Sentence examples for backbone dependent from inspiring English sources

To construct these ensembles we use a backbone dependent rotamer library and implement the concept of interaction sampling.

Moreover, the log-odd score is based on the popular backbone dependent rotamer library downloaded from Dunbrack's lab [ 24].

Further, side-chain torsion angles are assigned to the initial structure using backbone dependent rotamer library [ 51].

The energy function includes terms for the 12-6 Lennard-Jones potentimplicitlinteractionction with the solvent, electrostatics, a hydrogen-bonding potential, backbone dependent internal free energies of rotamers, and amino acid reference energies (wref).

New backbone-dependent rotamer libraries at varying levels of smoothing are available from http://dunbrack.fccc.edu.fccc.edu

The backbone-dependent rotamer library consists of rotamer frequencies, mean dihedral angles, and variances as a function of the backbone dihedral angles.

A new version of the backbone-dependent rotamer library has been developed using adaptive kernel density estimates for the rotamer frequencies and adaptive kernel regression for the mean dihedral angles and variances.

Here, we provide a backbone-dependent rotamer library, based on secondary structure ϕ/ψ regions, and an update to our 2011 backbone-independent library that addresses the doubling of our dataset since its original publication.

A standard backbone-dependent side chain rotamer library with expansions by one standard deviation about χ1 and χ2 was used [28].

The "swapaa" command was used to substitute amino acids, selecting the side chain from the Dunbrack backbone-dependent rotamer library based on lowest number of clashes, highest number of hydrogen bonds, and highest probability.

This was achieved by rebuilding side-chains with a backbone-dependent rotamer library implemented in the repack protocol using the score_membrane scoring function (Barth et al., 2007), followed by rescore using ProQM.