AIMC Topic: Protein Interaction Mapping

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Machine learning on protein-protein interaction prediction: models, challenges and trends.

Briefings in bioinformatics Mar 19, 2023
Protein-protein interactions (PPIs) carry out the cellular processes of all living organisms. Experimental methods for PPI detection suffer from high cost and false-positive rate, hence efficient computational methods are highly desirable for facilit...
Computational Biology Proteins Protein Interaction Mapping Machine Learning
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Growing ecosystem of deep learning methods for modeling protein-protein interactions.

Protein engineering, design & selection : PEDS Jan 21, 2023
Numerous cellular functions rely on protein-protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep learning has emerged as a...
Deep Learning Proteins Protein Interaction Mapping
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CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning.

Nucleic acids research Jul 5, 2022
Recent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computational appro...
Binding Sites Protein Interaction Mapping Membrane Proteins Software Ligands Deep Learning Protein Conformation
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An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph.

Briefings in bioinformatics May 13, 2022
Identifying the potential compound-protein interactions (CPIs) plays an essential role in drug development. The computational approaches for CPI prediction can reduce time and costs of experimental methods and have benefited from the continuously imp...
Protein Interaction Maps Drug Development Protein Interaction Mapping Neural Networks, Computer Software Proteins
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Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function.

Briefings in bioinformatics Nov 5, 2021
Deep residual learning has shown great success in protein contact prediction. In this study, a new deep residual learning-based protein contact prediction model was developed. Comparing with previous models, a new type of residual block hybridizing 1...
Proteins Protein Interaction Mapping Computational Biology Carrier Proteins Software Reproducibility of Results Deep Learning Protein Binding
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Improved prediction of protein-protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines.

Briefings in bioinformatics Nov 5, 2021
In this paper, for accurate prediction of protein-protein interaction (PPI), a novel hybrid classifier is developed by combining the functional-link Siamese neural network (FSNN) with the light gradient boosting machine (LGBM) classifier. The hybrid ...
Humans Reproducibility of Results Computational Biology Databases, Genetic Neural Networks, Computer Machine Learning Algorithms Protein Interaction Mapping Proteins Amino Acids
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Machine learning for phytopathology: from the molecular scale towards the network scale.

Briefings in bioinformatics Sep 2, 2021
With the increasing volume of high-throughput sequencing data from a variety of omics techniques in the field of plant-pathogen interactions, sorting, retrieving, processing and visualizing biological information have become a great challenge. Within...
Gene Expression Regulation Pathogen-Associated Molecular Pattern Molecules Fungal Proteins Support Vector Machine Plant Pathology Host-Pathogen Interactions Protein Serine-Threonine Kinases Viral Proteins Plants Receptors, Pattern Recognition Bayes Theorem Protein Interaction Mapping Plant Diseases Bacterial Proteins Disease Resistance NLR Proteins
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A survey on computational models for predicting protein-protein interactions.

Briefings in bioinformatics Sep 2, 2021
Proteins interact with each other to play critical roles in many biological processes in cells. Although promising, laboratory experiments usually suffer from the disadvantages of being time-consuming and labor-intensive. The results obtained are oft...
Proteins Databases, Protein Models, Molecular Protein Conformation Saccharomyces cerevisiae Gene Ontology Computational Biology Humans Support Vector Machine Protein Interaction Mapping Software Protein Interaction Domains and Motifs Databases, Genetic
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Current status and future perspectives of computational studies on human-virus protein-protein interactions.

Briefings in bioinformatics Sep 2, 2021
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 ...
CD40 Antigens TNF Receptor-Associated Factor 3 Viral Proteins Protein Binding Protein Interaction Mapping Computational Biology Receptors, Virus Databases, Genetic Gene Expression Amino Acid Sequence Virus Diseases Host-Pathogen Interactions Humans Viruses Machine Learning Antiviral Agents
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Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.

Briefings in bioinformatics May 20, 2021
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...
Protein Interaction Mapping Algorithms Humans Computational Biology Machine Learning Host-Pathogen Interactions
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