Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods

McGuffin, L. ORCID: https://orcid.org/0000-0003-4501-4767, Shuid, A. N., Kempster, R., Maghrabi, A. H.A., Nealon, J. O., Salehe, B. R., Atkins, J. D. and Roche, D. B. (2018) Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods. Proteins: Structure, Function, and Bioinformatics, 86. pp. 335-344. ISSN 0887-3585 doi: 10.1002/prot.25360

Abstract/Summary

Our aim in CASP12 was to improve our Template-Based Modeling (TBM) methods through better model selection, accuracy self-estimate (ASE) scores and refinement. To meet this aim, we developed two new automated methods, which we used to score, rank, and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4-TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple-template models that were generated using a number of alternative sequence-structure alignments. Overall, our selection of top models and ASE scores using ModFOLD6_rank was an improvement on our previous approaches. In addition, it was worthwhile attempting to repair the detected errors in the top selected models using ReFOLD, which gave us an overall gain in performance. According to the assessors' formula, the IntFOLD4 server ranked 3rd/5th (average Z-score > 0.0/–2.0) on the server only targets, and our manual predictions (McGuffin group) ranked 1st/2nd (average Z-score > −2.0/0.0) compared to all other groups.

Additional Information	Special Issue: Twelfth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/71838
Identification Number/DOI	10.1002/prot.25360
Refereed	Yes
Divisions	Interdisciplinary centres and themes > Institute for Cardiovascular and Metabolic Research (ICMR) Interdisciplinary centres and themes > Reading Systems Biology Network (RSBN) Life Sciences > School of Biological Sciences > Biomedical Sciences
Additional Information	Special Issue: Twelfth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Publisher	Wiley
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