[HTML][HTML] Structure-guided machine learning prediction of drug resistance mutations in Abelson 1 kinase
… within the ATP binding pocket, we found … affinity loss to 5-fold (ΔΔG = 0.95 Kcal/mol), the
model was able to detect five out of six resistance cases of E255 mutations, while still predicting …
model was able to detect five out of six resistance cases of E255 mutations, while still predicting …
Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein
… predicted to enlarge the binding pocket as rifampicin does. The analogs showed a marked
decrease in PXR binding affinity … validating our structural prediction in a cellular model. The …
decrease in PXR binding affinity … validating our structural prediction in a cellular model. The …
[HTML][HTML] Integrating structure-based approaches in generative molecular design
… to maximize the predicted on-target binding affinity of generated … pocket) such that it additionally
informs the GMD model of … optimizing the predicted activity according to a QSAR model. …
informs the GMD model of … optimizing the predicted activity according to a QSAR model. …
Peptide tethering: Pocket-directed fragment screening for peptidomimetic inhibitor discovery
AE Modell, F Marrone III, NR Panigrahi… - Journal of the …, 2022 - ACS Publications
… The computational method, AlphaSpace, was used to predict … The KIX/MLL complex serves
as a model system to explore … affinity protein mimics is to engage protein binding pockets …
as a model system to explore … affinity protein mimics is to engage protein binding pockets …
Protein structure prediction
… -based approach but may employ other methods of modeling … to understand the nature
and affinity of interactions for a … , are used for a cavity, or binding site predictions, and some …
and affinity of interactions for a … , are used for a cavity, or binding site predictions, and some …
Structure‐Guided Design of G‐Protein‐Coupled Receptor Polypharmacology
… affinities for both targets and was active in a rat model of … We hypothesized that the secondary
binding pockets could … compound 2, confirmed our predicted binding mode of the scaffold (…
binding pockets could … compound 2, confirmed our predicted binding mode of the scaffold (…
[HTML][HTML] Computing the relative binding affinity of ligands based on a pairwise binding comparison network
J Yu, Z Li, G Chen, X Kong, J Hu, D Wang… - Nature Computational …, 2023 - nature.com
… protein pocket alone. Then, the updated … model’s prediction value for a compound is
denoted as \({\hat{y}}\). Then, the compounds are split into substructures using the BRICS method. …
denoted as \({\hat{y}}\). Then, the compounds are split into substructures using the BRICS method. …
[HTML][HTML] Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites
… test our approach using a well characterized model … predicted affinity for the HDAC2. Designs
were ranked based on shape complementarity between the peptide and the protein pocket…
were ranked based on shape complementarity between the peptide and the protein pocket…
[HTML][HTML] Serotonin transporter: Recent progress of in silico ligand prediction methods and structural biology towards structure-guided in silico design of therapeutic …
K Nagayasu - Journal of Pharmacological Sciences, 2022 - Elsevier
… that a compound predicted to act on SERT by our prediction model are found to be high affinity
… and possible ligands to seek chemical structures fit to possible ligand binding pockets are …
… and possible ligands to seek chemical structures fit to possible ligand binding pockets are …
Water network-augmented two-state model for protein–ligand binding affinity prediction
X Qu, L Dong, D Luo, Y Si, B Wang - … Information and Modeling, 2023 - ACS Publications
… For the apo state, we considered the ligand in the pocket as a virtual ligand, enabling us to
… Model Architecture We present a novel protein–ligand binding affinity prediction model that …
… Model Architecture We present a novel protein–ligand binding affinity prediction model that …