Chlordiazepoxide against signalling, receptor and regulatory proteins of breast cancer: a structure-based in-silico approach

AA Alsaiari, AF Gharib, MM Bakhuraysah, AA Alrehaili… - Medical Oncology, 2024 - Springer
… and its target protein, capturing various aspects of the ligand–… 17 ring atoms and 0 rotatable
bonds, indicating a relatively … may exert therapeutic benefits beyond its anxiolytic actions, …

SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces

SMN Hönig, F Flachsenberg, C Ehrt… - Journal of Computer …, 2024 - Springer
… to more accurately describe fragments that extend beyond the … The flexible alignment of
LS-align involves generating a list … rotatable bonds are removed from the initial list of rotatable

Spatiotemporal Route to Understanding Metal Halide Perovskitoid Crystallization

MAN Nellikkal, R Keesey, M Zeile, V Shekar… - Chemistry of …, 2022 - ACS Publications
… The set of input descriptors used in this work are selected to capture “amine-”, “solvent-”, …
cation, rotatable bond count, number of C atoms, and aliphatic atom count nodes indicate the …

Pocket Crafter: a 3D generative modeling based workflow for the rapid generation of hit molecules in drug discovery

L Shen, J Fang, L Liu, F Yang, JL Jenkins… - Journal of …, 2024 - Springer
… and bonds, which restricts their ability to capture structural … number of aromatic rings and
rotatable bonds, as well as the … More encouragingly, this workflow can go beyond our diverse …

A spatial-temporal gated attention module for molecular property prediction based on molecular geometry

C Li, J Wang, Z Niu, J Yao, X Zeng - Briefings in Bioinformatics, 2021 - academic.oup.com
conformations because of the influence of rotating bond and … Namely, the count of channels
in 3D grid is 10. We randomly … based on 3D molecular descriptor, which can capture the 3D

[HTML][HTML] A guide to in silico drug design

Y Chang, BA Hawkins, JJ Du, PW Groundwater… - Pharmaceutics, 2023 - mdpi.com
Beyond locating the orthosteric binding site, these tools are … around rotatable bonds,
stereochemistry of double bonds, … Another important objective of MD is capturing conformational

Prediction of Melting Temperature of Organic Molecules using Machine Learning

A Dey - 2023 - nmbu.brage.unit.no
… to capture flexibility using rotatable bonds that are single bonds … We include this graph
descriptor since it describes the shape … x points that lie beyond the support vectors will be allowed. …

[PDF][PDF] Structural and functional analysis of proteins using rigidity theory

A Sljoka - … Computation Paradigm: Algorithmic Revolution in the …, 2022 - library.oapen.org
… The solution to such a homogenous system can be captured … , but such discussion is beyond
the scope of this chapter (… ) and a hinge is a rotatable bond, with corresponding body-bar …

A spatiotemporal route to understanding metal halide perovskite crystallization

MA Najeeb, R Keesey, M Zeile, V Shekar, Z Li, N Leiby… - 2022 - chemrxiv.org
… Specifically, charge of the organic ammonium cation, rotatable bond count, number of C …
RI, Beyond rotatable bond counts: capturing 3D conformational flexibility in a single descriptor. J…

[HTML][HTML] Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase

Y Zhou, S Portelli, M Pat, CHM Rodrigues… - Computational and …, 2021 - Elsevier
… of mutations on protein dynamics, flexibility, stability, as well as ligand … After that, we generated
a set of features capturing both … ionizable atom counts and the number of rotatable bonds, …