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 …

Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

DE Scott, AR Bayly, C Abell, J Skidmore - Nature Reviews Drug …, 2016 - nature.com
Protein–protein interactions (PPIs) are of pivotal importance in the regulation of biological
systems and are consequently implicated in the development of disease states. Recent work …

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

J Tubiana, D Schneidman-Duhovny, HJ Wolfson - Nature Methods, 2022 - nature.com
Predicting the functional sites of a protein from its structure, such as the binding sites of small
molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two …

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

D Kozakov, LE Grove, DR Hall, T Bohnuud… - Nature protocols, 2015 - nature.com
FTMap is a computational mapping server that identifies binding hot spots of
macromolecules—ie, regions of the surface with major contributions to the ligand-binding …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

Predicting protein–protein interactions from the molecular to the proteome level

O Keskin, N Tuncbag, A Gursoy - Chemical reviews, 2016 - ACS Publications
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …

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 …

Multifaceted roles of disulfide bonds. Peptides as therapeutics

M Gongora-Benitez, J Tulla-Puche… - Chemical Reviews, 2014 - ACS Publications
In the last century, small-molecule natural products were the main inspiration for most drug
discovery programs based either on high-throughput screening (HTS) or rational design …

X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in …

CD Putnam, M Hammel, GL Hura… - Quarterly reviews of …, 2007 - cambridge.org
Crystallography supplies unparalleled detail on structural information critical for mechanistic
analyses; however, it is restricted to describing low energy conformations of …

AGGRESCAN: a server for the prediction and evaluation of" hot spots" of aggregation in polypeptides

O Conchillo-Solé, NS de Groot, FX Avilés, J Vendrell… - BMC …, 2007 - Springer
Background Protein aggregation correlates with the development of several debilitating
human disorders of growing incidence, such as Alzheimer's and Parkinson's diseases. On …