Nonspecific binding—fundamental concepts and consequences for biosensing applications
A Frutiger, A Tanno, S Hwu, RF Tiefenauer… - Chemical …, 2021 - ACS Publications
Nature achieves differentiation of specific and nonspecific binding in molecular interactions
through precise control of biomolecules in space and time. Artificial systems such as …
through precise control of biomolecules in space and time. Artificial systems such as …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses …
Understanding protein–protein interactions (PPIs) is quite important to elucidate crucial
biological processes and even design compounds that interfere with PPIs with …
biological processes and even design compounds that interfere with PPIs with …
mCSM: predicting the effects of mutations in proteins using graph-based signatures
Motivation: Mutations play fundamental roles in evolution by introducing diversity into
genomes. Missense mutations in structural genes may become either selectively …
genomes. Missense mutations in structural genes may become either selectively …
Surfing the protein-protein interaction surface using docking methods: application to the design of PPI inhibitors
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates
biochemical pathways and has therapeutic significance. PPI inhibition for designing drug …
biochemical pathways and has therapeutic significance. PPI inhibition for designing drug …
Quantifying the underlying landscape, entropy production and biological path of the cell fate decision between apoptosis and pyroptosis
Pyroptosis, a recently identified type of cell death, and apoptosis are fundamental and
complex biological processes that underlie a multitude of diseases. However, the crosstalk …
complex biological processes that underlie a multitude of diseases. However, the crosstalk …
AREA-AFFINITY: A Web Server for Machine Learning-Based Prediction of Protein–Protein and Antibody–Protein Antigen Binding Affinities
YX Yang, JY Huang, P Wang… - Journal of Chemical …, 2023 - ACS Publications
Protein–Protein binding affinity reflects the binding strength between the binding partners.
The prediction of protein–protein binding affinity is important for elucidating protein functions …
The prediction of protein–protein binding affinity is important for elucidating protein functions …
SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity
Nucleic acids have been widely recognized as potential targets in drug discovery and
aptamer selection. Quantifying the interactions between small molecules and nucleic acids …
aptamer selection. Quantifying the interactions between small molecules and nucleic acids …
A minimal model of protein–protein binding affinities
J Janin - Protein Science, 2014 - Wiley Online Library
A minimal model of protein–protein binding affinity that takes into account only two structural
features of the complex, the size of its interface, and the amplitude of the conformation …
features of the complex, the size of its interface, and the amplitude of the conformation …
The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition
X Zheng, J Wang - PLoS Computational Biology, 2015 - journals.plos.org
We uncovered the universal statistical laws for the biomolecular recognition/binding
process. We quantified the statistical energy landscapes for binding, from which we can …
process. We quantified the statistical energy landscapes for binding, from which we can …
Physics of biomolecular recognition and conformational dynamics
Biomolecular recognition usually leads to the formation of binding complexes, often
accompanied by large-scale conformational changes. This process is fundamental to …
accompanied by large-scale conformational changes. This process is fundamental to …