TY - JOUR T1 - Prediction of Co-Receptor Usage of HIV-1 from Genotype A1 - Dybowski, J. Nikolaj A1 - Heider, Dominik A1 - Hoffmann, Daniel Y1 - 2010/04/15 N2 - Author Summary Human Immunodeficiency Virus is the pathogen causing the disease AIDS. A precondition for virus entry into human cells is the contact of its glycoprotein gp120 with two cellular proteins, a receptor and a co-receptor. Depending on the viral strain, one specific co-receptor is used. The type of co-receptor used is crucial for the aggressiveness of the viral strain and the available treatment options. Hence, it is important to identify which co-receptor is used by the virus in an individual patient. Since the genome of the virus in the patient can be readily sequenced, and thus the composition of the viral proteins be determined, it could be possible to predict co-receptor usage from the viral genome sequences. To this end, we developed a method that is motivated by the insight that physical properties of gp120 will determine its specificity for a co-receptor. The method learns a computational model from structures and sequences of a crucial part of gp120, and the corresponding experimentally measured co-receptor usage. It then employs the model to predict co-receptor usage for new sequences. The high accuracy of the method could make it helpful for diagnosis and suggests that the model captures the determinants of co-receptor usage. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 6 IS - 4 UR - https://doi.org/10.1371/journal.pcbi.1000743 SP - e1000743 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000743 ER -