DINC-ensemble:一个网络服务器,用于逐步将大型连接体对接到受体构造组合
Anja Conev1, Jing Chen2, Lydia E Kavraki1
1Computer Science Department, Rice University, 6100 Main Street, Houston 77005, TX, USA.
Journal of molecular biology
|April 23, 2025
概括
DINC-Ensemble通过模拟灵活的蛋白质 - 配体相互作用来增强药物发现. 它使用多个受体构造来预测最好的结合姿势,并识别连接体诱导的构造变化.
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:
- 蛋白质-连接体对接对于基于结构的药物发现至关重要,通过计算建模相互作用.
- 传统的对接方法假设受体灵活性有限,阻碍对灵活受体的准确预测.
- DINC (Docking INCrementally) 是大型带的元对接方法,但也假定受体灵活性有限.
研究的目的:
- 开发一种计算方法,以解释蛋白质-连接体对接中的受体骨干灵活性.
- 为了提高对接大型连接体到灵活的蛋白质结合点的准确性.
- 为了提供有关联体诱导的形状选择的见解.
主要方法:
- DINC-Ensemble在多个预定义的受体构造上并行运行DINC对接.
- 它需要一个连接体和一个受体构造列表作为输入.
- 对每个连接体-受体对进行增量元对接,生成多个姿势.
主要成果:
- DINC-Ensemble在不同的受体结构中产生多个连接体姿势.
- 姿势被排名,并选择了最佳得分姿势.
- 输出包括最好的连接体姿势和受体构造的排名列表.
结论:
- DINC-Ensemble隐性地模拟受体灵活性,以获得更准确的蛋白质-连接体对接.
- 该方法提供了对联结体-受体相互作用和联结体诱导的 conformational 选择的见解.
- DINC-Ensemble可以作为一个Python包和一个免费的Web服务器.
相关概念视频
Cooperative Allosteric Transitions
7.8K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
7.8K
Ligand Binding and Linkage
4.7K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.7K
Ligand Binding Sites
12.6K
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...
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...
12.6K
Drug-Receptor Interactions
4.7K
Drug-receptor interaction describes the binding of receptors by drugs, but not all drug-receptor interactions result in activation and tissue response. For instance, the binding of agonists activates the receptor to generate a cellular reaction, while antagonists bind to receptors without causing their activation.
Several parameters, such as the drug's affinity for its receptor and its efficacy, which is its ability to activate the receptor, determine the drug's effect on the tissue....
Several parameters, such as the drug's affinity for its receptor and its efficacy, which is its ability to activate the receptor, determine the drug's effect on the tissue....
4.7K
Receptor-mediated Endocytosis
103.4K
Overview
103.4K
GPCR Desensitization
5.6K
G protein-coupled receptor (GPCR) signaling plays a crucial role in cell functioning. GPCR desensitization is an equally essential process. It allows cells to respond to changing environments and regain sensitivity to new stimuli while preventing unnecessary stimulation when no longer needed. Prolonged exposure to stimuli leads to GPCR desensitization. It involves blocking the receptors from binding and activating additional G proteins. This inhibits activation of downstream effectors, thereby...
5.6K


