AIMC Topic: Protein Interaction Mapping

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A roadmap to multifactor dimensionality reduction methods.

Briefings in bioinformatics
Complex diseases are defined to be determined by multiple genetic and environmental factors alone as well as in interactions. To analyze interactions in genetic data, many statistical methods have been suggested, with most of them relying on statisti...

TENET: topological feature-based target characterization in signalling networks.

Bioinformatics (Oxford, England)
MOTIVATION: Target characterization for a biochemical network is a heuristic evaluation process that produces a characterization model that may aid in predicting the suitability of each molecule for drug targeting. These approaches are typically used...

Machine learning assisted design of highly active peptides for drug discovery.

PLoS computational biology
The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning ap...

Exploring the relationship between hub proteins and drug targets based on GO and intrinsic disorder.

Computational biology and chemistry
Protein-protein interactions (PPIs) play essential roles in many biological processes. In protein-protein interaction networks, hubs involve in numbers of PPIs and may constitute an important source of drug targets. The intrinsic disorder proteins (I...

Computationally predicting protein-RNA interactions using only positive and unlabeled examples.

Journal of bioinformatics and computational biology
Protein-RNA interactions (PRIs) are considerably important in a wide variety of cellular processes, ranging from transcriptional and post-transcriptional regulations of gene expression to the active defense of host against virus. With the development...

More challenges for machine-learning protein interactions.

Bioinformatics (Oxford, England)
MOTIVATION: Machine learning may be the most popular computational tool in molecular biology. Providing sustained performance estimates is challenging. The standard cross-validation protocols usually fail in biology. Park and Marcotte found that even...

DeepPhosPPI: a deep learning framework with attention-CNN and transformer for predicting phosphorylation effects on protein-protein interactions.

Briefings in bioinformatics
Protein phosphorylation regulates protein function and cellular signaling pathways, and is strongly associated with diseases, including neurodegenerative disorders and cancer. Phosphorylation plays a critical role in regulating protein activity and c...

InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.

Nucleic acids research
Predicting functional binding sites in proteins is crucial for understanding protein-protein interactions (PPIs) and identifying drug targets. While various computational approaches exist, many fail to assess PPI ligandability, which often involves c...

HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Nucleic acids research
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...

The signed two-space proximity model for learning representations in protein-protein interaction networks.

Bioinformatics (Oxford, England)
MOTIVATION: Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally expens...