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Accurate template‐based modeling in CASP12 using the IntFOLD4‐TS, ModFOLD6, and ReFOLD methods
Author(s) -
McGuffin Liam J.,
Shuid Ahmad N.,
Kempster Robert,
Maghrabi Ali H.A.,
Nealon John O.,
Salehe Bajuna R.,
Atkins Jennifer D.,
Roche Daniel B.
Publication year - 2018
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25360
Subject(s) - ranking (information retrieval) , rank (graph theory) , computer science , selection (genetic algorithm) , protocol (science) , data mining , sequence (biology) , artificial intelligence , mathematics , medicine , alternative medicine , pathology , combinatorics , biology , genetics
Abstract 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.