Evaluation of the template-based modeling in CASP12

Proteins: Structure, Function and Bioinformatics

Volumn 86, Issue , 2018, Pages 321-334

  Kryshtafovych, Andriy ^a   Monastyrskyy, Bohdan ^a   Fidelis, Krzysztof ^a   Moult, John ^b   Schwede, Torsten ^c,d   Tramontano, Anna ^e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^c UNIVERSITY OF BASEL   (Switzerland)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

CASP; high accuracy models; numerical evaluation measures; protein structure prediction; template based protein modeling

Indexed keywords

AB INITIO CALCULATION; ACCURACY; ANALYTICAL ERROR; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SOFTWARE; TEMPLATE BASED MODEL; BIOLOGY; CHEMISTRY; EVALUATION STUDY; HUMAN; MOLECULAR MODEL; PROCEDURES; PROTEIN CONFORMATION; PROTEIN DATABASE; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

PROTEIN;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 85037375235     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.25425     Document Type: Article

References (32)

1. Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007;35(Database issue):D301–D303.
2. Zemla A, Venclovas, Č, Moult J, Fidelis K. Processing and evaluation of predictions in CASP4. Proteins. 2001;45(S5):13–21.
3. Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5?. Bioinformatics. 2010;26(7):889–895.
4. Kinch LN, Shi S, Cheng H, et al. CASP9 target classification. Proteins. 2011;79(suppl 10):21–36.
5. Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP11 statistics and the prediction center evaluation system. Proteins. 2016;84(suppl 1):15–19.
6. Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL. Proteins. 2014;82(suppl 2):7–13.
7. Kryshtafovych A, Krysko O, Daniluk P, Dmytriv Z, Fidelis K. Protein structure prediction center in CASP8. Proteins. 2009;77(suppl 9):5–9.
8. Kryshtafovych A, Prlic A, Dmytriv Z, et al. New tools and expanded data analysis capabilities at the Protein Structure Prediction Center. Proteins. 2007;69(S8):19–26.
9. Kryshtafovych A, Milostan M, Szajkowski L, Daniluk P, Fidelis K. CASP6 data processing and automatic evaluation at the protein structure prediction center. Proteins. 2005;61(S7):19–23.
10. Tress M, Ezkurdia I, Grana O, Lopez G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins. 2005;61(S7):27–45.
11. Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins. 2007;69(suppl 8):38–56.
12. Mariani V, Biasini M, Barbato A, Schwede T. lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics. 2013;29(21):2722–2728.
13. Olechnovič K, Kulberkytė E, Venclovas Č. CAD-score: a new contact area difference-based function for evaluation of protein structural models. Proteins. 2013;81(1):149–162.
14. Kryshtafovych A, Barbato A, Monastyrskyy B, Fidelis K, Schwede T, Tramontano A. Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11. Proteins. 2016;84:349–369.
15. Huang YJ, Mao B, Aramini JM, Montelione GT. Assessment of template-based protein structure predictions in CASP10. Proteins. 2014;82(suppl 2):43–56.
16. Modi V, Xu Q, Adhikari S, Dunbrack RL. Jr., Assessment of template-based modeling of protein structure in CASP11. Proteins. 2016;84(suppl 1):200–220.
17. Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 2003;31(13):3370–3374.
18. Tramontano A, Morea V. Assessment of homology-based predictions in CASP5. Proteins. 2003;53(suppl 6):352–368.
19. Cozzetto D, Kryshtafovych A, Fidelis K, Moult J, Rost B, Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins. 2009;77(S9):18–28.
20. Mariani V, Kiefer F, Schmidt T, Haas J, Schwede T. Assessment of template based protein structure predictions in CASP9. Proteins. 2011;79(suppl 10):37–58.
21. Keedy DA, Williams CJ, Headd JJ, et al. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins. 2009;77(S9):29–49.
22. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction: progress and new directions in round XI. Proteins. 2016;84:4–14.
23. Kryshtafovych A, Fidelis K, Moult J. CASP10 results compared to those of previous CASP experiments. Proteins. 2014;82(suppl 2):164–174.
24. Kryshtafovych A, Fidelis K, Moult J. CASP9 results compared to those of previous casp experiments. Proteins. 2011;79(suppl 10):196–207.
25. Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins. 2005;61(suppl 7):225–236.
26. Johnson PM, Gucinski GC, Garza-Sanchez F, et al. Functional diversity of cytotoxic tRNase/immunity protein complexes from Burkholderia pseudomallei. J Biol Chem. 2016;291(37):19387–19400.
27. Ovchinnikov S, Park H, Kim DE, DiMaio F, Baker D. Protein structure prediction using Rosetta in CASP12. Proteins. 2017;1–9.
28. Abriata LA, Kinch LN, Tamo GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics. Proteins. 2017. https://doi.org/10.1002/prot.25403
29. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010;5(4):725–738.
30. Zhang C, Mortuza SM, He B, Wang Y, Zhang Y. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins. 2017;1–16.
31. Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV. Evaluation of free modeling targets in CASP11 and ROLL. Proteins. 2016;84:51–66.
32. Abriata LA, Tamo GE, Monastyrskyy B, Kryshtafovych A, Dal Peraro M. Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods. Proteins. 2017;1–16.