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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Conserved Binding Sites01:49

Conserved Binding Sites

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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

11.7K
The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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CoBRA: RNA言語モデルを用いた化合物結合部位予測

Wonkyeong Jang1, Woong-Hee Shin1,2

  • 1Department of Biomedical Informatics, Korea University College of Medicine, 161 Jeongneung-ro, Seongbuk-gu, Seoul 02708, Republic of Korea.

Briefings in bioinformatics
|January 11, 2026
PubMed
まとめ
この要約は機械生成です。

新しい深層学習ツールであるRNA（CoBRA）の化合物結合部位予測は、配列データのみを使用してRNA-薬物相互作用を正確に予測します。この手法は構造ベースのアプローチを上回り、新規RNA標的治療薬を発見するための柔軟な方法を提供します。

キーワード:
RNA言語モデルRNA-低分子結合部位予測畳み込みニューラルネットワーク深層学習事前学習済み埋め込み

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

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関連する実験動画

Last Updated: Jan 13, 2026

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions

Published on: September 28, 2017

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科学分野:

  • 生化学
  • 計算生物学
  • 創薬

背景:

  • リボ核酸（RNA）は、細胞機能において重要な役割を果たし、数多くのヒト疾患に関与しています。
  • タンパク質の druggability が限られているため、低分子でRNAを標的とすることは、有望な治療戦略を提示します。

研究 の 目的:

  • RNA分子上の低分子結合部位の正確な予測のための計算ツールの開発。
  • 結合部位予測におけるRNA言語モデルを利用した深層学習アプローチの有効性の評価。

主な方法:

  • CoBRA（Compound Binding Site Prediction for RNA）の導入。これは軽量な深層学習プログラムです。
  • 構造情報を必要とせずに、事前学習済みRNA言語モデルからの残基レベルの埋め込みを利用しました。
  • ニューロンネットワーク分類器を使用して、ヌクレオチド結合部位の二項分類を行いました。

主要な成果:

  • CoBRAは、既存の手法と比較して、Matthew相関係数で22.1%、感度で45.6%の相対的な改善を達成しました。
  • 配列ベースの言語モデル埋め込みは、構造ベースの予測手法に匹敵するか、それを超えるパフォーマンスを示しました。
  • このモデルはTR60およびHARIBOSSデータセットでトレーニングされ、4つの独立したベンチマークセットで検証されました。

結論:

  • CoBRAは、構造データを必要とせずにRNA-薬物結合部位を予測するための柔軟で効果的なツールを提供します。
  • この配列ベースのアプローチは、RNA標的治療薬の開発を進歩させます。
  • この発見は、RNA-リガンド相互作用の理解における言語モデルの可能性を強調しています。