AIMC Topic: Viral Proteins
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Current status and future perspectives of computational studies on human-virus protein-protein interactions.
Briefings in bioinformatics
Sep 2, 2021
The protein-protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human-virus PPIs can help us understand the principles of human-virus relationships and can thus guide the ...
DeepHPV: a deep learning model to predict human papillomavirus integration sites.
Briefings in bioinformatics
Jul 20, 2021
Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integr...
ModFOLD8: accurate global and local quality estimates for 3D protein models.
Nucleic acids research
Jul 2, 2021
Methods for estimating the quality of 3D models of proteins are vital tools for driving the acceptance and utility of predicted tertiary structures by the wider bioscience community. Here we describe the significant major updates to ModFOLD, which ha...
DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes.
Proceedings of the National Academy of Sciences of the United States of America
Jan 12, 2021
Information about macromolecular structure of protein complexes and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully aut...
UniProt: the universal protein knowledgebase in 2021.
Nucleic acids research
Jan 8, 2021
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over ...
Machine Learning Methods for Predicting Human-Adaptive Influenza A Viruses Based on Viral Nucleotide Compositions.
Molecular biology and evolution
Apr 1, 2020
Each influenza pandemic was caused at least partly by avian- and/or swine-origin influenza A viruses (IAVs). The timing of and the potential IAVs involved in the next pandemic are currently unpredictable. We aim to build machine learning (ML) models ...
Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks.
Journal of bioinformatics and computational biology
Feb 1, 2020
Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics due to rapid viral evolution. Vaccines are used to prevent influenza infections but the composition of the influenza vaccines have to be upd...
MSLVP: prediction of multiple subcellular localization of viral proteins using a support vector machine.
Molecular bioSystems
Jul 19, 2016
Knowledge of the subcellular location (SCL) of viral proteins in the host cell is important for understanding their function in depth. Therefore, we have developed "MSLVP", a two-tier prediction algorithm for predicting multiple SCLs of viral protein...
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