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Binding Sites

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A Point Cloud Graph Neural Network for Protein-Ligand Binding Site Prediction.

International journal of molecular sciences 39273227
Predicting protein-ligand binding sites is an integral part of structural biology and drug design. A comprehensive understanding of these binding sites is essential for advancing drug innovation, elucidating mechanisms of biological function, and exp...
Algorithms Binding Sites Databases, Protein Deep Learning Ligands Neural Networks, Computer Protein Binding Proteins
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Deciphering the Language of Protein-DNA Interactions: A Deep Learning Approach Combining Contextual Embeddings and Multi-Scale Sequence Modeling.

Journal of molecular biology 39214282
Deciphering the mechanisms governing protein-DNA interactions is crucial for understanding key cellular processes and disease pathways. In this work, we present a powerful deep learning approach that significantly advances the computational predictio...
Binding Sites Computational Biology Deep Learning DNA DNA-Binding Proteins Neural Networks, Computer Protein Binding
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Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure.

Journal of chemical information and modeling 39197011
We present a computational scheme for predicting the ligands that bind to a pocket of a known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations, and permutati...
Algorithms Binding Sites Ligands Machine Learning Models, Molecular Molecular Structure Protein Binding Protein Conformation Proteins Small Molecule Libraries
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iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites.

PLoS computational biology 39173070
Circular RNAs (circRNAs) play vital roles in transcription and translation. Identification of circRNA-RBP (RNA-binding protein) interaction sites has become a fundamental step in molecular and cell biology. Deep learning (DL)-based methods have been ...
Algorithms Binding Sites Computational Biology Deep Learning Humans Neural Networks, Computer RNA-Binding Proteins RNA, Circular
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FitScore: a fast machine learning-based score for 3D virtual screening enrichment.

Journal of computer-aided molecular design 39150579
Enhancing virtual screening enrichment has become an urgent problem in computational chemistry, driven by increasingly large databases of commercially available compounds, without a commensurate drop in in vitro screening costs. Docking these large d...
Binding Sites Drug Discovery Drug Evaluation, Preclinical Humans Ligands Machine Learning Molecular Docking Simulation Protein Binding Proteins Software
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Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.

Journal of chemical information and modeling 39283165
Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Compet...
Binding Sites Drug Discovery Ligands Machine Learning Molecular Dynamics Simulation Protein Binding Protein Conformation Proteins
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DeepDBS: Identification of DNA-binding sites in protein sequences by using deep representations and random forest.

Methods (San Diego, Calif.) 39270885
Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protei...
Algorithms Amino Acid Sequence Binding Sites Computational Biology Databases, Protein Deep Learning DNA DNA-Binding Proteins Neural Networks, Computer Protein Binding Random Forest Sequence Analysis, Protein
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Predicting splicing patterns from the transcription factor binding sites in the promoter with deep learning.

BMC genomics 39227799
BACKGROUND: Alternative splicing is a pivotal mechanism of post-transcriptional modification that contributes to the transcriptome plasticity and proteome diversity in metazoan cells. Although many splicing regulations around the exon/intron regions ...
Alternative Splicing Binding Sites Computational Biology Deep Learning Exons Humans Promoter Regions, Genetic Transcription Factors
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An integrated machine-learning model to predict nucleosome architecture.

Nucleic acids research 39162225
We demonstrate that nucleosomes placed in the gene body can be accurately located from signal decay theory assuming two emitters located at the beginning and at the end of genes. These generated wave signals can be in phase (leading to well defined n...
Binding Sites DNA Humans Machine Learning Nucleosomes Transcription Factors
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MMD-DTA: A Multi-Modal Deep Learning Framework for Drug-Target Binding Affinity and Binding Region Prediction.

IEEE/ACM transactions on computational biology and bioinformatics 39208057
The prediction of drug-target affinity (DTA) plays a crucial role in drug development and the identification of potential drug targets. In recent years, computer-assisted DTA prediction has emerged as a significant approach in this field. In this stu...
Binding Sites Computational Biology Deep Learning Drug Discovery Humans Neural Networks, Computer Pharmaceutical Preparations Protein Binding Proteins
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