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 …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

PIC: protein interactions calculator

KG Tina, R Bhadra, N Srinivasan - Nucleic acids research, 2007 - academic.oup.com
Interactions within a protein structure and interactions between proteins in an assembly are
essential considerations in understanding molecular basis of stability and functions of …

ProteinsPlus: a web portal for structure analysis of macromolecules

R Fährrolfes, S Bietz, F Flachsenberg… - Nucleic acids …, 2017 - academic.oup.com
With currently more than 126 000 publicly available structures and an increasing growth
rate, the Protein Data Bank constitutes a rich data source for structure-driven research in …

Principles of protein− protein interactions: what are the preferred ways for proteins to interact?

O Keskin, A Gursoy, B Ma, R Nussinov - Chemical reviews, 2008 - ACS Publications
Proteins are the working horse of the cellular machinery. They are responsible for diverse
functions ranging from molecular motors to signaling. They catalyze reactions, transport …

Transient protein–protein interactions

SE Acuner Ozbabacan, HB Engin… - … , Design & Selection, 2011 - academic.oup.com
Transient complexes are crucial for diverse biological processes such as biochemical
pathways and signaling cascades in the cell. Here, we give an overview of the transient …

Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein–protein interactions

M Guharoy, P Chakrabarti - Bioinformatics, 2007 - academic.oup.com
Motivation: The increasing amount of data on protein–protein interaction needs to be
rationalized for deriving guidelines for the alteration or design of an interface between two …

NOXclass: prediction of protein-protein interaction types

H Zhu, FS Domingues, I Sommer, T Lengauer - BMC bioinformatics, 2006 - Springer
Background Structural models determined by X-ray crystallography play a central role in
understanding protein-protein interactions at the molecular level. Interpretation of these …

A survey of available tools and web servers for analysis of protein–protein interactions and interfaces

N Tuncbag, G Kar, O Keskin, A Gursoy… - Briefings in …, 2009 - academic.oup.com
The unanimous agreement that cellular processes are (largely) governed by interactions
between proteins has led to enormous community efforts culminating in overwhelming …

Intra and inter-molecular communications through protein structure network

S Vishveshwara, A Ghosh… - Current Protein and …, 2009 - ingentaconnect.com
Communication within and across proteins is crucial for the biological functioning of
proteins. Experiments such as mutational studies on proteins provide important information …