[HTML][HTML] PREFMoDeL: A Systematic Review and Proposed Taxonomy of Biomolecular Features for Deep Learning
JL North, VL Hsu - Applied Sciences, 2023 - mdpi.com
… ”—specific subsets that capture relevant properties of the … in the feature table is beyond
the scope of this work, and … density [47]; RBC is the rotatable bond count [48]; and DRP is a …
the scope of this work, and … density [47]; RBC is the rotatable bond count [48]; and DRP is a …
dMXP: A De Novo Small-Molecule 3D Structure Predictor with Graph Attention Networks
… RDKit/mETKDG, CORINA, CSD Conformer Generator, and SDEGen (conformation … with
flexible scaffolds or longer side chains (such as a compound with more than 6 rotatable bonds) …
flexible scaffolds or longer side chains (such as a compound with more than 6 rotatable bonds) …
[HTML][HTML] SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction
… It should be remembered that RMSD values beyond 2 Å are … of H-bond donors and rotatable
bonds while the count of ring … be given to keeping molecules flexibility to a minimum. For …
bonds while the count of ring … be given to keeping molecules flexibility to a minimum. For …
Simulation models for prediction of bioavailability of medicinal drugs—the interface between experiment and computation
… In light of this, such models cannot capture accurately the … molecular flexibility (measured by
the number of rotatable bonds; … Examples of 3D calculation descriptors of the molecules are …
the number of rotatable bonds; … Examples of 3D calculation descriptors of the molecules are …
[HTML][HTML] In silico study approach on a series of 50 polyphenolic compounds in plants; A comparison on the bioavailability and bioactivity data
A Stefaniu, LC Pirvu - Molecules, 2022 - mdpi.com
… P), one descriptor related to the flexibility of molecules and the number of rotatable bonds
(nrotb… , and low polar surface area or total hydrogen bond count (sum of donors and acceptors) …
(nrotb… , and low polar surface area or total hydrogen bond count (sum of donors and acceptors) …
A review on the application of molecular descriptors and machine learning in polymer design
… ; therefore, the information captured by polymer descriptors is regarded as … Number of
rotatable bonds RBN … In this study, the author also found that calculated flexible descriptors can …
rotatable bonds RBN … In this study, the author also found that calculated flexible descriptors can …
Deep Learning for the Structure‐Based Binding Free Energy Prediction of Small Molecule Ligands
… multiple conformations accessible through its rotatable bonds… These vectorized 3D grids
of the binding site capture structural … global model can be shared beyond the individual sites. …
of the binding site capture structural … global model can be shared beyond the individual sites. …
Multibasin quasi-harmonic approach for the calculation of the configurational entropy of small molecules in solution
GP Pereira, M Cecchini - Journal of Chemical Theory and …, 2021 - ACS Publications
… In the following, we review the theory beyond the QHMB … and solvent effects are effectively
captured in the entropy calculation… up to 8 rotatable bonds, for which conformational sampling …
captured in the entropy calculation… up to 8 rotatable bonds, for which conformational sampling …
Rigorous free energy simulations in virtual screening
… scales sufficiently long to capture the biological time scales of … functions by penalizing each
rotatable bond in a ligand. This … ΔG via FEP or TI was beyond what was available at that time: …
rotatable bond in a ligand. This … ΔG via FEP or TI was beyond what was available at that time: …
Geometric deep learning for molecular crystal structure prediction
… that cannot capture important physical features such as bond … mostly to improve expressiveness
and flexibility of the model, … Beyond density prediction and sample ranking, our code …
and flexibility of the model, … Beyond density prediction and sample ranking, our code …