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ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates

Shuid, A. N., Kempster, R. and McGuffin, L. J. (2017) ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates. Nucleic Acids Research, 45 (W1). W422-W428. ISSN 1362-4962

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To link to this item DOI: 10.1093/nar/gkx249

Abstract/Summary

ReFOLD is a novel hybrid refinement server with integrated high performance global and local Accuracy Self Estimates (ASEs). The server attempts to identify and to fix likely errors in user supplied 3D models of proteins via successive rounds of refinement. The server is unique in providing output for multiple alternative refined models in a way that allows users to quickly visualize the key residue locations, which are likely to have been improved. This is important, as global refinement of a full chain model may not always be possible, whereas local regions, or individual domains, can often be much improved. Thus, users may easily compare the specific regions of the alternative refined models in which they are most interested e.g. key interaction sites or domains. ReFOLD was used to generate hundreds of alternative refined models for the CASP12 experiment, boosting our group's performance in the main tertiary structure prediction category. Our successful refinement of initial server models combined with our built-in ASEs were instrumental to our second place ranking on Template Based Modeling (TBM) and Free Modeling (FM)/TBM targets. The ReFOLD server is freely available at: http://www.reading.ac.uk/bioinf/ReFOLD/.

Item Type:Article
Refereed:Yes
Divisions:Interdisciplinary centres and themes > Food Chain and Health
Interdisciplinary centres and themes > Institute for Cardiovascular and Metabolic Research (ICMR)
Interdisciplinary centres and themes > Reading Systems Biology Network (RSBN)
Faculty of Life Sciences > School of Biological Sciences > Biomedical Sciences
ID Code:70122
Publisher:Oxford University Press

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