AIMC Topic: Databases, Protein

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Classification and prediction of protein-protein interaction interface using machine learning algorithm.

Scientific reports Jan 19, 2021
Structural insight of the protein-protein interaction (PPI) interface can provide knowledge about the kinetics, thermodynamics and molecular functions of the complex while elucidating its role in diseases and further enabling it as a potential therap...
Protein Binding Support Vector Machine Proteins Molecular Docking Simulation Protein Interaction Maps Binding Sites Thermodynamics Protein Interaction Mapping Databases, Protein Models, Molecular
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ELASPIC2 (EL2): Combining Contextualized Language Models and Graph Neural Networks to Predict Effects of Mutations.

Journal of molecular biology Jan 13, 2021
The ELASPIC web server allows users to evaluate the effect of mutations on protein folding and protein-protein interaction on a proteome-wide scale. It uses homology models of proteins and protein-protein interactions, which have been precalculated f...
Mutation Internet Protein Folding Computational Biology Databases, Protein Neural Networks, Computer Language Software Reproducibility of Results Algorithms User-Computer Interface
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TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features.

Journal of chemical information and modeling Jan 7, 2021
Protein-DNA interactions exist ubiquitously and play important roles in the life cycles of living cells. The accurate identification of DNA-binding proteins (DBPs) is one of the key steps to understand the mechanisms of protein-DNA interactions. Alth...
DNA-Binding Proteins Binding Sites Position-Specific Scoring Matrices Algorithms Support Vector Machine Databases, Protein
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iT3SE-PX: Identification of Bacterial Type III Secreted Effectors Using PSSM Profiles and XGBoost Feature Selection.

Computational and mathematical methods in medicine Jan 6, 2021
Identification of bacterial type III secreted effectors (T3SEs) has become a popular research topic in the field of bioinformatics due to its crucial role in understanding host-pathogen interaction and developing better therapeutic targets against th...
Databases, Protein Amino Acid Sequence Position-Specific Scoring Matrices Computational Biology Support Vector Machine Type III Secretion Systems Machine Learning Algorithms
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Template-based prediction of protein structure with deep learning.

BMC genomics Dec 29, 2020
BACKGROUND: Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary struct...
Software Algorithms Databases, Protein Deep Learning Protein Conformation Sequence Analysis, Protein Proteins
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Inter-protein residue covariation information unravels physically interacting protein dimers.

BMC bioinformatics Dec 17, 2020
BACKGROUND: Predicting physical interaction between proteins is one of the greatest challenges in computational biology. There are considerable various protein interactions and a huge number of protein sequences and synthetic peptides with unknown in...
Protein Interaction Maps Support Vector Machine Evolution, Molecular Proteins Databases, Protein Dimerization
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Deep learning embedder method and tool for mass spectra similarity search.

Journal of proteomics Dec 8, 2020
Spectral similarity calculation is widely used in protein identification tools and mass spectra clustering algorithms while comparing theoretical or experimental spectra. The performance of the spectral similarity calculation plays an important role ...
Cluster Analysis Databases, Protein Tandem Mass Spectrometry Algorithms Deep Learning Proteomics Humans Software
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PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids.

Genes Nov 28, 2020
Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant...
Lysine Support Vector Machine Computational Biology Protein Processing, Post-Translational Databases, Protein Proteome
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Classifying the superfamily of small heat shock proteins by using g-gap dipeptide compositions.

International journal of biological macromolecules Nov 17, 2020
Small heat shock protein (sHSP) is a superfamily of molecular chaperone and is found from archaea to human. Recent researches have demonstrated that sHSPs participate in a series of biological processes and are even closely associated with serious di...
Amino Acid Sequence Dipeptides Sequence Alignment Proteomics Databases, Protein Humans Heat-Shock Proteins, Small Machine Learning Animals Computational Biology
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AK-Score: Accurate Protein-Ligand Binding Affinity Prediction Using an Ensemble of 3D-Convolutional Neural Networks.

International journal of molecular sciences Nov 10, 2020
Accurate prediction of the binding affinity of a protein-ligand complex is essential for efficient and successful rational drug design. Therefore, many binding affinity prediction methods have been developed. In recent years, since deep learning tech...
Databases, Protein Molecular Dynamics Simulation Ligands User-Computer Interface Molecular Docking Simulation Humans Drug Discovery Protein Binding Computer-Aided Design Neural Networks, Computer Deep Learning Proteins Drug Design
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