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Methods for Improving Aptamer Binding Affinity [PDF]
Molecules, 2016 Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always ...
Hijiri Hasegawa +3 more
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Multiplexed Affinity Measurements of Extracellular Vesicles Binding Kinetics [PDF]
Sensors, 2021 Extracellular vesicles (EVs) have attracted significant attention as impactful diagnostic biomarkers, since their properties are closely related to specific clinical conditions.
Elisa Chiodi +3 more
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Distance plus attention for binding affinity prediction [PDF]
Journal of CheminformaticsProtein-ligand binding affinity plays a pivotal role in drug development, particularly in identifying potential ligands for target disease-related proteins.
Julia Rahman +3 more
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Ensembling methods for protein-ligand binding affinity prediction [PDF]
Scientific ReportsProtein-ligand binding affinity prediction is a key element of computer-aided drug discovery. Most of the existing deep learning methods for protein-ligand binding affinity prediction utilize single models and suffer from low accuracy and generalization ...
Jiffriya Mohamed Abdul Cader +4 more
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iScience, 2023 Summary: CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS).
Ester Marina-Zárate +4 more
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Learned features of antibody-antigen binding affinity
Frontiers in Molecular Biosciences, 2023 Defining predictors of antigen-binding affinity of antibodies is valuable for engineering therapeutic antibodies with high binding affinity to their targets.
Nathaniel L. Miller +7 more
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Probing high affinity sequences of DNA aptamer against VEGF165. [PDF]
PLoS ONE, 2012 Vascular endothelial growth factor (VEGF(165)) is a potent angiogenic mitogen commonly overexpressed in cancerous cells. It contains two main binding domains, the receptor-binding domain (RBD) and the heparin-binding domain (HBD). This study attempted to
Harleen Kaur, Lin-Yue Lanry Yung
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Multiplexed Small Molecule Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis [PDF]
, 2021 Small molecule binding assays to target proteins are a core component of drug discovery and development. While a number of assay formats are available, significant drawbacks still remain in cost, sensitivity, and throughput.
Krusemark, Casey J. +3 more
core +1 more source
Binding affinity and mechanisms of SARS-CoV-2 variants
Computational and Structural Biotechnology Journal, 2021 During the rapid worldwide spread of SARS-CoV-2, the viral genome has been undergoing numerous mutations, especially in the spike (S) glycoprotein gene that encode a type-I fusion protein, which plays an important role in the infectivity and ...
Yanqiang Han +4 more
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Method for computing protein binding affinity [PDF]
Journal of Computational Chemistry, 2004 AbstractA Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states.
Charles F. F. Karney +2 more
openaire +3 more sources