[HTML][HTML] PubChem3D: conformer generation
… 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 …
For example, what is the base-line conformer generation software accuracy as a function of …
[HTML][HTML] PubChem3D: conformer ensemble accuracy
… 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, …
… minimum accuracy of 90% or more of the PubChem3D ensembles to be 0.75, 1.09, 0.43, …
[HTML][HTML] PubChem3D: similar conformers
… 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 …
any two conformers with a shape-optimized superposition yielding a similar 3-D conformer …
[HTML][HTML] Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets
… 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 …
have both 2-D and 3-D descriptions and also removes any redundancy due to salt/mixture …
[HTML][HTML] PubChem3D: a new resource for scientists
… 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 …
biologically-relevant conformations that the molecule may have. In theory, one should have …
[HTML][HTML] PubChem3D: diversity of shape
… 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 …
PubChem 3-D conformer generation. This parameter set was employed for conformer generation …
[HTML][HTML] PubChem3D: biologically relevant 3-D similarity
… 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 …
conformer generation approach does not guarantee that the single (default) conformer used for …
[HTML][HTML] Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
… 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 …
to … both a single conformer per compound and ten diverse conformers per compound and …
[HTML][HTML] PubChem3D: shape compatibility filtering using molecular shape quadrupoles
… 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 …
conformer molecules were analyzed. The maximum quadrupole differences between neighbor …
[HTML][HTML] PubChem structure–activity relationship (SAR) clusters
… 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-…
ensure that 90% of the conformer models have at least one bioactive conformer whose root-mean-…