PubChem3D: conformer generation

EE Bolton, S Kim, SH Bryant - Journal of cheminformatics, 2011 - Springer
… the PubChem3D project, we attempt to answer questions regarding conformer model …
For example, what is the base-line conformer generation software accuracy as a function of …

PubChem3D: conformer ensemble accuracy

S Kim, EE Bolton, SH Bryant - Journal of Cheminformatics, 2013 - Springer
PubChem3D conformer models is operating as designed. In addition, the effect of PubChem3D
… minimum accuracy of 90% or more of the PubChem3D ensembles to be 0.75, 1.09, 0.43, …

PubChem3D: similar conformers

EE Bolton, S Kim, SH Bryant - Journal of cheminformatics, 2011 - Springer
… paper, the PubChem 3-D "Similar Conformers" … PubChem 3-D neighbors are defined as
any two conformers with a shape-optimized superposition yielding a similar 3-D conformer

Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets

S Kim, EE Bolton, SH Bryant - Journal of Cheminformatics, 2016 - Springer
PubChem3D conformer description. The Series B data sets ensure all considered chemicals
have both 2-D and 3-D descriptions and also removes any redundancy due to salt/mixture …

PubChem3D: a new resource for scientists

EE Bolton, J Chen, S Kim, L Han, S He, W Shi… - Journal of …, 2011 - Springer
… The PubChem3D conformer model for a chemical structure is meant to represent all possible
biologically-relevant conformations that the molecule may have. In theory, one should have …

PubChem3D: diversity of shape

EE Bolton, S Kim, SH Bryant - Journal of cheminformatics, 2011 - Springer
… C++ API [12] was used to compute conformer analytic volumes. In a recent study [20], a …
PubChem 3-D conformer generation. This parameter set was employed for conformer generation

PubChem3D: biologically relevant 3-D similarity

S Kim, EE Bolton, SH Bryant - Journal of cheminformatics, 2011 - Springer
conformer per compound in the analysis? After all, the current PubChem3D theoretical
conformer generation approach does not guarantee that the single (default) conformer used for …

Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis

S Kim, EE Bolton, SH Bryant - Journal of cheminformatics, 2012 - Springer
… to rigorously examine this question using all PubChem3D conformers, the approach used
to … both a single conformer per compound and ten diverse conformers per compound and …

PubChem3D: shape compatibility filtering using molecular shape quadrupoles

S Kim, EE Bolton, SH Bryant - Journal of cheminformatics, 2011 - Springer
… billion 3-D neighbor pairs resulting from PubChem 3-D neighboring of 17.1 million single
conformer molecules were analyzed. The maximum quadrupole differences between neighbor …

PubChem structure–activity relationship (SAR) clusters

S Kim, L Han, B Yu, VD Hähnke, EE Bolton… - Journal of …, 2015 - Springer
… the bioactive conformers. In fact, the PubChem 3-D conformer models are designed to
ensure that 90% of the conformer models have at least one bioactive conformer whose root-mean-…