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相关概念视频

Protein Organization01:24

Protein Organization

6.5K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Gene Families01:57

Gene Families

8.8K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
15.4K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
43.7K
Directing Proteins to the Rough Endoplasmic Reticulum01:34

Directing Proteins to the Rough Endoplasmic Reticulum

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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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Tail-anchoring of Proteins in the ER Membrane01:45

Tail-anchoring of Proteins in the ER Membrane

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Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
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相关实验视频

Updated: Jul 8, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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重新调整PDB的时间.

Florian Flachsenberg1, Christiane Ehrt1, Torben Gutermuth1

  • 1Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany.

Journal of chemical information and modeling
|December 18, 2023
PubMed
概括
此摘要是机器生成的。

我们开发了JAMDA,一个用于药物设计中的分子对接的自动化工作流. 它在高质量的蛋白质结构上取得了61.8%的成功率,与AutoDock Vina.相比.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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相关实验视频

Last Updated: Jul 8, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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科学领域:

  • 计算化学是一种计算化学.
  • 结构生物学是结构生物学.
  • 药物发现 药物发现

背景情况:

  • 分子对接对于基于结构的药物设计 (SBDD) 是至关重要的.
  • 当前的对接方法通常需要多种工具和手动干预.
  • 自动化对接过程可以提高效率并减少偏差.

研究的目的:

  • 介绍JAMDA (JACS分子对接分析) 预处理和对接工作流程.
  • 评估JAMDA的业绩,并确定影响其成功的因素.
  • 为了提供一个现实的估计自动化重制性能.

主要方法:

  • 开发了一个完全自动化的预处理和对接工作流程 (JAMDA).
  • 从蛋白质数据库 (PDB) 中对绑定站点进行了JAMDA评估.
  • 应用客观结构质量过器来创建PDBScan22-HQ数据集.

主要成果:

  • 在PDBScan22数据集中,30.1%的结构中,JAMDA在2年RMSD内获得了排名第一的位置.
  • 对于质量过的PDBScan22-HQ数据集,成功率增加到61.8%.
  • 在过的数据集上,JAMDA的性能与AutoDock Vina相当.

结论:

  • JAMDA 工作流提供了一个易于使用,完全自动化的分子对接解决方案.
  • 自动化预处理和质量过显著提高了对接成功率.
  • JAMDA为基于结构的药物设计提供了可靠和高效的工具.