Trends in small molecule drug properties: A developability molecule assessment perspective

P Agarwal, J Huckle, J Newman, DL Reid - Drug Discovery Today, 2022 - Elsevier
… , such as PSA, rotatable bonds (RB) and H-bond acceptors (HBA). … a given quadrant are
not captured by simply assigning a … of the P450 isozymes is beyond the scope this manuscript. …

Next generation 3D pharmacophore modeling

D Schaller, D Šribar, T Noonan, L Deng… - Wiley …, 2020 - Wiley Online Library
… field with various applications in drug discovery and beyond. … arrangement, 3D
pharmacophores can capture feature … is analyzed for rotatable bonds important for flexible

Leveraging 2D Molecular Graph Pretraining for Improved 3D Conformer Generation with Graph Neural Networks

K Alhamoud, Y Ghunaim, AS Alshehri, G Li… - Computers & Chemical …, 2024 - Elsevier
… strings, capturing up to five reactants and always one product. … more accurate and flexible
predictions of 3D conformations, … increasing the embedding size beyond 100 did not result in …

Reorganization energies of flexible organic molecules as a challenging target for machine learning enhanced virtual screening

K Chen, C Kunkel, K Reuter, JT Margraf - Digital Discovery, 2022 - pubs.rsc.org
… fully capturing the underlying structure–property relationships. … (4) rotatable bonds, with a
maximum of 5 rotatable bonds occurring … 2d), with 5 remaining outliers falling beyond the error …

When computation meets experiment: a combined approach towards understanding crystalline materials properties

L Spiteri - 2023 - um.edu.mt
flexibility was devised, given the proven lack of appropriateness of the number of rotatable
bonds … number per group and the strength of other non-bonding contacts, beyond HB. …

Dynamic Metallosupramolecular Cages Containing 12 Adaptable Pockets for High-Order Guest Binding Beyond Biomimicry

YH Huang, YL Lu, J Ruan, SP Zheng… - Journal of the …, 2023 - ACS Publications
… center lability and are able to capture 4–24 guests to manifest … to facilitate cage conformation
dynamics, the metastable 3d 6 … 8 Pd 6 cage conformationally flexible and fluctuate to exhibit …

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
… distorting ligand conformation beyond acceptable strain levels, … AICG can capture bioactive
conformations of molecules … conformation as a function of the number of rotatable bonds. …

Enhancing Semiempirical Quantum Mechanical Scoring with Machine Learning: a new scoring function that accounts for both the enthalpic and entropic contributions …

T Evangelidis, IC Giassa, M Lovrić - 2022 - chemrxiv.org
… terms of conformational sampling and protein flexibility, solvation, … between the multiple
rotatable bonds and the terminal CH3 … Non-bonded interactions beyond a cutoff distance of 18 Å …

An ecosystem for digital reticular chemistry

KM Jablonka, AS Rosen, AS Krishnapriyan, B Smit - 2023 - ACS Publications
… , for example, descriptors related to the flexibility of the linker … for reticular chemistry and
beyond without compromising rigor, … In this way, we attempt to capture the shapes of full building …

[HTML][HTML] Molecular modelling assisted design of napthalimide-dihydropyrimidinone conjugates as potential cytotoxic agents

MS Malik, SF Adil, ZS Seddigi, M Morad… - Journal of Saudi …, 2021 - Elsevier
… The conformational flexibility, molecular complexity and shape index … ) 3D bar chart
representation of the descriptors such as shape index, molecular complexity and molecular flexibility