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 …

Hot spots in protein–protein interfaces: Towards drug discovery

E Cukuroglu, HB Engin, A Gursoy, O Keskin - Progress in biophysics and …, 2014 - Elsevier
Identification of drug-like small molecules that alter protein–protein interactions might be a
key step in drug discovery. However, it is very challenging to find such molecules that target …

Pharmacological inactivation of Skp2 SCF ubiquitin ligase restricts cancer stem cell traits and cancer progression

CH Chan, JK Morrow, CF Li, Y Gao, G **, A Moten… - Cell, 2013 - cell.com
Skp2 E3 ligase is overexpressed in numerous human cancers and plays a critical role in cell-
cycle progression, senescence, metabolism, cancer progression, and metastasis. In the …

Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, signaling, and autoregulation

M Bernoux, T Ve, S Williams, C Warren, D Hatters… - Cell host & …, 2011 - cell.com
Summary The Toll/interleukin-1 receptor (TIR) domain occurs in animal and plant immune
receptors. In the animal Toll-like receptors, homodimerization of the intracellular TIR domain …

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

Y Dehouck, JM Kwasigroch, M Rooman… - Nucleic acids …, 2013 - academic.oup.com
The ability of proteins to establish highly selective interactions with a variety of (macro)
molecular partners is a crucial prerequisite to the realization of their biological functions. The …

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 …

[HTML][HTML] GTP-dependent K-Ras dimerization

S Muratcioglu, TS Chavan, BC Freed, H Jang… - Structure, 2015 - cell.com
Ras proteins recruit and activate effectors, including Raf, that transmit receptor-initiated
signals. Monomeric Ras can bind Raf; however, activation of Raf requires its dimerization. It …

KFC2: a knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features

X Zhu, JC Mitchell - Proteins: Structure, Function, and …, 2011 - Wiley Online Library
Hot spots constitute a small fraction of protein–protein interface residues, yet they account
for a large fraction of the binding affinity. Based on our previous method (KFC), we present …

Predicting and experimentally validating hot-spot residues at protein–protein interfaces

AA Ibarra, GJ Bartlett, Z Hegedus, S Dutt… - ACS chemical …, 2019 - ACS Publications
Protein–protein interactions (PPIs) are vital to all biological processes. These interactions
are often dynamic, sometimes transient, typically occur over large topographically shallow …

In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein–Protein Interactions

ZS Hashemi, M Zarei, MK Fath, M Ganji… - Frontiers in Molecular …, 2021 - frontiersin.org
Large contact surfaces of protein–protein interactions (PPIs) remain to be an ongoing issue
in the discovery and design of small molecule modulators. Peptides are intrinsically capable …