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 …

Template-based structure modeling of protein–protein interactions

A Szilagyi, Y Zhang - Current opinion in structural biology, 2014 - Elsevier
Highlights•The most accurate complex models are built by copying close homologous
templates.•Non-homologous templates can be detected by interface structure comparisons.• …

Graph-based prediction of protein-protein interactions with attributed signed graph embedding

F Yang, K Fan, D Song, H Lin - BMC bioinformatics, 2020 - Springer
Abstract Background Protein-protein interactions (PPIs) are central to many biological
processes. Considering that the experimental methods for identifying PPIs are time …

A multiple kernel learning algorithm for drug-target interaction prediction

ACA Nascimento, RBC Prudêncio, IG Costa - BMC bioinformatics, 2016 - Springer
Background Drug-target networks are receiving a lot of attention in late years, given its
relevance for pharmaceutical innovation and drug lead discovery. Different in silico …

Computational prediction of protein–protein interaction networks: algorithms and resources

J Zahiri, J Hannon Bozorgmehr… - Current …, 2013 - ingentaconnect.com
Protein interactions play an important role in the discovery of protein functions and pathways
in biological processes. This is especially true in case of the diseases caused by the loss of …

An integration of deep learning with feature embedding for protein–protein interaction prediction

Y Yao, X Du, Y Diao, H Zhu - PeerJ, 2019 - peerj.com
Protein–protein interactions are closely relevant to protein function and drug discovery.
Hence, accurately identifying protein–protein interactions will help us to understand the …

Predicting protein-protein interactions using sequence and network information via variational graph autoencoder

X Luo, L Wang, P Hu, L Hu - IEEE/ACM Transactions on …, 2023 - ieeexplore.ieee.org
Protein-protein interactions (PPIs) play a critical role in the proteomics study, and a variety of
computational algorithms have been developed to predict PPIs. Though effective, their …

HomPPI: a class of sequence homology based protein-protein interface prediction methods

LC Xue, D Dobbs, V Honavar - BMC bioinformatics, 2011 - Springer
Background Although homology-based methods are among the most widely used methods
for predicting the structure and function of proteins, the question as to whether interface …

Three-dimensional modeling of protein interactions and complexes is going 'omics

A Stein, R Mosca, P Aloy - Current opinion in structural biology, 2011 - Elsevier
High-throughput interaction discovery initiatives have revealed the existence of hundreds of
multiprotein complexes whose functions are regulated through thousands of protein–protein …

MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data

M Ohue, Y Matsuzaki, N Uchikoga… - Protein and peptide …, 2014 - ingentaconnect.com
The elucidation of protein-protein interaction (PPI) networks is important for understanding
cellular structure and function and structure-based drug design. However, the development …