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A high-dimensional microfluidic approach for selection of aptamers with programmable binding affinities
Aptamers are being applied as affinity reagents in analytical applications owing to their high stability, compact size and amenability to chemical...
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MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn
Carbonic anhydrase is an attractive drug target for the treatment of many diseases. This paper examines the ability of end-state MM/GBSA methods to...
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Computational insights into the differentiated binding affinities of Myc, Max, and Omomyc dimers to the E-boxes of DNA
Myc is a bHLHZip protein involved in growth control and cancer, which does not form a homodimer. Myc operates in a network with its...
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Molecular docking analysis reveals differential binding affinities of multiple classes of selective inhibitors towards cancer-associated KRAS mutants
KRAS is the most frequently mutated oncogene in solid cancers, and inhibitors that specifically target the KRAS-G12C mutant were recently approved...
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Evaluation of the Molecular Interaction Between CCN Protein and Its Binding Partners: A Solid-Phase Binding Assay and Surface Plasmon Resonance
CCN proteins are known to bind to various growth factors, cytokines, and membrane proteins. Since these bindings are closely involved in the function...
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Protein-Ligand Interactions and Binding
Why it is important to know this material? Protein binding is implied in all biological mechanisms, and the definition of quantitative models and...
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Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations
Omicron derived lineages viz. BA.2, BA.3, BA.4 BA.5, BF.7 and XBBs show prominence with improved immune escape, transmissibility, infectivity, and...
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The maximal and current accuracy of rigorous protein-ligand binding free energy calculations
Computational techniques can speed up the identification of hits and accelerate the development of candidate molecules for drug discovery. Among...
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SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations
Host–guest binding remains a major challenge in modern computational modelling. The newest 7th statistical assessment of the modeling of proteins and...
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Comparison of CD20 Binding Affinities of Rituximab Produced in Nicotiana benthamiana Leaves and Arabidopsis thaliana Callus
Plants are promising drug-production platforms with high economic efficiency, stability, and convenience in mass production. However, studies...
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Computational Protein Binding
Why it is important to know this material? The computational approach to protein binding has become a crucial methodology in drug design and...
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SAMPL7 TrimerTrip host–guest binding affinities from extensive alchemical and end-point free energy calculations
The prediction of host–guest binding affinities with computational modelling is still a challenging task. In the 7th statistical assessment of the...
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Study on the S239D/I332E mutation effect on the kinetics of Fc–Fc receptor binding through transition complex theory
The S239D/I332E mutation in both chain A and chain B of Fc is widely employed to enhance the binding affinity of Fc to its receptor (FcγRIIIa)....
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Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities
In this study, we developed a novel algorithm to improve the screening performance of an arbitrary docking scoring function by recalibrating the...
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PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
Protein mutations, especially those which occur in the binding site, play an important role in inter-individual drug response and may alter binding...
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The slow but steady rise of binding free energy calculations in drug discovery
Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affinities and to prioritize...
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A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors
Janus kinase 2 (JAK2) inhibitors are potential anticancer drugs in the treatment of lymphoma, leukemia, thrombocytosis and particularly...
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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant
End-point free energy calculations as a powerful tool have been widely applied in protein–ligand and protein–protein interactions. It is often...
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The selection of a hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamer with high binding affinity for the Heat Shock Protein 70
Nucleic acids aptamers often fail to efficiently target some proteins because of the hydrophilic character of the natural nucleotides. Here we...
