AIMC Topic: Proteome

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The Reactome Pathway Knowledgebase 2024.

Nucleic acids research Jan 5, 2024
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordere...
Humans Proteome Knowledge Bases Signal Transduction Metabolic Networks and Pathways
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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.

Nucleic acids research Jan 5, 2024
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural biology by amassing over 214 million predicted protein structures, expanding from the initial 300k structures released...
Artificial Intelligence Search Engine Amino Acid Sequence Proteins Protein Structure, Secondary Proteome Databases, Protein
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ASD2023: towards the integrating landscapes of allosteric knowledgebase.

Nucleic acids research Jan 5, 2024
Allosteric regulation, induced by perturbations at an allosteric site topographically distinct from the orthosteric site, is one of the most direct and efficient ways to fine-tune macromolecular function. The Allosteric Database (ASD; accessible onli...
Protein Interaction Maps Proteome Drug Discovery Allosteric Site Humans Knowledge Bases Allosteric Regulation Ligands
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PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk.

Briefings in bioinformatics Mar 19, 2023
Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk...
Protein Domains Neural Networks, Computer Proteome Signal Transduction Protein Processing, Post-Translational
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Searching and Navigating UniProt Databases.

Current protocols Mar 1, 2023
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt website receives about 800,000 unique visitors per month and is the primary means to access UniProt. It provides 10 searchable ...
Knowledge Bases Archives Proteome Amino Acid Sequence Databases, Protein
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UniProt: the Universal Protein Knowledgebase in 2023.

Nucleic acids research Jan 6, 2023
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing...
Amino Acid Sequence Proteome Machine Learning Knowledge Bases Databases, Protein
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Discovering misannotated lncRNAs using deep learning training dynamics.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: Recent experimental evidence has shown that some long non-coding RNAs (lncRNAs) contain small open reading frames (sORFs) that are translated into functional micropeptides, suggesting that these lncRNAs are misannotated as non-coding. Cur...
Deep Learning Proteome RNA, Long Noncoding Open Reading Frames Amino Acid Sequence Micropeptides
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DockNet: high-throughput protein-protein interface contact prediction.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: Over 300 000 protein-protein interaction (PPI) pairs have been identified in the human proteome and targeting these is fast becoming the next frontier in drug design. Predicting PPI sites, however, is a challenging task that traditionally...
Computational Biology Proteome Area Under Curve Pharmacophore Neural Networks, Computer Algorithms Humans
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Multi-omic integration by machine learning (MIMaL).

Bioinformatics (Oxford, England) Oct 31, 2022
MOTIVATION: Cells respond to environments by regulating gene expression to exploit resources optimally. Recent advances in technologies allow for measuring the abundances of RNA, proteins, lipids and metabolites. These highly complex datasets reflect...
Machine Learning Metabolic Networks and Pathways Proteome Cluster Analysis
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The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.

Molecular biology and evolution Oct 7, 2022
The recent development of artificial intelligence provides us with new and powerful tools for studying the mysterious relationship between organism evolution and protein evolution. In this work, based on the AlphaFold Protein Structure Database (Alph...
Databases, Protein Phylogeny Artificial Intelligence Proteome
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