Beyond rotatable bond counts: capturing 3D conformational flexibility in a single descriptor
JGP Wicker, RI Cooper - Journal of Chemical Information and …, 2016 - ACS Publications
A new molecular descriptor, nConf20, based on chemical connectivity, is presented which
captures the accessible conformational space of a molecule. Currently the best available …
captures the accessible conformational space of a molecule. Currently the best available …
Flexophore, a new versatile 3D pharmacophore descriptor that considers molecular flexibility
M von Korff, J Freyss, T Sander - Journal of chemical information …, 2008 - ACS Publications
A novel pharmacophore descriptor Flexophore is presented, which considers molecular
flexibility when comparing descriptor similarities. The descriptor is a complete reduced …
flexibility when comparing descriptor similarities. The descriptor is a complete reduced …
xMaP An Interpretable Alignment-Free Four-Dimensional Quantitative Structure–Activity Relationship Technique Based on Molecular Surface Properties and …
J Dreher, J Scheiber, N Stiefl… - Journal of Chemical …, 2018 - ACS Publications
A novel alignment-free molecular descriptor called xMaP (flexible MaP descriptor) is
introduced. The descriptor is the advancement of the previously published translationally …
introduced. The descriptor is the advancement of the previously published translationally …
Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns
J Auer, J Bajorath - Journal of chemical information and modeling, 2008 - ACS Publications
To systematically compare bioactive and theoretically derived compound conformations, we
have analyzed 18 different sets of active small molecules with experimentally determined …
have analyzed 18 different sets of active small molecules with experimentally determined …
Variable selection and model validation of 2D and 3D molecular descriptors
A Nicholls, NE MacCuish, JD MacCuish - Journal of computer-aided …, 2004 - Springer
We have found that molecular shape and electrostatics, in conjunction with 2D structural
fingerprints, are important variables in discriminating classes of active and inactive …
fingerprints, are important variables in discriminating classes of active and inactive …
PubChem3D: shape compatibility filtering using molecular shape quadrupoles
Background PubChem provides a 3-D neighboring relationship, which involves finding the
maximal shape overlap between two static compound 3-D conformations, a computationally …
maximal shape overlap between two static compound 3-D conformations, a computationally …
Conformer generation with OMEGA: learning from the data set and the analysis of failures
PCD Hawkins, A Nicholls - Journal of chemical information and …, 2012 - ACS Publications
We recently published a high quality validation set for testing conformer generators,
consisting of structures from both the PDB and the CSD (Hawkins, PCD et al. J. Chem. Inf …
consisting of structures from both the PDB and the CSD (Hawkins, PCD et al. J. Chem. Inf …
Generative topographic mapping of conformational space
Abstract Herein, Generative Topographic Mapping (GTM) was challenged to produce planar
projections of the high‐dimensional conformational space of complex molecules (the 1LE1 …
projections of the high‐dimensional conformational space of complex molecules (the 1LE1 …
TFD: torsion fingerprints as a new measure to compare small molecule conformations
T Schulz-Gasch, C Scharfer, W Guba… - Journal of chemical …, 2012 - ACS Publications
Advantages like intuitive interpretation, objectivity, general applicability, and its easy,
automated calculation make the rmsd (root-mean-squared deviation) the measure of choice …
automated calculation make the rmsd (root-mean-squared deviation) the measure of choice …
Using diffusion distances for flexible molecular shape comparison
Background Many molecules are flexible and undergo significant shape deformation as part
of their function, and yet most existing molecular shape comparison (MSC) methods treat …
of their function, and yet most existing molecular shape comparison (MSC) methods treat …