Active site prediction of phosphorylated SARS-CoV-2 N-Protein using molecular simulationCovid-19Machine learningMolecular simulationN-ProteinThe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) nucleocapsid protein (N-protein) is responsible for viral replication by assisting in viral RNA ...
There exist many tools for computing both sequence-based and structure-based features for proteins. Previous research by Jones and Thornton [55] into identifying important features for PPI site prediction has revealed solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion, ...
For instance, a protein might have more than one active or functionally relevant sites. The activation score does not allow to discern active site a given residue is part of. We anticipate that evolutionary information will enable statistics-informed learning approaches to effectively characterize ...
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...
NRTIs are chemical analogs of the natural nucleoside substrates of the HIV RT that bind to the protein active site and block its activity in synthesizing DNA from viral RNA. The inhibitors in the NNRTI class also decrease the enzymatic activities of RT, however, they bind in an allosteric ...
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics) - kexinhuang12345/DeepPurpose
Method development for RBP binding-site prediction is an active area of research in the domain of computational RNA biology and an abundance of RBP binding-site prediction methods have been developed in recent years [8, 9, 10]. Development of new methods further accelerated with the advent of ...
(that is, cosine similarities of a protein’s representations across cell type contexts) based on the number of cell types in which the protein is active (Extended Data Fig.5a,b). Representational similarities of proteins negatively correlate with the number of cell types in which they act (...
In the third experiment we study the impact of using bidirectional constraints between pairs of levels; the level not appearing in the rules is predicted independently, as above. In theP⇔Dcase, both theP→DandD→Prules are active, meaning that the protein and domain levels are enforced to ...
Adhikari UK, Tayebi M, Rahman MM (2018) Immunoinformatics approach for epitope-based peptide vaccine design and active site prediction against polyprotein of emerging oropouche virus. J Immunol Res 2018:6718083. https://doi.org/10.1155/2018/6718083 Article CAS PubMed PubMed Central Google Scholar...