DREAMweb:一种在线工具,用于基于图形的NMR蛋白质结构建模
Niladri Ranajan Das1, Kunal Narayan Chaudhury2, Debnath Pal3
1IISc Mathematics Initiative, Indian Institute of Science, Bangalore, Karnataka, India.
Proteomics
|April 17, 2024
概括
改进的DREAMv2算法通过减少工件和提高二次结构精度来增强蛋白质结构建模. 这种方法有效地处理稀疏的实验数据,有利于基于NMR的工作流.
科学领域:
- 生物物理学的生物物理.
- 计算生物学 计算生物学
- 结构生物学 结构生物学
背景情况:
- 准确的蛋白质结构模型对于理解生物功能至关重要.
- 现有的算法可能会产生文物或与稀疏的实验数据作斗争.
- 距离几何问题 (DGP) 是蛋白质结构决定的核心.
研究的目的:
- 介绍DREAMv2,一种用于蛋白质结构建模的增强算法.
- 为了提高准确性,减少人工物,并提高蛋白质模型中的二级结构一致性.
- 为蛋白质结构确定提供一个高效的网络资源 (DREAMweb).
主要方法:
- DREAMv2 在优化约束集中包含了一个更紧密的边界.
- 采用自下而上的策略,建立和巩固较小的基础结构.
- 模型区域与稀疏的实验数据高效地,减少文物.
- 在特定条件下通过解决较小的子结构 (原子) 来平衡性能和准确性.
主要成果:
- 与DREAM相比,DREAMv2显著减少了蛋白质结构建模中的工件.
- 实现了与实验数据相一致的改进的二次结构合规性.
- 在10个结构上的基准证明了该方法的有效性.
- 有效地模拟具有稀疏实验数据的区域.
结论:
- DREAMv2为蛋白质结构建模提供了更准确,更可靠的方法.
- DREAMweb资源使用NMR数据促进了蛋白质结构的确定.
- DREAMv2与各种基于NMR的蛋白质结构确定工作流程兼容,包括具有不完整或模两可的赋值的代方法.
相关概念视频
02:00Molecular Models
38.3K
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.
38.3K
01:12Two-Dimensional (2D) NMR: Overview
666
The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse....
666
02:06Newman Projections
16.8K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
16.8K
01:25Applications Of NMR In Biology
3.7K
Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
3.7K
01:20NMR Spectrometers: Overview
1.1K
NMR spectrometers consist of a strong magnet, a radiofrequency transmitter, and a detector attached to a computer console for recording spectra of samples containing NMR-active nuclei. In first-generation NMR instruments called continuous-wave spectrometers, the resonance frequencies of the nuclei are determined by frequency-sweep or field-sweep methods. The magnetic field strength is fixed and the rf signal is swept in the former, while the radiofrequency signal is fixed and the magnetic field...
1.1K
02:15Protein and Protein Structures
10.4K
10.4K