Proteins frequently bind together in pairs or larger complexes to take part in biological processes. Understanding such protein functions and biological processes in a cell across the entire genome is an important goal with diverse implications about protein function. In this paper, we propose a method to detect protein-protein interaction (PPI) based on sequence neighboring information and sup...

Pathogens usually evade and manipulate host-immune pathways through pathogen-host protein-protein interactions (PPIs) to avoid being killed by the host immune system. Therefore, uncovering pathogen-host PPIs is critical for determining the mechanisms underlying pathogen infection and survival. In this study, we developed a computational method, which we named pairwise structure similarity (PSS)...

Accelerated efforts to identify intervention strategies for the COVID-19 pandemic caused by SARS-CoV-2 need be supported deeper investigations into host invasion and response mechanisms. We constructed neighborhood interactome network of 332 human proteins targeted proteins, augmenting it with 1,941 novel protein-protein interactions predicted using our High-precision Protein-Protein Interactio...

Molecular function in cellular processes is governed by protein-protein interactions (PPIs) within biological networks. Selective yet specific association of these protein partners contributes to diverse functionality such as catalysis, regulation, assembly, immunity, and inhibition in a cell. Therefore, understanding the principles of protein-protein association has been of immense interest fo...

The prediction of protein-protein interactions (PPIs) is essential to understand the cellular processes from a medical perspective. Among various machine learning techniques, kernel-based Support Vector Machine (SVM) has been commonly employed discriminate between interacting and non-interacting protein pairs. main drawback employing SVM datasets with many features, such as primary sequence-bas...

A goal of the post-genomics era has been to elucidate a detailed global map of protein-protein interactions (PPIs) within a cell. Here, we show that the presence of co-occurring short polypeptide sequences between interacting protein partners appears to be conserved across different organisms. We present an algorithm to automatically generate PPI prediction method parameters for various organis...

As an increasing number of reliable protein-protein interactions (PPIs) become available and high-throughput experimental methods provide systematic identification of PPIs, there is a growing need for fast and accurate methods for discovering homologous PPIs of a newly determined PPI. PPISearch is a web server that rapidly identifies homologous PPIs (called PPI family) and infers transferabilit...

PrePPI (http://bhapp.c2b2.columbia.edu/PrePPI) is a database that combines predicted and experimentally determined protein-protein interactions (PPIs) using a Bayesian framework. Predicted interactions are assigned probabilities of being correct, which are derived from calculated likelihood ratios (LRs) by combining structural, functional, evolutionary and expression information, with the most ...

Protein-protein interactions (PPIs) are crucial in many biological processes. The first step towards the molecular characterisation of PPIs implies the charting of their interfaces, that is, the surfaces mediating the interaction. To this end, we present here iFrag, a sequence-based computational method that infers possible interacting regions between two proteins by searching minimal common se...