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 …

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 …

F Chen, H Liu, H Sun, P Pan, Y Li, D Li… - Physical Chemistry …, 2016 - pubs.rsc.org
Understanding protein–protein interactions (PPIs) is quite important to elucidate crucial
biological processes and even design compounds that interfere with PPIs with …

mCSM: predicting the effects of mutations in proteins using graph-based signatures

DEV Pires, DB Ascher, TL Blundell - Bioinformatics, 2014 - academic.oup.com
Motivation: Mutations play fundamental roles in evolution by introducing diversity into
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

R Sable, S Jois - Molecules, 2015 - mdpi.com
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates
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

J Jin, F Xu, Z Liu, J Shuai, X Li - Chaos, Solitons & Fractals, 2024 - Elsevier
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 …

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 …

SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity

Z Yan, J Wang - Nucleic acids research, 2017 - academic.oup.com
Nucleic acids have been widely recognized as potential targets in drug discovery and
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 …

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 …

Physics of biomolecular recognition and conformational dynamics

WT Chu, Z Yan, X Chu, X Zheng, Z Liu… - Reports on Progress …, 2021 - iopscience.iop.org
Biomolecular recognition usually leads to the formation of binding complexes, often
accompanied by large-scale conformational changes. This process is fundamental to …