Sentence examples for validation suite from inspiring English sources
The homology based protein structure of human tubulin was validated using PSVS validation suite.
Our implementation was fully validated against the official validation suite provided by the MMFF authors.
The final ensemble containing the 20 lowest-energy structures, contained neither distance violations > 0.5 A, nor dihedral angle violation > 5°, and was validated by using the iCing validation suite [ 53].
The MMFF94 forcefield code is tested against the MMFF94 validation suite.
Obviously, since now the rebuilt conformations were different from those in the validation suite, energies could not be compared anymore.
Some examples of tests that are run each night are: (1) The MMFF94 forcefield code is tested against the MMFF94 validation suite.
Our MMFF implementation was validated against the MMFF94 and MMFF94s official validation suites deposited by Halgren and Kearsley in the CCL data archive [20],[21], which contain the kekulized 3D structures of 761 and 235 molecules, respectively.
The validation suites include a detailed log file generated by OPTIMOL, a molecular-mechanics program developed at Merck where the force field was first implemented, which lists for each molecule the MMFF atom types and charges and the overall potential energy, decomposed into the seven energy terms which appear in Equation 1.
Secondly, we converted the 3D structures provided in the MMFF validation suites into SMILES strings using the MolToSmiles RDKit function, and then rebuilt 3D coordinates with DGeomHelpers::EmbedMolecule; the raw 3D geometries were finally optimized with our MMFF implementation (see Additional files 1, 2 and 3).
Analysis by two standard validation suites, PSVS (Bhattacharya et al., 2007) and iCing (http://nmr.cmbi.ru.nl/icing/ welcome), revealed that the PONDEROSA-derived structures were of equivalent quality to the structures of the same proteins in the Protein Data Bank (1D3Z and 2KQK) determined by less automated means.
To establish the power and identify caveats of the new PDB_REDO pipeline incorporating the above developments, we chose to apply it to a selection of models from the PDB and evaluate all results both with validation suites, and also by manual inspection.
