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Assessment of the model refinement category in CASP12

Hovan, L; Oleinikovas, V; Yalinca, H; Kryshtafovych, A; Saladino, G; Gervasio, FL; (2017) Assessment of the model refinement category in CASP12. Proteins - Structure. Function and Bioinformatics , 86 pp. 152-167. 10.1002/prot.25409. Green open access

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We here report on the assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12). This is the fifth refinement experiment since CASP8 (2008) and, as with the previous experiments, the predictors were invited to refine selected server models received in the regular (nonrefinement) stage of the CASP experiment. We assessed the submitted models using a combination of standard CASP measures. The coefficients for the linear combination of Z‐scores (the CASP12 score) have been obtained by a machine learning algorithm trained on the results of visual inspection. We identified eight groups that improve both the backbone conformation and the side chain positioning for the majority of targets. Albeit the top methods adopted distinctively different approaches, their overall performance was almost indistinguishable, with each of them excelling in different scores or target subsets. What is more, there were a few novel approaches that, while doing worse than average in most cases, provided the best refinements for a few targets, showing significant latitude for further innovation in the field.

Type: Article
Title: Assessment of the model refinement category in CASP12
Open access status: An open access version is available from UCL Discovery
DOI: 10.1002/prot.25409
Publisher version: https://doi.org/10.1002/prot.25409
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, Biophysics, CASP, CASP12, enhanced sampling algorithms, model refinement, molecular dynamics, protein structure prediction, PROTEIN-STRUCTURE REFINEMENT, MOLECULAR-DYNAMICS SIMULATIONS, STRUCTURE PREDICTIONS, STRUCTURE SELECTION, FORCE-FIELD, SIDE-CHAIN, POTENTIALS, ENSEMBLES, FF99SB
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry
URI: https://discovery.ucl.ac.uk/id/eprint/10049347
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