The torsion library: Semiautomated improvement of torsion rules with SMARTScompare
P Penner, W Guba, R Schmidt, A Meyder… - Journal of Chemical …, 2022 - ACS Publications
… rule can then most specifically describe the likelihood of a dihedral angle for the chemical
… Otherwise patterns with similar chemistry but describing very different torsion angles may …
… Otherwise patterns with similar chemistry but describing very different torsion angles may …
Defining and navigating macrocycle chemical space
LA Viarengo-Baker, LE Brown, AA Rzepiela… - Chemical Science, 2021 - pubs.rsc.org
… 3 MC drug-like chemical space as defined by PCA. (A) The oral MC drugs and clinical …
We speculate that this high preference for peripheral oxygens over nitrogens may be because …
We speculate that this high preference for peripheral oxygens over nitrogens may be because …
Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation
Z Zhang, G Wang, R Li, L Ni, RZ Zhang… - Journal of …, 2023 - Springer
… Its performance is particularly high for drug-like molecules with rotatable bonds less than
10… , some hyperparameters of the model, the settings of loss functions and the implementation …
10… , some hyperparameters of the model, the settings of loss functions and the implementation …
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
… chemical diversity represented in crystal structure databases. A rigorous analysis of strain
with adequate coverage of druglike chemical space … to analyze torsion angle preferences were…
with adequate coverage of druglike chemical space … to analyze torsion angle preferences were…
Torsionnet: A deep neural network to rapidly predict small-molecule torsional energy profiles with the accuracy of quantum mechanics
BK Rai, V Sresht, Q Yang, R Unwalla… - Journal of Chemical …, 2022 - ACS Publications
… by insufficient coverage of drug-like chemical space and accurate … of dihedral preference
characterization and torsional strain … explored the available chemical space of our corporate …
characterization and torsional strain … explored the available chemical space of our corporate …
Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules
E Raush, R Abagyan, M Totrov - Journal of Chemical Information …, 2022 - ACS Publications
… We trained a GCNN model of torsion angle distributions using … Our torsion profile model
correctly captures this preference (… for large libraries of drug-like compounds is essential for fast …
correctly captures this preference (… for large libraries of drug-like compounds is essential for fast …
Structure-based drug design with geometric deep learning
… prediction of amino acid preference for the atomic environment … a binding site for small,
drug-like ligands, or as an interaction … , whereas the torsion angle outputs and confidence model …
drug-like ligands, or as an interaction … , whereas the torsion angle outputs and confidence model …
Useful Computational Chemistry Tools for Medicinal Chemistry
DVS Green, CM Edge - 2023 - books.rsc.org
… , comprises the cosine of the torsional angle. The final term is a … experimental error for
drug-like molecules. Unfortunately, … This method clearly shows the preference of an ester to use …
drug-like molecules. Unfortunately, … This method clearly shows the preference of an ester to use …
Computer-aided drug design towards new psychotropic and neurological drugs
… cannot capture the full breadth of chemical space, it is … using standard and extra precision
settings in Glide indicated 32 … that the small molecules possessed drug-like properties. The …
settings in Glide indicated 32 … that the small molecules possessed drug-like properties. The …
Shape-based methods for Structure-based Fragment Growing
P Penner - 2022 - ediss.sub.uni-hamburg.de
… at torsion angle preferences and conformations of druglike … consider the torsion angle
preferences of druglike molecules… specific SMARTS defines a subset of the chemical space[85]. …
preferences of druglike molecules… specific SMARTS defines a subset of the chemical space[85]. …