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 …

[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review

F Soleymani, E Paquet, H Viktor, W Michalowski… - Computational and …, 2022 - Elsevier
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

Inference of macromolecular assemblies from crystalline state

E Krissinel, K Henrick - Journal of molecular biology, 2007 - Elsevier
We discuss basic physical–chemical principles underlying the formation of stable
macromolecular complexes, which in many cases are likely to be the biological units …

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 …

Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues

O Keskin, B Ma, R Nussinov - Journal of molecular biology, 2005 - Elsevier
Structurally conserved residues at protein–protein interfaces correlate with the experimental
alanine-scanning hot spots. Here, we investigate the organization of these conserved …

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 …

Deciphering protein–protein interactions. Part I. Experimental techniques and databases

BA Shoemaker, AR Panchenko - PLoS computational biology, 2007 - journals.plos.org
Proteins interact with each other in a highly specific manner, and protein interactions play a
key role in many cellular processes; in particular, the distortion of protein interfaces may lead …

Cation–π interactions in protein–protein interfaces

PB Crowley, A Golovin - Proteins: Structure, Function, and …, 2005 - Wiley Online Library
Arginine is an abundant residue in protein–protein interfaces. The importance of this residue
relates to the versatility of its side chain in intermolecular interactions. Different classes of …

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM

N Tuncbag, A Gursoy, R Nussinov, O Keskin - Nature protocols, 2011 - nature.com
Prediction of protein-protein interactions at the structural level on the proteome scale is
important because it allows prediction of protein function, helps drug discovery and takes …

Crystal contacts as nature's docking solutions

E Krissinel - Journal of computational chemistry, 2010 - Wiley Online Library
The assumption that crystal contacts reflect natural macromolecular interactions makes a
basis for many studies in structural biology. However, the crystal state may correspond to a …