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For the critical assessment of techniques for protein structure prediction (CASP) 11, we have built a protocol of protein structure prediction that has novel coarse\u2010grained scoring functions for selecting decoys as the heart of its pipeline. The score named PRESCO (Protein Residue Environment SCOre) developed recently by our group evaluates the native\u2010likeness of local structural environment of residues in a structure decoy considering positions and the depth of side\u2010chains of spatially neighboring residues. We also introduced a helix interaction potential as an additional scoring function for selecting decoys. The best models selected by PRESCO and the helix interaction potential underwent structure refinement, which includes side\u2010chain modeling and relaxation with a short molecular dynamics simulation. Our protocol was successful, achieving the top rank in the free modeling category with a significant margin of the accumulated Z\u2010score to the subsequent groups when the top 1 models were considered. Proteins 2016; 84(Suppl 1):105\u2013117. \u00a9 2015 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/prot.24920","type":"journal-article","created":{"date-parts":[[2015,9,7]],"date-time":"2015-09-07T23:44:46Z","timestamp":1441669486000},"page":"105-117","source":"Crossref","is-referenced-by-count":18,"title":["Protein structure prediction using residue\u2010 and fragment\u2010environment potentials in <scp>CASP<\/scp>11"],"prefix":"10.1002","volume":"84","author":[{"given":"Hyungrae","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Biological Sciences Purdue University West Lafayette Indiana 47906"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daisuke","family":"Kihara","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences Purdue University West Lafayette Indiana 47906"},{"name":"Department of Computer Science Purdue University West Lafayette Indiana 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