Thus, over the past two decades, a number of protein domain identification approaches have been developed, and a variety of protein domain databases have also been constructed. This review divides protein domain prediction methods into two categories, namely sequence-based and structure-based. These ...
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...
Overview WoLF PSORT is an extension of the PSORT II program for protein subcellular localization prediction, which is based on the PSORT principle. WoLF PSORT converts a protein's amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functiona...
To date, there have been a plethora of works that employed traditional machine learning (ML) techniques to solve several problems in the computational biology domain, such as protein classification, structure prediction, protein interaction prediction, etc. Support vector machines (SVMs), Random forest...
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 ...
A protein function prediction tool that takes only the sequences as input About S2F S2F brings the power of label propagation in biological networks for prediciting protein function for newly sequenced organisms. You can read more about S2F in the project'swebsite. ...
To meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools. These tools include secondary structure prediction, solvent accessibility prediction, disorder region prediction, domain boundary prediction, contact map pre...
In addition to commonly used baselines in the automatic function prediction tasks, we also considered machine learning methods that had an open-source implementation that we could train from scratch on our dataset. BLAST—basic local alignment search tool This method transfers annotations from sequence...
2 and 3). Therefore, the WSME-L model quantitatively improves the prediction accuracy of the folding mechanisms of small proteins compared with the original WSME models. Folding of large multidomain proteins Next, to test whether the WSME-L model (Fig. 1e) can predict the folding mechanisms ...
FunFams is a domain-based approach that leverages CATH super-families to transfer function annotation from a protein to another40. Given a protein, its sequence is searched against the CATH using the HMMER tool57, and its function annotation (EC numbers and GO terms) is copied from the FunFa...