In the last decade, deep learning has led to unprecedented improvements in performance of methods tackling a broad spectrum of problems, ranging from learning protein sequence embeddings for contact map prediction35to predicting protein structure36,37and function38. In particular, convolutional neural net...
In particular, the technology disclosed relates to specifying a particular amino acid at a particular position in a protein as a gap amino acid, and specifying remaining amino acids at remaining positions in the protein as non-gap amino acids. The technology disclosed further relates to generating...
Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents. A variety of computational approaches have been developed for predicting a protein’s interfaci...
1.96 Å). The structure of A310W variant was obtained from the wild-type AmAT7-3. Ac-CoA was docked into both structures in the same manner as with the wild-type protein. MD simulations showed that the substrate binding
The PUXANO technology platforms aim to accelerate structure-based protein research, from sequence to structure
Secondary structure-based protein topologies are represented uniquely as undirected labeled graphs in four different ways allowing for exploration under different aspects. The linear notations, and the 2D and 3D diagrams of each notation facilitate a deeper understanding of protein topologies. Several ...
There are many components which govern the function of a protein within a cell. Here, we focus on the molecular recognition of small molecules and the prediction of common recognition by similarity between protein-ligand binding sites. SitesBase is an easily accessible database which is simple to...
Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Theref
论文地址: Enhancing Protein Language Models with Structure-based Encoder and Pre-training 看完GearNet再看这篇文章,其实就是加了一个语言模型在结构编码器前面,并且做预训练的时候fix语言模型。 GearNet记录:nlinp:《Protein Representation Learning by Geometric Structure Pretraining》阅读记录 摘要 蛋白质语言模...
这个作业将花费大约一分钟的时间,并将在您的工作目录中写入一个名为“glide-grid_1fjs”的文件夹。 4. Docking the Cognate Ligand with Hydrogen-Bond Constraint 运行Glide虚拟筛选所需的最低要求是一个网格文件和一个配体文件。强烈建议使用蛋白质准备工作流程(Protein Preparation Workflow)生成网格文件,并使用LigPr...