GalaxyWEB

These sets consists of backbone perturbed crystal structures and templated-based models constructed for loop modeling as described in Park/Lee et al, "Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments", PLoS ONE, 2014.

For the backbone-perturbed set, the set is composed of two parts, targets with 8 residue length loops and 12 residue length loops each. The list of crystal structures used is derived from the work of Sellers/Zhu et al [1]. The backbone-perturbed structures were generated by running 2-ns molecular dynamics simulations using AMBER. Details can be found in the article. Each directory contains 20 backbone perturbed structures, XXXX.bbpert.pdb. XXXX is the native crystal structure PDB ID and the file named 'trglist_X' contains loop information.

For the template-based model set, targets were selected from the HOMSTRAD set [2] and the models were generated using MODELLER 9.6 [3] with the templates and alignments taken from the SALIGN study 4,5]. The set consists of total 23 loops with loop length from 6 to 11 residue. The model qualities are between GDT-TS 70.0 and 90.0. In the text file trglist_tbm', native crystal structure PDB ID with the range of the loop is written. Template-based models are supplied in the 'tbm' directory with the file names marked with the native PDB ID and the loop range. For the corresponding native crystal structure, the whole chain structure is given as [PDB_ID]_[loop_range].nat.pdb and the loop region with its environment superposed to the model structure as it was used to calculate loop RMSD in the study is also given as PDB_ID]_[loop_range].nat.env.pdb in the 'native' directory. Please be aware that the residue numbers for both TBM and the native structures were rearranged after generating the structure model.