AIMC Topic: Protein Interaction Mapping

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Recent advances in predicting and modeling protein-protein interactions.

Trends in biochemical sciences Apr 14, 2023
Protein-protein interactions (PPIs) drive biological processes, and disruption of PPIs can cause disease. With recent breakthroughs in structure prediction and a deluge of genomic sequence data, computational methods to predict PPIs and model spatial...
Protein Interaction Mapping Computational Biology Proteome Artificial Intelligence Machine Learning Algorithms
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Graph-BERT and language model-based framework for protein-protein interaction identification.

Scientific reports Apr 6, 2023
Identification of protein-protein interactions (PPI) is among the critical problems in the domain of bioinformatics. Previous studies have utilized different AI-based models for PPI classification with advances in artificial intelligence (AI) techniq...
Artificial Intelligence Amino Acid Sequence Protein Interaction Mapping Protein Interaction Maps Proteins
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Cracking the code of cellular protein-protein interactions: Alphafold and whole-cell crosslinking to the rescue.

Molecular systems biology Mar 10, 2023
Integration of experimental and computational methods is crucial to better understanding protein-protein interactions (PPIs), ideally in their cellular context. In their recent work, Rappsilber and colleagues (O'Reilly et al, 2023) identified bacteri...
Protein Interaction Mapping Artificial Intelligence Proteins
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Hierarchical graph learning for protein-protein interaction.

Nature communications Feb 25, 2023
Protein-Protein Interactions (PPIs) are fundamental means of functions and signalings in biological systems. The massive growth in demand and cost associated with experimental PPI studies calls for computational tools for automated prediction and und...
Humans Proteins Amino Acid Sequence Deep Learning Protein Interaction Maps Protein Interaction Mapping
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ISPRED-SEQ: Deep Neural Networks and Embeddings for Predicting Interaction Sites in Protein Sequences.

Journal of molecular biology Jan 13, 2023
The knowledge of protein-protein interaction sites (PPIs) is crucial for protein functional annotation. Here we address the problem focusing on the prediction of putative PPIs considering as input protein sequences. The issue is important given the h...
Protein Interaction Mapping Amino Acid Sequence Molecular Sequence Annotation Deep Learning Proteins
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SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction.

BMC genomics Jun 27, 2022
BACKGROUND: Protein-protein interactions (PPIs) dominate intracellular molecules to perform a series of tasks such as transcriptional regulation, information transduction, and drug signalling. The traditional wet experiment method to obtain PPIs info...
Saccharomyces cerevisiae Protein Interaction Mapping Computational Biology Amino Acid Sequence Mice Humans Neural Networks, Computer Animals
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Identifying Protein Subcellular Locations With Embeddings-Based node2loc.

IEEE/ACM transactions on computational biology and bioinformatics Apr 1, 2022
Identifying protein subcellular locations is an important topic in protein function prediction. Interacting proteins may share similar locations. Thus, it is imperative to infer protein subcellular locations by taking protein-protein interactions (PP...
Protein Interaction Mapping Proteins Saccharomyces cerevisiae Humans Neural Networks, Computer
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BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction.

Journal of molecular biology Mar 21, 2022
Computational approaches for predicting protein-protein interfaces are extremely useful for understanding and modelling the quaternary structure of protein assemblies. In particular, partner-specific binding site prediction methods allow delineating ...
Datasets as Topic Binding Sites Proteins Protein Interaction Mapping Internet Use Machine Learning Software Protein Binding
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PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning.

Journal of molecular biology Mar 5, 2022
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, ...
Proteomics Proteome Bayes Theorem Protein Interaction Mapping COVID-19 SARS-CoV-2 Software Humans Machine Learning
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Recent advances in predicting protein-protein interactions with the aid of artificial intelligence algorithms.

Current opinion in structural biology Feb 23, 2022
Protein-protein interactions (PPIs) are essential in the regulation of biological functions and cell events, therefore understanding PPIs have become a key issue to understanding the molecular mechanism and investigating the design of drugs. Here we ...
Protein Interaction Mapping Algorithms Computational Biology Artificial Intelligence
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