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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
使用模拟模式移动的蒙特卡洛模拟来快速预测蛋白质结构
Paolo Carnevali1, Gergely Tóth, Garrick Toubassi
1Protein Mechanics Inc., 280 Hope Street, Mountain View, CA 94041, USA. PCarnevali@ProteinMechanics.com
Journal of the American Chemical Society
|November 20, 2003
概括
模式蒙特卡洛模拟有效地预测小蛋白质结构. 与传统技术相比,这种方法显著减少了初始蛋白质结构预测的计算时间.
科学领域:
- 计算生物学 计算生物学
- 生物物理学的生物物理.
- 结构生物学 结构生物学
背景情况:
- 正常模式是分子模拟中生成扭力空间移动的强大工具.
- 尽管它们具有潜力,但基于正常模式的方法尚未被广泛采用用于和蛋白质模拟.
研究的目的:
- 为了证明模态蒙特卡洛方法对初始蛋白质结构预测的效率.
- 应用模态蒙特卡洛模型来预测Trp子的结构,一个小的,快速折叠的多.
主要方法:
- 利用正常模式在蒙特卡洛模拟中产生扭矩空间移动.
- 将模态蒙特卡洛方法应用于20个残留聚 (Trp).
主要成果:
- 实现了Trp子的高质量的初始结构预测.
- 证明Modal Monte Carlo比标准的分子动力学技术在计算上显著更高效,将计算时间缩短了大约两个数量级.
结论:
- 模式蒙特卡洛是一个有效和强大的工具,用于初始预测小蛋白质结构.
- 这种方法比现有的蛋白质结构预测方法提供了实质性的计算优势.
相关概念视频
Molecular Models
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Protein Dynamics in Living Cells
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

