AIMC Topic: Binding Sites

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Predicting cryptic ligand binding sites based on normal modes guided conformational sampling.

Proteins Dec 5, 2020
To greatly expand the druggable genome, fast and accurate predictions of cryptic sites for small molecules binding in target proteins are in high demand. In this study, we have developed a fast and simple conformational sampling scheme guided by norm...
Area Under Curve Antigens, CD Molecular Dynamics Simulation Hepacivirus Ligands Antigens, Neoplasm Interleukin-2 Models, Statistical Regression Analysis Coronavirus 3C Proteases Coronavirus Papain-Like Proteases Karyopherins Protein Tyrosine Phosphatase, Non-Receptor Type 1 Exportin 1 Protein Elasticity Protein Conformation Receptors, Cytoplasmic and Nuclear Binding Sites Humans SARS-CoV-2 Machine Learning ROC Curve Computational Biology Algorithms Reproducibility of Results
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DeepA-RBPBS: A hybrid convolution and recurrent neural network combined with attention mechanism for predicting RBP binding site.

Journal of biomolecular structure & dynamics Dec 4, 2020
It's important to infer the binding site of RNA-binding proteins (RBP) for understanding the interaction between RBP and its RNA targets and decipher the mechanisms of transcriptional regulation. However, experimental detection of RBP binding sites i...
RNA Binding Sites Neural Networks, Computer Protein Binding RNA-Binding Proteins
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Learning and interpreting the gene regulatory grammar in a deep learning framework.

PLoS computational biology Nov 2, 2020
Deep neural networks (DNNs) have achieved state-of-the-art performance in identifying gene regulatory sequences, but they have provided limited insight into the biology of regulatory elements due to the difficulty of interpreting the complex features...
Gene Regulatory Networks Mice Computational Biology Models, Genetic Transcription Factors Neural Networks, Computer Computer Simulation Animals Deep Learning Genes, Regulator Databases, Genetic Terminology as Topic Binding Sites Enhancer Elements, Genetic
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Spatiotemporal identification of druggable binding sites using deep learning.

Communications biology Oct 27, 2020
Identification of novel protein binding sites expands druggable genome and opens new opportunities for drug discovery. Generally, presence or absence of a binding site depends on the three-dimensional conformation of a protein, making binding site id...
Models, Molecular Models, Biological Software Receptors, Purinergic P2X3 Deep Learning Binding Sites Adenosine Triphosphate Drug Delivery Systems Protein Binding Protein Conformation Ion Channel Gating Receptors, G-Protein-Coupled
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COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2.

The journal of physical chemistry letters Oct 26, 2020
Chemical similarity-based approaches employed to repurpose or develop new treatments for emerging diseases, such as COVID-19, correlates molecular structure-based descriptors of drugs with those of a physiological counterpart or clinical phenotype. W...
Coronavirus Infections Nucleotides Binding Sites Betacoronavirus Pneumonia, Viral RNA-Dependent RNA Polymerase Principal Component Analysis RNA, Viral Drug Evaluation, Preclinical Quantum Theory Pandemics COVID-19 SARS-CoV-2 Molecular Docking Simulation Humans Machine Learning
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SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features.

International journal of molecular sciences Oct 1, 2020
Protein Hot-Spots (HS) are experimentally determined amino acids, key to small ligand binding and tend to be structural landmarks on protein-protein interactions. As such, they were extensively approached by structure-based Machine Learning (ML) pred...
Amino Acid Sequence Datasets as Topic Binding Sites Protein Interaction Mapping Computational Biology Proteins Databases, Protein Amino Acids Humans Machine Learning Protein Binding
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iDRBP_MMC: Identifying DNA-Binding Proteins and RNA-Binding Proteins Based on Multi-Label Learning Model and Motif-Based Convolutional Neural Network.

Journal of molecular biology Sep 11, 2020
DNA-binding protein (DBP) and RNA-binding protein (RBP) are playing crucial roles in gene expression. Accurate identification of them is of great significance, and accurately computational predictors are highly required. In previous studies, DBP reco...
Machine Learning Protein Binding Computational Biology Humans Neural Networks, Computer RNA-Binding Proteins DNA-Binding Proteins RNA Binding Sites
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Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs.

Frontiers in immunology Aug 25, 2020
Current sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. Currents too...
Signal Transduction Peptides Binding Sites Databases, Protein Deep Learning Humans Protein Interaction Domains and Motifs Ligands Software Receptors, Antigen, T-Cell Antigens T-Lymphocytes Protein Binding Epitopes, T-Lymphocyte
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A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes.

Nature communications Aug 21, 2020
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identif...
Proteolysis Binding Sites Phosphotransferases Botrytis Cell Survival Ligands HeLa Cells Saccharomyces cerevisiae Computational Biology Proteomics Humans Proteome Machine Learning Mass Spectrometry Drug Delivery Systems Drug Discovery Protein Binding
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The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target.

Computers in biology and medicine Aug 13, 2020
Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subse...
Amino Acid Sequence Coronavirus Infections Viral Nonstructural Proteins Binding Sites COVID-19 SARS-CoV-2 Computational Biology Drug Development Humans Conserved Sequence Artificial Intelligence Betacoronavirus Pandemics Pneumonia, Viral Coronavirus Papain-Like Proteases
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