Related Experiment Video
Updated: Apr 19, 2026

Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
Published on: December 21, 2019
State of the art prediction of HIV-1 protease cleavage sites
Thorsteinn Rögnvaldsson1, Liwen You1, Daniel Garwicz1
1CAISR, School of Information Science, Computer and Electrical Engineering, Halmstad University, Halmstad, Sweden and Division of Clinical Chemistry and Pharmacology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
Motivation:
Understanding the substrate specificity of human immunodeficiency virus (HIV)-1 protease is important when designing effective HIV-1 protease inhibitors. Furthermore, characterizing and predicting the cleavage profile of HIV-1 protease is essential to generate and test hypotheses of how HIV-1 affects proteins of the human host. Currently available tools for predicting cleavage by HIV-1 protease can be improved.
Results:
The linear support vector machine with orthogonal encoding is shown to be the best predictor for HIV-1 protease cleavage. It is considerably better than current publicly available predictor services. It is also found that schemes using physicochemical properties do not improve over the standard orthogonal encoding scheme. Some issues with the currently available data are discussed.
Availability And Implementation:
The datasets used, which are the most important part, are available at the UCI Machine Learning Repository. The tools used are all standard and easily available.
Contact:
thorsteinn.rognvaldsson@hh.se.
More Related Videos
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Predicting Reaction Outcomes
Protein-protein Interfaces
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

