AIMC Topic: Protein Interaction Domains and Motifs

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GGIP: Structure and sequence-based GPCR-GPCR interaction pair predictor.

Proteins Jun 8, 2016
G Protein-Coupled Receptors (GPCRs) are important pharmaceutical targets. More than 30% of currently marketed pharmaceutical medicines target GPCRs. Numerous studies have reported that GPCRs function not only as monomers but also as homo- or hetero-d...
Mice Support Vector Machine Databases, Protein Receptors, G-Protein-Coupled Area Under Curve Models, Molecular Amino Acid Sequence Binding Sites Humans Animals ROC Curve Protein Binding Protein Structure, Secondary Protein Multimerization Protein Interaction Domains and Motifs
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Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

Journal of theoretical biology Apr 23, 2016
Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic si...
Molecular Sequence Annotation Gene Ontology Protein Interaction Mapping Humans Protein Interaction Domains and Motifs Machine Learning Support Vector Machine Yeasts
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Accurate contact predictions using covariation techniques and machine learning.

Proteins Aug 14, 2015
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effectiv...
Models, Molecular Internet Amino Acid Sequence Humans Viruses Computational Biology Protein Structure, Secondary Neural Networks, Computer Models, Statistical Protein Folding Machine Learning Proteins Sequence Alignment Software Databases, Protein Protein Interaction Domains and Motifs Computer Simulation Bacteria
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Efficient prediction of progesterone receptor interactome using a support vector machine model.

International journal of molecular sciences Mar 3, 2015
Protein-protein interaction (PPI) is essential for almost all cellular processes and identification of PPI is a crucial task for biomedical researchers. So far, most computational studies of PPI are intended for pair-wise prediction. Theoretically, p...
Receptors, Progesterone Protein Interaction Domains and Motifs Cluster Analysis Area Under Curve Humans Receptors, Androgen ROC Curve Receptors, Estrogen Proteome Support Vector Machine
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LR-GNN: a graph neural network based on link representation for predicting molecular associations.

Briefings in bioinformatics Jan 17, 2022
In biomedical networks, molecular associations are important to understand biological processes and functions. Many computational methods, such as link prediction methods based on graph neural networks (GNNs), have been successfully applied in discov...
Humans Neural Networks, Computer Algorithms RNA, Long Noncoding Research Design Cell Communication Drug Interactions Biomedical Technology Deep Learning Protein Interaction Domains and Motifs Computational Biology MicroRNAs
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Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins.

Briefings in bioinformatics Nov 5, 2021
Accurate variant effect prediction has broad impacts on protein engineering. Recent machine learning approaches toward this end are based on representation learning, by which feature vectors are learned and generated from unlabeled sequences. However...
Neural Networks, Computer Algorithms Reproducibility of Results Deep Learning Amino Acid Sequence Protein Interaction Domains and Motifs Protein Binding Computational Biology Proteins Protein Domains
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The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis.

Briefings in bioinformatics Nov 5, 2021
Cancerlectins, lectins linked to tumor progression, have become the focus of cancer therapy research for their carbohydrate-binding specificity. However, the specific characterization for cancerlectins involved in tumor progression is still unclear. ...
Protein Interaction Domains and Motifs Amino Acid Sequence Disease Susceptibility Gene Ontology Lectins Computational Biology Neoplasms Databases, Genetic Machine Learning Peptides Structure-Activity Relationship Algorithms Phylogeny Workflow Protein Binding
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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 Software Protein Conformation Computational Biology Support Vector Machine Databases, Genetic Saccharomyces cerevisiae Humans Gene Ontology Protein Interaction Mapping Protein Interaction Domains and Motifs
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Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes.

Briefings in bioinformatics Sep 2, 2021
Protein-protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein-protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting the protein-protein inte...
Protein Binding Proteins Datasets as Topic Binding Sites Humans Software Molecular Docking Simulation Deep Learning Protein Multimerization Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical Protein Conformation, beta-Strand
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Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology Mar 3, 2021
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...
Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Membrane Transport Modulators Models, Molecular Artificial Intelligence Humans Protein Interaction Domains and Motifs Molecular Dynamics Simulation Software Ligands Animals Binding Sites Ion Channel Gating Quantitative Structure-Activity Relationship Protein Binding Ion Channels Structural Homology, Protein
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