AIMC Topic: Binding Sites

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dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains.

Nucleic acids research Jul 21, 2021
Domains are instrumental in facilitating protein interactions with DNA, RNA, small molecules, ions and peptides. Identifying ligand-binding domains within sequences is a critical step in protein function annotation, and the ligand-binding properties ...
Humans RNA Ions Ligands Binding Sites Machine Learning Peptides DNA Protein Domains
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GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues.

Nucleic acids research May 21, 2021
Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this pap...
Neural Networks, Computer Software Protein Binding RNA-Binding Proteins DNA DNA-Binding Proteins RNA Protein Conformation Binding Sites
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Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology Mar 3, 2021
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...
Software Animals Protein Binding Models, Molecular Humans Artificial Intelligence Structural Homology, Protein Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Membrane Transport Modulators Binding Sites Molecular Dynamics Simulation Ion Channels Ligands Protein Interaction Domains and Motifs Quantitative Structure-Activity Relationship Ion Channel Gating
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A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America Feb 9, 2021
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...
Binding Sites RNA Polymerase II Nucleotide Motifs RNA Splicing Base Sequence Genome, Human Histones RNA Splice Sites Transcription Elongation, Genetic Machine Learning Epigenesis, Genetic DNA Methylation Protein Processing, Post-Translational Models, Biological HeLa Cells HEK293 Cells Humans
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Application and assessment of deep learning for the generation of potential NMDA receptor antagonists.

Physical chemistry chemical physics : PCCP Jan 21, 2021
Uncompetitive antagonists of the N-methyl d-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzheimer's, but some also cause dissociative effects that have led to the ...
Animals Drug Design Deep Learning Mice Molecular Structure Ligands Xenopus laevis Receptors, N-Methyl-D-Aspartate Binding Sites Small Molecule Libraries
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Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Nucleic acids research Jan 11, 2021
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Polymorphism, Single Nucleotide Epigenomics Models, Genetic Transcription Factors Causality Epigenome Datasets as Topic Organ Specificity Humans Deep Learning Genome-Wide Association Study Genetic Diseases, Inborn Chromatin Immunoprecipitation Histone Code Molecular Sequence Annotation Binding Sites Linkage Disequilibrium
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Bionoi: A Voronoi Diagram-Based Representation of Ligand-Binding Sites in Proteins for Machine Learning Applications.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
Bionoi is a new software to generate Voronoi representations of ligand-binding sites in proteins for machine learning applications. Unlike many other deep learning models in biomedicine, Bionoi utilizes off-the-shelf convolutional neural network arch...
Neural Networks, Computer Machine Learning Histidine Kinase Proteins Ligands Databases, Chemical Binding Sites Software Drug Discovery Deep Learning
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DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleic acids research Jul 27, 2020
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling...
Mice Computational Biology RNA-Binding Proteins Mutation Humans Animals Computer Simulation Deep Learning Protein Binding Binding Sites Nucleotide Motifs RNA Base Sequence Nucleic Acid Conformation
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Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.

Bioinformatics (Oxford, England) May 1, 2020
MOTIVATION: Knowledge of protein-ligand binding residues is important for understanding the functions of proteins and their interaction mechanisms. From experimentally solved protein structures, how to accurately identify its potential binding sites ...
Protein Binding Computational Biology Proteins Ligands Binding Sites Machine Learning Algorithms
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BionoiNet: ligand-binding site classification with off-the-shelf deep neural network.

Bioinformatics (Oxford, England) May 1, 2020
MOTIVATION: Fast and accurate classification of ligand-binding sites in proteins with respect to the class of binding molecules is invaluable not only to the automatic functional annotation of large datasets of protein structures but also to projects...
Ligands Binding Sites Neural Networks, Computer Proteins Molecular Structure
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