Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments

   Hahnbeom Park, Gyu Rie Lee, Lim Heo, and Chaok Seok

   Seoul National University

Backbone-perturbed crystal structure test set and templated-based model test set
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.


[1] Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP (2008) Toward better refinement of
comparative models: predicting loops in inexact environments. Proteins 72: 959-971.
[2] Mizuguchi K, Deane CM, Blundell TL, Overington JP (1998) HOMSTRAD: a database of protein
structure alignments for homologous families. Protein Science 7: 2469-2471.
[3] Sali A, Blundell TL (1993) Comparative Protein Modeling by satisfaction of Spatial Restraints.
Journal of Molecular Biology 234: 779-815.
[4] Marti-Renom MA, Madhusudhan MS, Sali A (2004) Alignment of protein sequences by their
profiles. Protein Science 13: 1071-1087.
[5] Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, et al. (2012) SALIGN: a web server for alignment
of multiple protein sequences and structures. Bioinformatics 28: 2072-2073.