Predicting protein-protein interactions based on rotation of proteins in 3D-space

12/22/2017
by   Samaneh Aghajanbaglo, et al.
0

Protein-Protein Interactions (PPIs) perform essential roles in biological functions. Although some experimental techniques have been developed to detect PPIs, they suffer from high false positive and high false negative rates. Consequently, efforts have been devoted during recent years to develop computational approaches to predict the interactions utilizing various sources of information. Therefore, a unique category of prediction approaches has been devised which is based on the protein sequence information. However, finding an appropriate feature encoding to characterize the sequence of proteins is a major challenge in such methods. In presented work, a sequence based method is proposed to predict protein-protein interactions using N-Gram encoding approaches to describe amino acids and a Relaxed Variable Kernel Density Estimator (RVKDE) as a machine learning tool. Moreover, since proteins can rotate in 3D-space, amino acid compositions have been considered with "undirected" property which leads to reduce dimensions of the vector space. The results show that our proposed method achieves the superiority of prediction performance with improving an F-measure of 2.5 Dataset (HPRD).

READ FULL TEXT
POST COMMENT

Comments

There are no comments yet.

Authors

page 4

page 5

07/08/2021

Network and Sequence-Based Prediction of Protein-Protein Interactions

Background:Typically, proteins perform key biological functions by inter...
01/30/2018

A novel methodology on distributed representations of proteins using their interacting ligands

The effective representation of proteins is a crucial task that directly...
12/06/2020

Align-gram : Rethinking the Skip-gram Model for Protein Sequence Analysis

Background: The inception of next generations sequencing technologies ha...
07/26/2021

Protein-RNA interaction prediction with deep learning: Structure matters

Protein-RNA interactions are of vital importance to a variety of cellula...
07/18/2020

Deep Learning of High-Order Interactions for Protein Interface Prediction

Protein interactions are important in a broad range of biological proces...
11/21/2017

Training large margin host-pathogen protein-protein interaction predictors

Detection of protein-protein interactions (PPIs) plays a vital role in m...
07/24/2021

Identifying similar functional modules by a new hybrid spectral clustering method

Recently, a large number of researches have focused on finding cellular ...
This week in AI

Get the week's most popular data science and artificial intelligence research sent straight to your inbox every Saturday.