A distributional model of bound ligand conformational strain: From small molecules up to large peptidic macrocycles
… (1.0 kcal/mol/Å 2 for deviations beyond 0.1 Å). Positionally restrained minimization reduced
… molecular flexibility (the total number of exocyclic and macrocyclic rotatable bonds plus one)…
… molecular flexibility (the total number of exocyclic and macrocyclic rotatable bonds plus one)…
Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks
… and transition-metal catalysts, extending beyond the scope of common GNN benchmarks …
capture their properties. Hence, we only retain molecules with more than 5 rotatable bonds. …
capture their properties. Hence, we only retain molecules with more than 5 rotatable bonds. …
Understanding ring puckering in small molecules and cyclic peptides
… Beyond ring puckers, our models also explain the change in … conformational flexibility
of rings, including endocyclic double … not contain any acyclic rotatable bonds. The lowest-energy …
of rings, including endocyclic double … not contain any acyclic rotatable bonds. The lowest-energy …
Comparative Analysis of Chemical Descriptors by Machine Learning Reveals Atomistic Insights into Solute–Lipid Interactions
… is arguably not one set of “best” descriptors that captures all … to the presence of a rotatable
bond, the amide structure and … it offers novel perspectives beyond 2D and 3D descriptors. It is …
bond, the amide structure and … it offers novel perspectives beyond 2D and 3D descriptors. It is …
ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents
L Pattanaik, A Menon, V Settels… - The Journal of …, 2023 - ACS Publications
… with a large number of rotatable bonds but few conformers. … flexible solutes with an increasing
number of rotatable bonds, … to the free energy change of solution beyond the LEC. This …
number of rotatable bonds, … to the free energy change of solution beyond the LEC. This …
Integrating multiscale and machine learning approaches towards the SAMPL9 log P challenge
MR Draper, A Waterman, JE Dannatt… - Physical Chemistry …, 2024 - pubs.rsc.org
… enhance the description of the electronic energy beyond a … One of the causes is the large
rotational flexibility exhibited … sampled from the umbrella sampling capture the wide range of …
rotational flexibility exhibited … sampled from the umbrella sampling capture the wide range of …
Permeability prediction in the beyond-Rule-of 5 chemical space: Focus on cyclic hexapeptides
V Digiesi, V de la Oliva Roque, M Vallaro… - European Journal of …, 2021 - Elsevier
… for cyclic compounds than the number of rotatable bonds [9]. … model with ΔG I and the flexibility
descriptor PHI (Eq. 1) log P … to find the states that best capture the dynamics of the system …
descriptor PHI (Eq. 1) log P … to find the states that best capture the dynamics of the system …
Can small drugs predict the intrinsic aqueous solubility of 'beyond Rule of 5'big drugs?
A Avdeef, M Kansy - ADMET and DMPK, 2020 - hrcak.srce.hr
… number of rotatable bonds, which suggests that flexibility may … acceptor count increases,
but not so much the donor count. … search for 3D-based descriptors arising from ‘conformational …
but not so much the donor count. … search for 3D-based descriptors arising from ‘conformational …
The hapten rigidity improves antibody performances in immunoassay for rifamycins: Immunovalidation and molecular mechanism
Y Zhang, W Wu, Q Li, P Zhou, K Wen, J Shen… - Journal of Hazardous …, 2024 - Elsevier
… ) flexibility index that counts the number of conformers with an … molecular descriptors,
which considers rotatable bonds, 2D … of rotatable bonds, 2D topology, and 3D conformation, …
which considers rotatable bonds, 2D … of rotatable bonds, 2D topology, and 3D conformation, …
Design principles for balancing lipophilicity and permeability in beyond rule of 5 space
H Möbitz - ChemMedChem, 2024 - Wiley Online Library
… , and high number of rotatable bonds typical for bRo5 drugs. … and 24 replicates of highly
flexible molecules also showed a strong … compartment to reduce lysosomal and cellular trapping. …
flexible molecules also showed a strong … compartment to reduce lysosomal and cellular trapping. …