@article {Boniecki2003, title = {Protein fragment reconstruction using various modeling techniques}, journal = {Journal of Computer-Aided Molecular Design}, volume = {17}, number = {11}, year = {2003}, month = {nov}, pages = {725{\textendash}38}, abstract = {Recently developed reduced models of proteins with knowledge-based force fields have been applied to a specific case of comparative modeling. From twenty high resolution protein structures of various structural classes, significant fragments of their chains have been removed and treated as unknown. The remaining portions of the structures were treated as fixed - i.e., as templates with an exact alignment. Then, the missed fragments were reconstructed using several modeling tools. These included three reduced types of protein models: the lattice SICHO (Side Chain Only) model, the lattice CABS (Calpha + Cbeta + Side group) model and an off-lattice model similar to the CABS model and called REFINER. The obtained reduced models were compared with more standard comparative modeling tools such as MODELLER and the SWISS-MODEL server. The reduced model results are qualitatively better for the higher resolution lattice models, clearly suggesting that these are now mature, competitive and complementary (in the range of sparse alignments) to the classical tools of comparative modeling. Comparison between the various reduced models strongly suggests that the essential ingredient for the sucessful and accurate modeling of protein structures is not the representation of conformational space (lattice, off-lattice, all-atom) but, rather, the specificity of the force fields used and, perhaps, the sampling techniques employed. These conclusions are encouraging for the future application of the fast reduced models in comparative modeling on a genomic scale.}, keywords = {Amino Acid Sequence, Binding Sites, Hydrogen Bonding, Models, Molecular, Peptide Fragments, Peptide Fragments: chemistry, Protein Conformation, Protein Structure, Proteins, Proteins: chemistry, Secondary}, issn = {0920-654X}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15072433}, author = {Michal Boniecki and Piotr Rotkiewicz and Jeffrey Skolnick and Andrzej Koli{\'n}ski} } @article {Skolnick1993, title = {From independent modules to molten globules: observations on the nature of protein folding intermediates}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {90}, number = {6}, year = {1993}, pages = {2099{\textendash}100}, keywords = {Binding Sites, Isomerases, Isomerases: chemistry, Protein Disulfide-Isomerases, Protein Folding, Protein Structure, Proteins, Proteins: chemistry, Secondary}, issn = {0027-8424}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=46030\&tool=pmcentrez\&rendertype=abstract}, author = {Jeffrey Skolnick and Andrzej Koli{\'n}ski and Adam Godzik} }