AIMC Topic: Binding Sites

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Interaction of systemic drugs causing ocular toxicity with organic cation transporter: an artificial intelligence prediction.

Journal of biomolecular structure & dynamics Jun 20, 2023
Chronic disease patients (cancer, arthritis, cardiovascular diseases) undergo long-term systemic drug treatment. Membrane transporters in ocular barriers could falsely recognize these drugs and allow their trafficking into the eye from systemic circu...
Molecular Docking Simulation Protein Binding Artificial Intelligence Machine Learning Binding Sites Organic Cation Transport Proteins Organic Cation Transporter 1 Molecular Dynamics Simulation Ligands Humans
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CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization.

BMC bioinformatics May 30, 2023
BACKGROUND: Circular RNAs (circRNAs) play a significant role in some diseases by acting as transcription templates. Therefore, analyzing the interaction mechanism between circRNA and RNA-binding proteins (RBPs) has far-reaching implications for the p...
RNA, Circular RNA-Binding Proteins Neural Networks, Computer Binding Sites Computational Biology
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Identification of SH2 domain-containing proteins and motifs prediction by a deep learning method.

Computers in biology and medicine May 29, 2023
The Src Homology 2 (SH2) domain plays an important role in the signal transmission mechanism in organisms. It mediates the protein-protein interactions based on the combination between phosphotyrosine and motifs in SH2 domain. In this study, we desig...
Signal Transduction Binding Sites src Homology Domains Proteins Phosphotyrosine Deep Learning Protein Binding
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CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion.

Interdisciplinary sciences, computational life sciences May 26, 2023
Circular RNAs (circRNAs) participate in the regulation of biological processes by binding to specific proteins and thus influence transcriptional processes. In recent years, circRNAs have become an emerging hotspot in RNA research. Due to powerful le...
RNA-Binding Proteins RNA Binding Sites RNA, Circular Neural Networks, Computer
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Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus.

Journal of biomolecular structure & dynamics May 23, 2023
Monkeypox virus (MPXV) outbreak is a serious public health concern that requires international attention. P37 of MPXV plays a pivotal role in DNA replication and acts as one of the promising targets for antiviral drug design. In this study, we intent...
Antiviral Agents Protein Binding Machine Learning Molecular Docking Simulation Hydrogen Bonding Binding Sites Viral Envelope Proteins Molecular Dynamics Simulation Hydrophobic and Hydrophilic Interactions Monkeypox virus
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Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins.

Nature communications May 11, 2023
Metal ions are essential cofactors for many proteins and play a crucial role in many applications such as enzyme design or design of protein-protein interactions because they are biologically abundant, tether to the protein using strong interactions,...
Ions Binding Sites Zinc Metalloproteins Deep Learning Metals
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De novo design of protein interactions with learned surface fingerprints.

Nature Apr 26, 2023
Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. ...
Binding Sites Humans Proteins Computer Simulation Synthetic Biology Protein Binding Deep Learning Proteomics Protein Interaction Maps
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Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches.

International journal of molecular sciences Apr 25, 2023
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protei...
Membrane Proteins Artificial Intelligence Protein Binding Binding Sites Peptides Peptide Library
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Modulation of DNA-protein Interactions by Proximal Genetic Elements as Uncovered by Interpretable Deep Learning.

Journal of molecular biology Apr 24, 2023
Transcription factors (TF) recognize specific motifs in the genome that are typically 6-12 bp long to regulate various aspects of the cellular machinery. Presence of binding motifs and favorable genome accessibility are key drivers for a consistent T...
Protein Binding Transcription Factors DNA Binding Sites Deep Learning
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Self-Attention Based Neural Network for Predicting RNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
Proteins binding to Ribonucleic Acid (RNA) inside cells are called RNA-binding proteins (RBP), which play a crucial role in gene regulation. The identification of RNA-protein binding sites helps to understand the function of RBP better. Although many...
RNA Neural Networks, Computer Binding Sites Protein Binding
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