De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

• DOI: 10.1002/prot.23059
• Publication Date: 2011-04-20T20:07:54Z
• Authors: Juyong Lee; Jinhyuk Lee; Takeshi N. Sasaki; Masaki Sasai; Chaok Seok; Jooyoung Lee
• Keywords: Fragment (logic); Energy landscape

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of and efficient conformational sampling method for successful modeling. In this article, we present ab which combines recently suggested novel way fragment assembly, dynamic assembly (DFA) space annealing (CSA) algorithm. DFA, model structures are scored by continuous functions constructed based on short- long-range structural restraint information from library. Here, DFA represented the full-atom CHARMM with addition empirical potential DFIRE. The relative contributions between various energy terms optimized using linear programming. was carried out CSA algorithm, can find low conformations more efficiently than simulated used in existing study. newly introduced function algorithm implemented into CHARMM. Test results 30 small single-domain proteins 13 template-free modeling targets 8th Critical Assessment Structure Prediction show current provides comparable complementary to top methods.