A kinematic view of protein loop flexibility, with applications to conformational exploration

T O'Donnell - 2022 - theses.hal.science
… loop conformations beyond tripeptides, the third contribution develops a loop sampling
strategy based on solutions of individualrotatable bonds of a loop L. (A) Kinematic chain with n …

Comprehensive assessment of torsional strain in crystal structures of small molecules and protein–ligand complexes using ab initio calculations

BK Rai, V Sresht, Q Yang, R Unwalla… - Journal of chemical …, 2019 - ACS Publications
… the given bond, is both necessary and sufficient for capturing the … This analysis, however,
is beyond the scope of the present … n is the number to rotatable bonds in the given molecule—…

A distributional model of bound ligand conformational strain: From small molecules up to large peptidic macrocycles

AN Jain, AC Brueckner, AE Cleves… - Journal of Medicinal …, 2023 - ACS Publications
… (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)…

Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks

Y Zhu, J Hwang, K Adams, Z Liu, B Nan… - The Twelfth …, 2023 - openreview.net
… 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. …

Understanding ring puckering in small molecules and cyclic peptides

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

Comparative Analysis of Chemical Descriptors by Machine Learning Reveals Atomistic Insights into Solute–Lipid Interactions

JJ Lange, A Anelli, J Alsenz, M Kuentz… - Molecular …, 2024 - ACS Publications
… 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 …

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 …

A million crystal structures: The whole is greater than the sum of its parts

R Taylor, PA Wood - Chemical reviews, 2019 - ACS Publications
… The Internet and World Wide Web must have been almost beyond imagination (… descriptors
were used in the model: the rotatable bond count (obviously measuring molecular flexibility) …

Quantitative structure–selectivity relationships in enantioselective catalysis: past, present, and future

AF Zahrt, SV Athavale, SE Denmark - Chemical reviews, 2019 - ACS Publications
… , 3D-QSSR methods have the greatest potential for capturing … nonobvious contributions,
perhaps beyond the chemists’ … perform similarly to previously published work, but for flexible

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 …