[HTML][HTML] Benchmark assessment of molecular geometries and energies from small molecule force fields
… molecular structures such that conformers of the same … likely in the high TFD subset than the
full molecule set, we compared … in the torsion fingerprint, and (2) torsions in the centre of the …
full molecule set, we compared … in the torsion fingerprint, and (2) torsions in the centre of the …
Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences
S Wang, J Witek, GA Landrum… - Journal of chemical …, 2020 - ACS Publications
… space to sample is much broader than for small molecules, … For this, we employ the torsion
fingerprint deviation (TFD) … for comparing conformers of macrocycles, in contrast to small …
fingerprint deviation (TFD) … for comparing conformers of macrocycles, in contrast to small …
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters
… for comparing the geometries of small molecule conformers. … project, we flag molecule pairs
yielding a TFD score above 0.2 and … Molecule pairs were assessed using Torsion Fingerprint …
yielding a TFD score above 0.2 and … Molecule pairs were assessed using Torsion Fingerprint …
Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings
… the conformational space of small molecules and compare the … and understanding of
conformational ensembles. After this … a torsion fingerprint (TF) [6] are inherently different as the TFs …
conformational ensembles. After this … a torsion fingerprint (TF) [6] are inherently different as the TFs …
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G Hutchison - Efficient Fragment-Based, 2019 - … .s3.amazonaws.com
… Bcl:: Conf: small molecule conformational sampling using a knowledge based rotamer
library. … Tfd: torsion fingerprints as a new measure to compare small molecule conformations. …
library. … Tfd: torsion fingerprints as a new measure to compare small molecule conformations. …
A simple representation of three-dimensional molecular structure
… 3D fingerprint, we generate a library of potential conformers … torsion fingerprint deviation
(TFD), (29) using 10000 random same-… same-molecule conformer pairs, in addition to the TFD …
(TFD), (29) using 10000 random same-… same-molecule conformer pairs, in addition to the TFD …
[PDF][PDF] Benchmark assessment of molecular geometries and energies from small molecule force
… three associated conformers of an example molecule from … positions (RMSD), and torsion
fingerprint deviation (TFD)87–89. … likely in the high TFD subset than the full molecule set, we …
fingerprint deviation (TFD)87–89. … likely in the high TFD subset than the full molecule set, we …
[PDF][PDF] Benchmark Assessment of Molecular Geometries
D Mobley - 2020 - … .s3.amazonaws.com
… conformers a molecule may have did not have a bearing on this analysis. For each molecule
in the high TFD … (RMSD) and Torsion Fingerprint Deviation (TFD) scores with reference to …
in the high TFD … (RMSD) and Torsion Fingerprint Deviation (TFD) scores with reference to …
Understanding ring puckering in small molecules and cyclic peptides
… to map puckering preferences to torsion space, which allows … The best RMSD between
conformations are 0.60 Å and 0.67 … and the TFD value of the corresponding conformation were …
conformations are 0.60 Å and 0.67 … and the TFD value of the corresponding conformation were …
Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field
… conformer geometries, torsion fingerprint deviations (TFD), and … properties, including
comparison against experimental data … molecule, we use no more than 10 optimized conformers in …
comparison against experimental data … molecule, we use no more than 10 optimized conformers in …