DeepPPI: boosting prediction of protein–protein interactions with deep neural networks

X Du, S Sun, C Hu, Y Yao, Y Yan… - Journal of chemical …, 2017 - ACS Publications
The complex language of eukaryotic gene expression remains incompletely understood.
Despite the importance suggested by many proteins variants statistically associated with …

Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

Y Guo, L Yu, Z Wen, M Li - Nucleic acids research, 2008 - academic.oup.com
Compared to the available protein sequences of different organisms, the number of revealed
protein–protein interactions (PPIs) is still very limited. So many computational methods have …

PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

ZR Li, HH Lin, LY Han, L Jiang, X Chen… - Nucleic acids …, 2006 - academic.oup.com
Sequence-derived structural and physicochemical features have frequently been used in the
development of statistical learning models for predicting proteins and peptides of different …

Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity

L Han, J Cui, H Lin, Z Ji, Z Cao, Y Li, Y Chen - Proteomics, 2006 - Wiley Online Library
Protein sequence contains clues to its function. Functional prediction from sequence
presents a challenge particularly for proteins that have low or no sequence similarity to …

[HTML][HTML] PPIevo: Protein–protein interaction prediction from PSSM based evolutionary information

J Zahiri, O Yaghoubi, M Mohammad-Noori… - Genomics, 2013 - Elsevier
Protein–protein interactions regulate a variety of cellular processes. There is a great need
for computational methods as a complement to experimental methods with which to predict …

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 …

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

HB Rao, F Zhu, GB Yang, ZR Li… - Nucleic acids research, 2011 - academic.oup.com
Sequence-derived structural and physicochemical features have been extensively used for
analyzing and predicting structural, functional, expression and interaction profiles of proteins …

[HTML][HTML] Domain-mediated protein interaction prediction: From genome to network

J Reimand, S Hui, S Jain, B Law, GD Bader - FEBS letters, 2012 - Elsevier
Protein–protein interactions (PPIs), involved in many biological processes such as cellular
signaling, are ultimately encoded in the genome. Solving the problem of predicting protein …

Prediction of protein-protein interactions based on protein-protein correlation using least squares regression

DS Huang, L Zhang, K Han, S Deng… - Current Protein and …, 2014 - ingentaconnect.com
In order to transform protein sequences into the feature vectors, several works have been
done, such as computing auto covariance (AC), conjoint triad (CT), local descriptor (LD) …

Detecting protein complexes based on uncertain graph model

B Zhao, J Wang, M Li, FX Wu… - IEEE/ACM Transactions …, 2014 - ieeexplore.ieee.org
Advanced biological technologies are producing large-scale protein-protein interaction (PPI)
data at an ever increasing pace, which enable us to identify protein complexes from PPI …