AIMC Topic: Protein Interaction Mapping

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Current status and future perspectives of computational studies on human-virus protein-protein interactions.

Briefings in bioinformatics
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the ...

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.

Briefings in bioinformatics
In recent years, high-throughput experimental techniques have significantly enhanced the accuracy and coverage of protein-protein interaction identification, including human-pathogen protein-protein interactions (HP-PPIs). Despite this progress, expe...

Deep Learning for Protein-Protein Interaction Site Prediction.

Methods in molecular biology (Clifton, N.J.)
Protein-protein interactions (PPIs) are central to cellular functions. Experimental methods for predicting PPIs are well developed but are time and resource expensive and suffer from high false-positive error rates at scale. Computational prediction ...

Network Analysis of Integrin Adhesion Complexes.

Methods in molecular biology (Clifton, N.J.)
Cell-surface adhesion receptors mediate interactions with the extracellular matrix (ECM) to control many fundamental aspects of cell behavior, including cell migration, survival, and proliferation. Integrin adhesion receptors recruit structural and s...

Improved Prediction of Protein-Protein Interaction Mapping on by Using Amino Acid Sequence Features in a Supervised Learning Framework.

Protein and peptide letters
BACKGROUND: Protein-Protein Interaction (PPI) has emerged as a key role in the control of many biological processes including protein function, disease incidence, and therapy design. However, the identification of PPI by wet lab experiment is a chall...

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions.

Nucleic acids research
Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predic...

NetGO: improving large-scale protein function prediction with massive network information.

Nucleic acids research
Automated function prediction (AFP) of proteins is of great significance in biology. AFP can be regarded as a problem of the large-scale multi-label classification where a protein can be associated with multiple gene ontology terms as its labels. Bas...

Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences.

Bioinformatics (Oxford, England)
MOTIVATION: In bioinformatics, machine learning-based methods that predict the compound-protein interactions (CPIs) play an important role in the virtual screening for drug discovery. Recently, end-to-end representation learning for discrete symbolic...

canSAR: update to the cancer translational research and drug discovery knowledgebase.

Nucleic acids research
canSAR (http://cansar.icr.ac.uk) is a public, freely available, integrative translational research and drug discovery knowlegebase. canSAR informs researchers to help solve key bottlenecks in cancer translation and drug discovery. It integrates genom...

Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research.

Current cancer drug targets
BACKGROUND: Autophagy and apoptosis are the basic physiological processes in cells that clean up aged and mutant cellular components or even the entire cells. Both autophagy and apoptosis are disrupted in most major diseases such as cancer and neurol...