title: Template-free modeling by LEE and LEER in CASP11.
abstract: For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc.
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.|School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
authors.forename: InSuk
authors.initials: I
authors.lastname: Joung
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
authors.forename: Sun Young
authors.initials: SY
authors.lastname: Lee
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.|School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
authors.forename: Qianyi
authors.initials: Q
authors.lastname: Cheng
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
authors.forename: Jong Yun
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.|Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, 130-722, Korea.
authors.forename: Keehyoung
authors.initials: K
authors.lastname: Joo
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.|Department of Physics, University of Suwon, Hwaseong-Si, Gyeonggi-Do 445-743, Korea.
authors.forename: Sung Jong
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Center for In Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea. jlee@kias.re.kr.|School of Computational Sciences, Korea Institute for Advanced Study, Seoul, 130-722, Korea. jlee@kias.re.kr.|Center for Advanced Computation, Korea Institute for Advanced Study, Seoul, 130-722, Korea. jlee@kias.re.kr.
authors.forename: Jooyoung
authors.initials: J
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D001419:Bacteria / Q000737:chemistry; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data*; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D015233:Models, Statistical; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013237:Stereoisomerism; D013816:Thermodynamics; D014780:Viruses / Q000737:chemistry
chemical_list: D011506:Proteins
keywords: CASP; global optimization; protein structure modeling; template free modeling