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Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Updated: May 17, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

基准测试HelixFold3-预测全息结构的相对自由能量扰动计算.

Kairi Furui¹, Masahito Ohue¹

¹Department of Computer Science, School of Computing, Institute of Science Tokyo, Yokohama 226-8501, Japan.

|March 31, 2025

概括

此摘要是机器生成的。

HelixFold3准确地预测了蛋白质连接体复合体,表现优于AlphaFold2.2. 它的预测结构使可靠的自由能量扰动计算成为可能,与水晶结构相比,推动了药物发现.

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Published on: September 15, 2010

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

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Last Updated: May 17, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

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科学领域:

计算化学是一种计算化学.
结构生物学是结构生物学.
药物发现药物发现

背景情况:

自由能量扰动 (FEP) 的计算对于预测药物发现中的结合亲和关系至关重要.
准确的蛋白质 - 连接体复合结构对于FEP准确性至关重要.
虽然AlphaFold2是先进的,但它无法预测全息结构,这限制了它在基于结构的药物设计中的使用.

研究的目的:

为了评估HelixFold3在预测FEP计算中的蛋白质 - 配体复合物的性能.
将HelixFold3的准确性与AlphaFold2.2等现有方法进行比较.
评估HelixFold3预测结构在早期药物发现中的实用性.

主要方法:

HelixFold3被用来预测一个基准集的八个目标的蛋白质-连接体复合体.
结合点的形状被分析,以确定其准确性.
使用预测的Holo和Apo结构以及晶体结构进行了自由能量扰动计算.

主要成果:

与AlphaFold2.2.3相比,HelixFold3在预测结合部位形状方面表现优越,与AlphaFold2.3相比,它在预测结合部位形状方面表现优越.
预测的全息结构显示了比apo结构更高的结合点准确度.
使用HelixFold3预测结构的FEP计算实现了与水晶结构相美的精度.
HelixFold3成功预测了新型联体的结构,保持了FEP的准确性.

结论:

HelixFold3准确地预测了蛋白质-连接体复杂结构,包括全息形状.
在FEP计算中,HelixFold3预测的结构可以作为晶体结构的有效替代品.
这一进步支持在早期药物发现中应用基于结构的药物设计.