AIMC Topic: Binding Sites

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TFscope: systematic analysis of the sequence features involved in the binding preferences of transcription factors.

Genome biology Jul 10, 2024
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. Here, we develop TFscope, a machine learning approach that identifies sequence fea...
Protein Binding Humans Transcription Factors Machine Learning Binding Sites Nucleotide Motifs Chromatin Immunoprecipitation Sequencing
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Machine-learning-based structural analysis of interactions between antibodies and antigens.

Bio Systems Jul 2, 2024
Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many dise...
Deep Learning Protein Binding Computational Biology Humans Machine Learning Binding Sites Antigen-Antibody Complex Binding Sites, Antibody Antibodies Epitopes Antigens
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Highly accurate carbohydrate-binding site prediction with DeepGlycanSite.

Nature communications Jun 17, 2024
As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how carbohydrates regulate proteins in the physiological and pathological processes presents opportunities to address crucial biological problems a...
Deep Learning Models, Molecular Humans Protein Binding Carbohydrates Neural Networks, Computer Binding Sites Proteins
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A Machine Learning Approach to Identify Key Residues Involved in Protein-Protein Interactions Exemplified with SARS-CoV-2 Variants.

International journal of molecular sciences Jun 13, 2024
Human infection with the coronavirus disease 2019 (COVID-19) is mediated by the binding of the spike protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the human angiotensin-converting enzyme 2 (ACE2). The frequent mutatio...
Binding Sites Protein Interaction Domains and Motifs Humans Mutation Machine Learning Molecular Dynamics Simulation SARS-CoV-2 Angiotensin-Converting Enzyme 2 COVID-19 Protein Binding Spike Glycoprotein, Coronavirus
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DP-site: A dual deep learning-based method for protein-peptide interaction site prediction.

Methods (San Diego, Calif.) Jun 12, 2024
BACKGROUND: Protein-peptide interaction prediction is an important topic for several applications including various biological processes, understanding drug discovery, protein function abnormal cellular behaviors, and treating diseases. Over the year...
Protein Interaction Mapping Protein Binding Computational Biology Proteins Databases, Protein Binding Sites Software Peptides Deep Learning Humans Neural Networks, Computer
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Protein embeddings predict binding residues in disordered regions.

Scientific reports Jun 12, 2024
The identification of protein binding residues helps to understand their biological processes as protein function is often defined through ligand binding, such as to other proteins, small molecules, ions, or nucleotides. Methods predicting binding re...
Machine Learning Protein Binding Computational Biology Humans Databases, Protein Intrinsically Disordered Proteins Binding Sites
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Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning.

Molecules (Basel, Switzerland) Jun 5, 2024
CDK6 plays a key role in the regulation of the cell cycle and is considered a crucial target for cancer therapy. In this work, conformational transitions of CDK6 were identified by using Gaussian accelerated molecular dynamics (GaMD), deep learning (...
Principal Component Analysis Molecular Dynamics Simulation Protein Conformation Protein Kinase Inhibitors Binding Sites Cyclin-Dependent Kinase 6 Humans Deep Learning Thermodynamics Protein Binding Normal Distribution
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MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling.

IEEE/ACM transactions on computational biology and bioinformatics Jun 5, 2024
RNA-binding proteins (RBPs) can regulate biological functions by interacting with specific RNAs, and play an important role in many life activities. Therefore, the rapid identification of RNA-protein binding sites is crucial for functional annotation...
RNA Neural Networks, Computer Algorithms Binding Sites Computational Biology RNA-Binding Proteins
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SOFB is a comprehensive ensemble deep learning approach for elucidating and characterizing protein-nucleic-acid-binding residues.

Communications biology Jun 3, 2024
Proteins and nucleic-acids are essential components of living organisms that interact in critical cellular processes. Accurate prediction of nucleic acid-binding residues in proteins can contribute to a better understanding of protein function. Howev...
Deep Learning Protein Binding Computational Biology Binding Sites Proteins Nucleic Acids
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Geometry Optimization Algorithms in Conjunction with the Machine Learning Potential ANI-2x Facilitate the Structure-Based Virtual Screening and Binding Mode Prediction.

Biomolecules May 31, 2024
Structure-based virtual screening utilizes molecular docking to explore and analyze ligand-macromolecule interactions, crucial for identifying and developing potential drug candidates. Although there is availability of several widely used docking pro...
Binding Sites Molecular Docking Simulation Machine Learning Protein Binding Algorithms Ligands
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