domain linker prediction assessmentDomNet approachinter‐domain linker predictionprotein structuresimulated annealingThe accurate and stable prediction of protein domains is an important stage for the prediction of protein structure, function, evolution, and design. Predicting inter-domain linkers is very ...
DOMpro also achieved a sensitivity and specificity of 71% and 71% respectively in the Critical Assessment of Fully Automated Structure Prediction 4 (CAFASP-4) (Fisher et al., 1999 ; Saini and Fischer, 2005 ) and was ranked among the top ab initio domain predictors. The DOMpro server, ...
This review divides protein domain prediction methods into two categories, namely sequence-based and structure-based. These methods are introduced in detail, and their advantages and limitations are compared. Furthermore, this review also provides a comprehensive overview of popular online protein domain...
Annotation-guided Protein Design with Multi-Level Domain Alignment Chaohao Yuan, Songyou Li, Geyan Ye, Yikun Zhang, Long-Kai Huang, Wenbing Huang, Wei Liu, Jianhua Yao, Yu Rong arXiv:2404.16866 Open-Source Protein Language Models for Function Prediction and Protein Design Shivasankaran Vanaja ...
We call the prediction algorithm based on this new definition as DSCP (Domain combination Similarity in context of protein complexes). The following pseudo code illustrates the procedure of calculating the functional similarity by using algorithm DSCP. Protein function prediction Given the protein ...
Enhancing protein stability prediction with geometric learning and pre-training strategies A recent study introduces a series of approaches that predict protein fitness and stability after the introduction of mutations. The work focuses on combining different data and pre-training to overcome data scarcity...
Yao, S. et al. NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information.Nucleic Acids Res.49, W469–W475 (2021). ArticleCASPubMed Krissinel, E. On the relationship between sequence and structure similarities in proteomics...
GlobPlot is less accurate than DisEMBL in coils prediction; however, it was designed as a visual inspection tool for finding both domain boundaries, repeats and unstructured regions. Furthermore, the GlobPlot algorithm is very simple and intuitive, which might appeal to some users. The web ...
Domain-PFP allows protein function prediction using function-aware domain embedding representations Nabil Ibtehaz Yuki Kagaya Daisuke Kihara Communications Biology (2023) Combining views for newly sequenced organisms Yingying Zhang Shayne D. Wierbowski Haiyuan Yu Nature Machine Intelligence (2021)Associa...
We call the prediction algorithm based on this new definition as DSCP (Domain combination Similarity in context of protein complexes). The following pseudo code illustrates the procedure of calculating the functional similarity by using algorithm DSCP. Protein function prediction Given the protein ...