AIMC Topic: Protein Domains

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Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues.

Scientific reports Dec 21, 2016
The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a com...
Amino Acid Motifs GTPase-Activating Proteins Dishevelled Proteins Carcinoma, Hepatocellular Computational Biology RNA, Messenger Cluster Analysis Protein Domains Gene Expression Regulation, Neoplastic Signal Transduction Gene Expression Profiling Real-Time Polymerase Chain Reaction Liver Neoplasms Machine Learning Algorithms Phylogeny Humans
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gDNA-Prot: Predict DNA-binding proteins by employing support vector machine and a novel numerical characterization of protein sequence.

Journal of theoretical biology Jul 1, 2016
DNA-binding proteins are the functional proteins in cells, which play an important role in various essential biological activities. An effective and fast computational method gDNA-Prot is proposed to predict DNA-binding proteins in this paper, which ...
Models, Molecular Databases, Protein Protein Domains Principal Component Analysis DNA-Binding Proteins ROC Curve DNA Computational Biology Numerical Analysis, Computer-Assisted Support Vector Machine Amino Acid Sequence Genome
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Effectively Identifying Compound-Protein Interactions by Learning from Positive and Unlabeled Examples.

IEEE/ACM transactions on computational biology and bioinformatics May 18, 2016
Prediction of compound-protein interactions (CPIs) is to find new compound-protein pairs where a protein is targeted by at least a compound, which is a crucial step in new drug design. Currently, a number of machine learning based methods have been d...
Protein Domains Caenorhabditis elegans Proteins Pharmaceutical Preparations Humans Protein Interaction Mapping Support Vector Machine Drug Discovery Proteins Computational Biology Databases, Protein
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PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.

Journal of molecular modeling Mar 11, 2016
The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based ...
Discriminant Analysis Protein Domains Caspase 9 Caspase 10 Caspase 8 Sequence Analysis, Protein Structural Homology, Protein Humans Decision Trees Databases, Protein Bayes Theorem Neural Networks, Computer Computational Biology Support Vector Machine
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UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.

BMC systems biology Jan 11, 2016
BACKGROUND: The conjugation of ubiquitin to a substrate protein (protein ubiquitylation), which involves a sequential process--E1 activation, E2 conjugation and E3 ligation, is crucial to the regulation of protein function and activity in eukaryotes....
Models, Molecular Ubiquitination Amino Acid Motifs Protein Domains Machine Learning Amino Acid Sequence Sequence Analysis, Protein Software Datasets as Topic Proteomics Proteome Lysine Mass Spectrometry Ubiquitin
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Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities.

Journal of chemical information and modeling Jun 9, 2025
The leucine-rich repeat kinase 2 (LRRK2) is the most mutated gene in familial Parkinson's disease, and its mutations lead to pathogenic hallmarks of the disease. The LRRK2 WDR domain is an understudied drug target for Parkinson's disease, with no kno...
Humans Machine Learning Ligands Protein Kinase Inhibitors Thermodynamics Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 Protein Binding Protein Domains Molecular Dynamics Simulation
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DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Due to the breakthrough in protein structure prediction by AlphaFold, the scientific community has access to 200 million predicted protein structures with near-atomic accuracy from the AlphaFold protein structure DataBase (AFDB), covering...
Protein Folding Proteins Databases, Protein Protein Domains Neural Networks, Computer Algorithms Computational Biology Artificial Intelligence Software
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Chainsaw: protein domain segmentation with fully convolutional neural networks.

Bioinformatics (Oxford, England) May 2, 2024
MOTIVATION: Protein domains are fundamental units of protein structure and play a pivotal role in understanding folding, function, evolution, and design. The advent of accurate structure prediction techniques has resulted in an influx of new structur...
Databases, Protein Protein Domains Algorithms Computational Biology Proteins Humans Neural Networks, Computer Software
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Insights into the inner workings of transformer models for protein function prediction.

Bioinformatics (Oxford, England) Mar 4, 2024
MOTIVATION: We explored how explainable artificial intelligence (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such that latent ...
Artificial Intelligence Protein Domains Amino Acids Gene Ontology Neural Networks, Computer
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Lactylation prediction models based on protein sequence and structural feature fusion.

Briefings in bioinformatics Jan 22, 2024
Lysine lactylation (Kla) is a newly discovered posttranslational modification that is involved in important life activities, such as glycolysis-related cell function, macrophage polarization and nervous system regulation, and has received widespread ...
Protein Processing, Post-Translational Natural Language Processing Protein Domains Amino Acid Sequence Lysine
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