Computer-aided Drug Discovery

4. 计算机辅助药物发现

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Receptor-based
Drug Discovery
从受体结构出发的药物发现
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Ligand-based
Drug Discovery
以配体为基础的药物发现
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Molecular Dynamics Simulations
分子动力学模拟
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I. Structure-based Drug Discovery

以受体结构为基础的药物发现

通过分析靶标受体的三维结构,结合分子模拟和虚拟筛选技术,为客户设计和优化候选药物分子。SBDD 利用结构信息高效筛选出与受体结合力强的分子,并通过自由能微扰(FEP)和分子力学泊松-玻尔兹曼表面积(MMPBSA)等方法预测亲和力,从而优化分子活性和成药性。这种方法广泛应用于蛋白酶、G 蛋白偶联受体(GPCR)和离子通道等靶标的药物研发,为客户的靶向治疗项目提供强有力的支持。

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Through analysis of the three-dimensional structure of target receptors, combined with molecular simulation and virtual screening technologies, we design and optimize candidate drug molecules for clients. RBDD efficiently screens molecules with strong receptor binding affinity using structural information, and predicts binding affinity through methods such as free energy perturbation (FEP) and molecular mechanics Poisson-Boltzmann surface area (MMPBSA), thereby optimizing molecular activity and druggability. This method is widely applied in drug development for targets such as proteases, G protein-coupled receptors (GPCRs), and ion channels, providing powerful support for clients' targeted therapy projects.

3D Structures

The 3D structure can be obtained from the Protein Data Bank (PDB). For novel proteins not in the database, we offer protein structure elucidation services to determine structures at atomic resolution.

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Molecular Docking

We offer high-throughput virtual screening services to identify promising drug candidates. Our comprehensive in silico analysis encompass binding affinity predictions and detailed molecular interaction assessments.

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II. Ligand-based Drug Discovery

以配体为基础的药物发现

我们的药物设计服务采用药效团建模和定量构效关系(QSAR)技术。我们通过相似性搜索进行高效筛选,将分子描述符与机器学习模型相结合,并加强分子活性和成药性评估,从而优化候选药物分子。

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Our drug design services employ Pharmacophore Modeling and Quantitative Structure-Activity Relationship (QSAR) techniques. We optimize candidate drug molecules through efficient screening via Similarity Search, integration of molecular descriptors with machine learning models, and enhanced molecular activity and druggability assessment.

III. Molecular Dynamics (MD) Simulation

分子动力学模拟

生物分子动力学模拟用于研究分子系统随时间的演化。基于经典力学原理,MD模拟通过初始化、力场选择、能量最小化、平衡和生产模拟等步骤,精确地模拟蛋白质、核酸等生物大分子的动态过程。

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MD simulations accurately model the dynamic processes of biological macromolecules—such as proteins and nucleic acids—through steps including initialization, force field selection, energy minimization, equilibration, and reaction simulation.

Key Advantages of MD Simulation 技术优势

分子动力学(MD)能揭示了在实验环境中通常难以观察到的相互作用和运动,分析了极短时间尺度内的生物分子过程,加深了我们对分子结构、动力学和功能之间复杂关系的理解,并通过提供详细的原子级洞察来增强实验技术。这些能力使MD模拟成为生物物理学、生物化学和相关领域研究人员不可或缺的工具。它提供了对生物系统在原子水平上动态行为的独特视角,为分子相互作用提供了一个通过其他方法难以实现的窗口。
MD simulation is a powerful computational tool for studying molecular behavior. It reveals interactions and movements often hidden in experiments, analyzes biomolecular processes at ultra-short timescales, enhances our understanding of molecular structure-function relationships, and complements experimental techniques with atomic-level details. These features make MD simulation essential for biophysics and biochemistry research, offering unique insights into biological systems' dynamic behavior at the atomic level.
  • 结构分析和优化:评估和提高实验确定或计算机建模结构的精确度。Evaluating and enhancing the precision of experimentally determined or computationally modeled structures.

  • 制药研究与开发:支持基于结构和基于配体的药物设计,包括虚拟筛选和结合亲和力估算。Supporting structure-based and ligand-based drug design, including virtual screening and binding affinity estimations.

  • 膜转运分析:研究分子穿过生物膜的运动。Investigating the movement of molecules across biological membranes.

  • 生物分子相互作用研究:仔细研究蛋白质-蛋白质、蛋白质-配体和蛋白质-核酸相互作用。Scrutinizing protein-protein, protein-ligand, and protein-nucleic acid interactions.

  • 蛋白质动力学研究:检查蛋白质内部的灵活性、构象变化和变构机制。Examining flexibility, conformational changes, and allosteric mechanisms within proteins.

  • 蛋白质折叠研究:探索蛋白质折叠过程中涉及的复杂机制和途径。Exploring the intricate mechanisms involved in protein folding processes.

  • 酶催化研究:深入研究酶反应中的反应机制和过渡态。Delving into reaction mechanisms and transition states in enzymatic reactions.

  • 材料科学研究:在分子水平上检查各种材料的性质。Examining the properties of various materials at the molecular level.

  • 微信号 / wechat ID: shangjinbiomedical
  • E-mail: consultants@shangjin-biomedical.com
  • Address: 5/F, Block 1, Hang Tai Yue South China Medical Valley Industrial Park, Guangming District, Shenzhen, China
  • 地    址: 深圳市光明区华南医谷恒泰裕大厦一栋五楼
微信 / Wechat ID
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E-mail
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Address
5/F, Block 1, Hang Tai Yue South China Medical Valley Industrial Park, Guangming District, Shenzhen, China

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