICS, 2022, 38 (07) :1895-1903
[5]   Highly accurate protein structure prediction with AlphaFold [J].
Jumper, John ;
Evans, Richard ;
Pritzel, Alexander ;
Green, Tim ;
Figurnov, Michael ;
Ronneberger, Olaf ;
Tunyasuvunakool, Kathryn ;
Bates, Russ ;
Zidek, Augustin ;
Potapenko, Anna ;
Bridgland, Alex ;
Meyer, Clemens ;
Kohl, Simon A. A. ;
Ballard, Andrew J. ;
Cowie, Andrew ;
Romera-Paredes, Bernardino ;
Nikolov, Stanislav ;
Jain, Rishub ;
Adler, Jonas ;
Back, Trevor ;
Petersen, Stig ;
Reiman, David ;
Clancy, Ellen ;
Zielinski, Michal ;
Steinegger, Martin ;
Pacholska, Michalina ;
Berghammer, Tamas ;
Bodenstein, Sebastian ;
Silver, David ;
Vinyals, Oriol ;
Senior, Andrew W. ;
Kavukcuoglu, Koray ;
Kohli, Pushmeet ;
Hassabis, Demis .
NATURE, 2021, 596 (7873) :583-+
[6]   Docking and scoring protein complexes: CAPRI 3rd edition [J].
Lensink, Marc F. ;
Mendez, Raul ;
Wodak, Shoshana J. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 69 (04) :704-718
[7]  
Liu J., 2023, BIORXIV, DOI [10.1101/2022.01.11.475831, DOI 10.1101/2022.01.11.475831]
[8]   ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models [J].
Maghrabi, Ali H. A. ;
McGuffin, Liam J. .
NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) :W416-W421
[9]   Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers [J].
McGuffin, Liam J. ;
Edmunds, Nicholas S. ;
Genc, Ahmet G. ;
Alharbi, Shuaa M. A. ;
Salehe, Bajuna R. ;
Adiyaman, Recep .
NUCLEIC ACIDS RESEARCH, 2023, 51 (W1) :W274-W280
[10]   ModFOLD8: accurate global and local quality estimates for 3D protein models [J].
McGuffin, Liam J. ;
Aldowsari, Fand M. F. ;
Alharbi, Shuaa M. A. ;
Adiyaman, Recep .
NUCLEIC ACIDS RESEARCH, 2021, 49 (W1) :W425-W430