>>"Example of Download Page" of 2010 Smooth Backbone-Dependent Rotamer Library
β turns & Lib
Example of Download Page
Here is an example download page you will be provided, once you have applied for a 2010 library license and have been approved by us. For more details on the available download options, please rerefer to Tutorial. The links of this example download page will lead you to Licensing.
Welcome to 2010 Backbone-dependent Rotamer Library Download Page
An original dataset that was prepared to compile the 2010 Rotamer Library itself. To download the dataset click here. This is not a rotamer library, the rotamer libraries are provided below.
A set of different 2010 backbone-dependent rotamer libraries is available. Choose the default option if you have no specific preference. The default option is the 2010 rotamer library with a 5%-stepdown smoothness. In addition we provide smoother but less detailed libraries with 10%-stepdown, 20%-stepdown and 25%-stepdown. We also provide less smooth libraries and with more details than in the default, 5%-stepdown option: 2%-stepdown and 0%-stepdown. Our benchmarking with different structural biology applications showed that the default, 5%-stepdown library provides the best modeling and structure prediction rates in most tests. For further details please refer to Shapovalov and Dunbrack, Structure, 2011 (in press).
Simple Mode: all residue types are represented as discrete rotamers as it was done in 1997 and 2002 libraries. The 8 non-rotameric residue types (ASN, ASP, GLN, GLU, HIS, TRP, PHE and TYR) have their last torsion angle, chi(n) are not well described in terms of rotamers (chi2 for ASN, ASP, TRP, PHE and HIS and chi3 for GLN and GLU). They rather have broader and asymmetric chi(n) distributions. The chi(n) space was broken up into 30 deg bins (12 bins for ASN, GLN, HIS and TRP and 6 bins for ASP, GLU, PHE and TYR). Here the 8 non-rotameric residue types are modeled with rotamers only. The chi(n) rotamer defintions for these 8 non-rotameric residue types are not fixed, i.e. backbone-dependent, meaning their bin positions move as a function of phi and psi. If one is interested in a model where the chi(n) rotamer definitions are fixed for the non-rotameric residues, please see the next option, Extended Mode.
All 22 residue types with their rotamer probabilities, chi means and standard deviations are stored in a single file. The chi(n) rotamer definitions for the 8 non-rotameric residue types are backbone-dependent. 22 residue types = 18 standard amino acids + trans PRO + cis PRO + non-disulfide-bonded CYS and disulfide-bonded CYS. Default, 5%-stepdown ; 0%-stepdown ; 2%-stepdown ; 10%-stepdown ; 20%-stepdown ; 25%-stepdown
Extended Mode: the rotameric residue types are modeled with rotamers only while the non-rotameric residue types are described in terms of chi(n) discrete rotamers (as in the case of Simple Mode for backward compatibility) and chi(n) densities. The chi(n) rotamer definitions for the non-rotameric residues are fixed, i.e. backbone-independent, meaning their bin positions are the same across all phi and psi values.
Each of 22 residue types is stored in its own separate file(s). For each of 8 non-rotameric residue types three files are provided: 1) file with backbone-dependent chi(n) densities, 2) file with backbone-dependent chi(n) rotamer probabilities (for backward compatibility) and 3) file with backbone-independent chi(n) rotamer definitions. Each of the 14 remaining rotameric residue types has its own separate, single file with backbone-dependent probabilities. Default, 5%-stepdown ; 0%-stepdown ; 2%-stepdown ; 10%-stepdown ; 20%-stepdown ; 25%-stepdown
All 22 residue types are treated as rotamers only and are stored in a single file. The difference from a similar option in Simple Mode is that the chi(n) rotamers of the 8 non-rotameric residue types have backbone-independent definitions. The 8 smaller files with the backbone-independent definitions are also included. Default, 5%-stepdown ; 0%-stepdown ; 2%-stepdown ; 10%-stepdown ; 20%-stepdown ; 25%-stepdown