based technique. First, there are constraints that limit the possibilities for local region modeling. One such constraint is that loop termini are required to end at the correct anchor position. Also, the Ramachandran space cannot contain a backbone of dihedral angles. Second, a modeling program has to use a set procedure. Some programs use the “spare parts” approach as mentioned above. Other programs use a de novo approach that samples sterically feasible loop conformations and selects the best one. Third, determining the best model means that a scoring method must be created to compare the various conformations. See also Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology" Structure 4: 1123–27. Fiser A, Gian Do RK, Sali A. (2000) Modeling of loops in protein structures" Protein Science 9: 1753-73 Ko J. et al. The FALC-Loop web server for protein loop modeling" Nucleic Acids Research 39, W210-W214 (2011). Lee J, Lee D, Park H, Coutsias EA, Seok C. "Protein loop modeling by using fragment assembly and analytical loop closure. Proteins: Structure, Function, and Bioinformatics 78, 1-9 (2010). Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY. Soto C. et al. "Loop modeling: Sampling, filtering, and scoring. Proteins: Structure, Function, and Bioinformatics 70, 1-10 (2008). Tang K., Zhang J., Liang J. (2014) Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method. PLOS Computational Biology 10 (4), e1003539. References External links MODLOOP, public server for access to MODELLER's loop modeling facility RAPPER, public server for access to RAPPER’s protein modeling facility SuperLooper2, SuperLooper2 homepage FALC-Loop, FALC-Loop homepage DiSGro, DiSGro homepage Bioinformatics Protein methods Protein structure