[HTML][HTML] Benchmark assessment of molecular geometries and energies from small molecule force fields

VT Lim, DF Hahn, G Tresadern, CI Bayly… - …, 2020 - ncbi.nlm.nih.gov
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 …

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

Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters

JN Ehrman, VT Lim, CC Bannan, N Thi, DY Kyu… - … -aided molecular design, 2021 - Springer
… 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

Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings

J Braun, P Katzberger, GA Landrum, S Riniker - 2024 - chemrxiv.org
… 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

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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. …

A simple representation of three-dimensional molecular structure

SD Axen, XP Huang, EL Cáceres… - Journal of medicinal …, 2017 - ACS Publications
… 3D fingerprint, we generate a library of potential conformerstorsion fingerprint deviation
(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

V Lim, D Hahn, G Tresadern - 2020 - academia.edu
… 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 …

[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 …

Understanding ring puckering in small molecules and cyclic peptides

L Chan, GR Hutchison, GM Morris - Journal of Chemical …, 2021 - ACS Publications
… 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 …

Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field

S Boothroyd, PK Behara, OC Madin… - Journal of chemical …, 2023 - ACS Publications
… conformer geometries, torsion fingerprint deviations (TFD), and … properties, including
comparison against experimental data … molecule, we use no more than 10 optimized conformers in …