AIMC Topic: Multiprotein Complexes

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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Computer Simulation Deep Learning Homologous Recombination Chromosome Segregation Ligases Ribosomes Multiprotein Complexes Acyltransferases Protein Conformation Saccharomyces cerevisiae Ubiquitin Membrane Proteins DNA Repair Evolution, Molecular Protein Biosynthesis Models, Molecular Protein Interaction Mapping Protein Interaction Maps Saccharomyces cerevisiae Proteins Computational Biology Proteome
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Accurate prediction of protein structures and interactions using a three-track neural network.

Science (New York, N.Y.) Jul 15, 2021
DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track ...
Amino Acid Sequence ADAM Proteins Crystallography, X-Ray Protein Conformation Databases, Protein Receptors, G-Protein-Coupled Models, Molecular Protein Subunits Sphingosine N-Acyltransferase Cryoelectron Microscopy Protein Folding Multiprotein Complexes Neural Networks, Computer Membrane Proteins Proteins Computer Simulation Deep Learning
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Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry.

Nature communications May 28, 2021
Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits t...
Multiprotein Complexes Cross-Linking Reagents Escherichia coli Proteins Chromatography, Reverse-Phase Protein Interaction Mapping Escherichia coli Chromatography, High Pressure Liquid Tandem Mass Spectrometry Time Factors Proteomics Neural Networks, Computer Peptides
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Protein complex identification based on weighted PPI network with multi-source information.

Journal of theoretical biology Jun 11, 2019
Proteins form complexes to accomplish biological functions such as transcription of DNA, translation of mRNA and cell growth. Detection of protein complexes from protein-protein interaction (PPI) networks is the first step for the analysis of biologi...
Protein Interaction Maps Gene Ontology Multiprotein Complexes
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Integrating network topology, gene expression data and GO annotation information for protein complex prediction.

Journal of bioinformatics and computational biology Oct 30, 2018
The prediction of protein complexes based on the protein interaction network is a fundamental task for the understanding of cellular life as well as the mechanisms underlying complex disease. A great number of methods have been developed to predict p...
Transcriptome Protein Interaction Maps Algorithms Gene Ontology Protein Interaction Mapping Saccharomyces cerevisiae Proteins Computational Biology Multiprotein Complexes Cluster Analysis Databases, Protein
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A Type-2 fuzzy data fusion approach for building reliable weighted protein interaction networks with application in protein complex detection.

Computers in biology and medicine Jun 23, 2017
Detecting the protein complexes is an important task in analyzing the protein interaction networks. Although many algorithms predict protein complexes in different ways, surveys on the interaction networks indicate that about 50% of detected interact...
Databases, Protein Semantics Protein Interaction Mapping Multiprotein Complexes Protein Interaction Maps Computational Biology Fuzzy Logic Algorithms Gene Expression Profiling
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Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.

Scientific reports Apr 18, 2017
Protein-protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. We tested our method on a previously used large ...
Multiprotein Complexes Protein Binding Machine Learning Models, Chemical Predictive Value of Tests Monte Carlo Method
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Nano Random Forests to mine protein complexes and their relationships in quantitative proteomics data.

Molecular biology of the cell Jan 5, 2017
Ever-increasing numbers of quantitative proteomics data sets constitute an underexploited resource for investigating protein function. Multiprotein complexes often follow consistent trends in these experiments, which could provide insights about thei...
DNA-Binding Proteins Machine Learning Datasets as Topic Computer Simulation Multiprotein Complexes Adenosine Triphosphatases Proteomics Kinetochores Structure-Activity Relationship
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Detection of overlapping protein complexes in gene expression, phenotype and pathways of Saccharomyces cerevisiae using Prorank based Fuzzy algorithm.

Gene Jan 22, 2016
Proteins show their functional activity by interacting with other proteins and forms protein complexes since it is playing an important role in cellular organization and function. To understand the higher order protein organization, overlapping is an...
Databases, Protein Fungal Proteins Saccharomyces cerevisiae Signal Transduction Algorithms Multiprotein Complexes Gene Expression Regulation, Fungal Fuzzy Logic Phenotype Protein Interaction Mapping Cluster Analysis Computational Biology
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Deep learning and protein structure modeling.

Nature methods Jan 1, 2022
Algorithms Models, Molecular Protein Conformation Sequence Alignment Multiprotein Complexes Deep Learning Computational Biology Proteins
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