相关实验视频

Updated: Jul 13, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

基于结构的虚拟选机器学习评分的实用指南

Viet-Khoa Tran-Nguyen¹, Muhammad Junaid¹, Saw Simeon¹

¹Centre de Recherche en Cancérologie de Marseille, Marseille, France.

Nature protocols

|October 16, 2023

概括

本研究介绍了一种用于构建和评估基于结构的虚拟选 (SBVS) 的特定目标机器学习评分函数 (SF) 的协议. 这种方法增强了对治疗点的活性分子的发现.

科学领域:

计算化学的计算化学
药物发现药物发现药物发现
生物信息学是一种生物信息学.

背景情况:

基于结构的虚拟查 (SBVS) 使用对接来识别治疗点的活性分子.
随着生物活性信息的大量化学和蛋白质数据集的可用性显著增加.
机器学习 (ML),包括深度学习,有效地利用这些数据集来开发SBVS的评分函数 (SF).

研究的目的:

为SBVS提供一个全面和用户友好的协议,用于构建和评估针对特定目标的基于ML的SF.
为增强SBVS性能提供关于数据增强,算法选择和SF优化的实际指导.
为了促进发现具有较高活动可能性的分子对特定目标的发现.

主要方法:

该协议涉及四个关键步骤:在公共基准上评估通用SF,准备特定目标的实验数据,为ML建模分区数据,并生成/评估特定目标的MLSF.
使用公共存储库来获取数据,并为ML建模准备培训和测试数据集.
使用可访问的软件 (Smina,CNN-Score,RF-Score-VS,DeepCoy) 和用于SF生成和评估的网络资源.

主要成果:

该协议使用三个示例目标来演示:乙胆化酶,HMG-CoA减少酶和过氧酶增殖器激活受体-α.
所有必要的代码和数据都是公开可用的,使得可复制性和应用.
该过程可以在一周内在一台计算机上执行,突出其效率.

结论:

针对特定目标的基于ML的SFs代表了SBVS的最先进的状态,通常表现优于通用方法.
提出的协议提供了通过增强训练数据和选择适当的ML算法来优化SBVS的实际指导.
该协议的成功实施可以显著提高发现新疗法剂的效率和成功率.

更多相关视频

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Published on: May 29, 2021

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

相关概念视频

Structure-Activity Relationships and Drug Design

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Viral Structure

Viral Structure

Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.