Software for molecular docking: a review

NS Pagadala, K Syed, J Tuszynski - Biophysical reviews, 2017 - Springer
Molecular docking methodology explores the behavior of small molecules in the binding site
of a target protein. As more protein structures are determined experimentally using X-ray …

A survey on computational models for predicting protein–protein interactions

L Hu, X Wang, YA Huang, P Hu… - Briefings in …, 2021 - academic.oup.com
Proteins interact with each other to play critical roles in many biological processes in cells.
Although promising, laboratory experiments usually suffer from the disadvantages of being …

[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 …

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 …

Computational identification of protein-protein interactions in model plant proteomes

Z Ding, D Kihara - Scientific reports, 2019 - nature.com
Protein-protein interactions (PPIs) play essential roles in many biological processes. A PPI
network provides crucial information on how biological pathways are structured and …

Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments

G Grassmann, M Miotto, F Desantis… - Chemical …, 2024 - ACS Publications
Investigating protein–protein interactions is crucial for understanding cellular biological
processes because proteins often function within molecular complexes rather than in …

MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers

M Ohue, T Shimoda, S Suzuki, Y Matsuzaki… - …, 2014 - academic.oup.com
The application of protein–protein docking in large-scale interactome analysis is a major
challenge in structural bioinformatics and requires huge computing resources. In this work …

Exploring protein-protein interactions at the proteome level

H Elhabashy, F Merino, V Alva, O Kohlbacher… - Structure, 2022 - cell.com
Proteins are central to all of the processes of life. For their activity, they almost invariably
need to interact with other macromolecules, be they nucleic acids, membranes, glycans, or …

Computational methods for predicting protein‐protein interactions using various protein features

Z Ding, D Kihara - Current protocols in protein science, 2018 - Wiley Online Library
Understanding protein‐protein interactions (PPIs) in a cell is essential for learning protein
functions, pathways, and mechanism of diseases. PPIs are also important targets for …

Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions

M Baranwal, A Magner, J Saldinger, ES Turali-Emre… - BMC …, 2022 - Springer
Background Development of new methods for analysis of protein–protein interactions (PPIs)
at molecular and nanometer scales gives insights into intracellular signaling pathways and …