MELD-Adapt:在整合性分子动力学中随时更新信念
Bhumika Singh1, Arup Mondal1, Kari Gaalswyk2
1Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611-7011, United States.
Journal of chemical theory and computation
|October 2, 2024
概括
MELD-Adapt动态评估生物分子建模的数据可靠性. 这种方法通过适应未知的数据准确性来改善结构预测,这在高分辨率数据不可用时至关重要.
科学领域:
- 整合性结构生物学 整合性结构生物学
- 计算生物物理学的计算生物物理.
- 结构生物信息学 结构生物信息学
背景情况:
- 准确的生物分子结构对于理解功能至关重要,特别是当高分辨率实验数据有限时.
- 整合各种实验数据与计算模型需要知道每个数据点的可靠性.
- 以前的方法,如采用有限数据建模 (MELD),需要对数据可靠性的初始估计,这些估计通常是未知的.
研究的目的:
- 引入MELD-Adapt,这是一个用于整合性结构生物学的新型计算方法.
- 在结构建模中实现输入数据可靠性的动态评估和推断.
- 确定与推断数据可靠性相兼容的最佳结构解释.
主要方法:
- 开发MELD-Adapt,一个计算框架,以适应方式评估数据可靠性.
- MELD-Adapt应用于蛋白质折叠和-蛋白质结合系统.
- 使用基准数据集进行测试,包括粗略的物理见解和化学转移扰动数据.
主要成果:
- MELD-Adapt成功地推断了数据的可靠性,并纠正了结构建模的初始假设.
- 该方法在不同的系统和数据类型中展示了稳定性,识别了可靠的结构模型.
- 分析表明,数据结构和最初的信念影响预测结果,突出了适应性方法的必要性.
结论:
- 通过适应未知的数据可靠性,MELD-Adapt为整合性结构生物学提供了一个强大的管道.
- 这种方法提高了生物分子结构预测在缺乏高分辨率数据的情况下的准确性.
- 数据满意度的差异有效地识别了低于最佳的建模设置,确保可靠的结构洞察力.
更多相关视频
05:00Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
Published on: August 9, 2024
1.2K
07:31Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
Published on: September 1, 2023
2.1K
相关概念视频
01:12Adaptability of Cytoskeletal Filaments
3.7K
The cytoskeleton is a complex dynamic structure performing varied functions based on cellular requirements. The adaptability of the individual filaments in the cytoskeleton determines their ability to perform various functions within the cell. It can undergo rapid reorganization during processes like cell division or remain stable for several hours as in the interphase. The adaptability of these filaments depends on stringent regulatory mechanisms. The microfilament and microtubules of the...
3.7K
00:53Olefin Metathesis Polymerization: Acyclic Diene Metathesis (ADMET)
1.9K
Acyclic diene metathesis polymerization or ADMET polymerization involves cross-metathesis of terminal dienes, such as 1,8-nonadiene, to give linear unsaturated polymer and ethylene. As ADMET is a reversible process, the formed ethylene gas must be removed from the reaction mixture to complete the polymerization process.
Similar to cross-metathesis, ADMET also involves the formation of metallacyclobutane intermediate by [2+2] cycloaddition of one of the double bonds of a terminal diene with...
Similar to cross-metathesis, ADMET also involves the formation of metallacyclobutane intermediate by [2+2] cycloaddition of one of the double bonds of a terminal diene with...
1.9K
02:18The Equilibrium Binding Constant and Binding Strength
12.8K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.8K
01:58Cooperative Allosteric Transitions
7.9K
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...
7.9K
01:17Intracellular Signaling Affects Focal Adhesions
2.6K
Integrins act both as extracellular input receivers and as intracellular processing activators. As their name suggests, integrins are entirely integrated into the membrane structure. Their hydrophobic membrane-spanning regions interact with the phospholipid bilayer's hydrophobic region. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors. They activate intracellular response cascades when their effectors are bound and active.
Some...
Some...
2.6K
01:15Activation of Integrins
3.3K
Integrins bind ligands and transmit information from outside the cell to inside or vice-versa through an "outside-in signaling" or "inside-out signaling."
In "outside-in signaling," external factors in the extracellular space bind to exposed ligand binding sites on integrins. This causes the inactive protein to undergo a conformational change to become active. Integrins are often clustered on the cell membrane. Repetitive and regularly spaced ligand binding...
In "outside-in signaling," external factors in the extracellular space bind to exposed ligand binding sites on integrins. This causes the inactive protein to undergo a conformational change to become active. Integrins are often clustered on the cell membrane. Repetitive and regularly spaced ligand binding...
3.3K