Accurate and Rapid Ranking of Protein–Ligand Binding Affinities Using Density Matrix Fragmentation and Physics‐Informed Machine Learning Dispersion Potentials
Sign Up to like & getrecommendations! Published in 2025 at "Chemphyschem"
DOI: 10.1002/cphc.202500094
Abstract: The generalized many‐body expansion for building density matrices (GMBE‐DM), truncated at the one‐body level and combined with a purification scheme, is applied to rank protein–ligand binding affinities across two cyclin‐dependent kinase 2 (CDK2) datasets and… read more here.
Keywords: physics informed; protein ligand; dispersion; ligand binding ... See more keywords
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
Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism
Sign Up to like & getrecommendations! Published in 2024 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.4c01523
Abstract: Since their inception in antibacterial therapy, macrolide-based antibiotics have significantly shaped the evolutionary pathways of pathogenic bacteria, driving them to develop diverse antimicrobial resistance (AMR) mechanisms. Among these, macrolide esterase, commonly referred to as erythromycin… read more here.
Keywords: macrolide binding; flytrap mechanism; venus flytrap; erythromycin esterase ... See more keywords
Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands
Sign Up to like & getrecommendations! Published in 2025 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.4c01708
Abstract: Accurate prediction of the affinity of ligand binding to nucleic acids represents a formidable challenge for current computational approaches. This limitation has hindered the use of computational methods to develop small-molecule drugs that modulate the… read more here.
Keywords: physics; targeting ligands; prediction; rna dna ... 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