Accurate prediction of relative binding affinities of a series of HIV‐1 protease inhibitors using semi‐empirical quantum mechanical charge
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26218
Abstract: A major challenge in computer‐aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi‐empirical quantum… read more here.
Keywords: semi empirical; binding affinities; relative binding; empirical quantum ... See more keywords
Use of Microscale Thermophoresis (MST) to Measure Binding Affinities of Components of the Fusion Machinery.
Sign Up to like & getrecommendations! Published in 2019 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-8760-3_11
Abstract: Microscale thermophoresis is a relatively new technique used by an increasing number of academic laboratories to estimate relative binding affinities between ligand (analyte) that is titrated and a target (generally protein) that is either fluorescently… read more here.
Keywords: thermophoresis; binding affinities; microscale thermophoresis; fusion machinery ... See more keywords
Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-017-0075-9
Abstract: Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design… read more here.
Keywords: binding affinities; challenge; relative binding; physics based ... See more keywords
Dietary anthocyanin–human serum albumin interaction
Sign Up to like & getrecommendations! Published in 2017 at "Free Radical Biology and Medicine"
DOI: 10.1016/j.freeradbiomed.2017.10.049
Abstract: Dietary anthocyanins occurring with different chemical structures are claimed to be beneficial for human health. The bioavailability of anthocyanins is the key factor influencing their health benefits. Fluorescence quenching method was applied to determine the… read more here.
Keywords: human serum; groups ring; binding affinities; serum albumin ... See more keywords
P081 ST14 protease resistant peptides, from glioblastoma multiforme mutant proteins, represent higher binding affinities as potential HLA class I epitopes
Sign Up to like & getrecommendations! Published in 2018 at "Human Immunology"
DOI: 10.1016/j.humimm.2018.07.140
Abstract: Aim We previously identified a set of the most frequently mutated cytoskeleton- and extracellular matrix-related proteins (CECMPs) in numerous cancer datasets. Mutations in the cytoskeleton and extracellular matrix can induce resistance or sensitivity to proteolysis.… read more here.
Keywords: binding affinities; protease; st14 protease; glioblastoma multiforme ... See more keywords
Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations.
Sign Up to like & getrecommendations! Published in 2017 at "Bioconjugate chemistry"
DOI: 10.1021/acs.bioconjchem.7b00367
Abstract: Biocompatible gold nanoclusters can be utilized as contrast agents in virus imaging. The labeling of viruses can be achieved noncovalently but site-specifically by linking the cluster to the hydrophobic pocket of a virus via a… read more here.
Keywords: binding affinities; labeling viruses; molecular dynamics; pocket factor ... See more keywords
When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00604
Abstract: Accurate determination of binding free energy is pivotal for the study of many biological processes and has been applied in a number of theoretical investigations to compare the affinity of severe acute respiratory syndrome coronavirus… read more here.
Keywords: binding free; methodology; affinity; free energy ... See more keywords
Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.7b00885
Abstract: Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective… read more here.
Keywords: binding affinities; drug; accurate reliable; prediction binding ... See more keywords
On the Frustration to Predict Binding Affinities from Protein-Ligand Structures with Deep Neural Networks.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of medicinal chemistry"
DOI: 10.1021/acs.jmedchem.2c00487
Abstract: Accurate prediction of binding affinities from protein-ligand atomic coordinates remains a major challenge in early stages of drug discovery. Using modular message passing graph neural networks describing both the ligand and the protein in their… read more here.
Keywords: neural networks; deep neural; affinities protein; binding affinities ... See more keywords
Rotenoids and Other Specialized Metabolites from the Roots of Mirabilis multiflora: Opioid and Cannabinoid Receptor Radioligand Binding Affinities.
Sign Up to like & getrecommendations! Published in 2021 at "Journal of natural products"
DOI: 10.1021/acs.jnatprod.0c00939
Abstract: Mirabilis multiflora is an acclaimed hallucinogen consumed traditionally by the Hopi Indians to induce diagnostic visions. Its root extract afforded a new (3) and four known (2, 5, 6, and 7) 12a-hydroxyrotenoids, a known rotenoid… read more here.
Keywords: radioligand binding; binding affinities; mirabilis multiflora; receptor ... See more keywords
Novel Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species
Sign Up to like & getrecommendations! Published in 2020 at "ACS Omega"
DOI: 10.1021/acsomega.0c01295
Abstract: The interaction between the main carrier (serum albumin, SA) of endogenous and exogenous compounds in the bloodstream of different species (human, bovine, canine, rat, rabbit, and sheep) and a general anesthetic agent (propofol, PR) was… read more here.
Keywords: binding affinities; propofol binding; characterizing propofol; novel approach ... See more keywords