Biomedical subjects

Jinbo Xu

Publications and source records attributed to Jinbo Xu.

3 recordsLinked to original sources

PubMed2003

Assessment of RAPTOR's linear programming approach in CAFASP3.

We have developed a new algorithm based on the mathematical theory of linear programming (LP) and implemented it in our program RAPTOR. Our new approach provides an elegant formulation of the protein-threading problem, overcomes the intractability problem of protein threading, in practice, and allows us to use existing powerful linear programming software to obtain optimal protein threading solutions. CASP5 and CAFASP3 gave us the first chance to test RAPTOR in an unbiased way. RAPTOR was ranked as the top individual (automatic) server for fold recognition by the CAFASP3 organizers. In this short article, we describe RAPTOR's LP formulation, assess RAPTOR's performance in CAFASP3/CASP5, explain why it has superceded other existing automatic individual methods, and point out its strengths, limitations, extensions, and prospects for improvement.

Algorithms↗

PubMed2003

Protein threading by linear programming.

Protein three-dimensional structure prediction through threading approach has been extensively studied and various models and algorithms have been proposed. In order to further explore ways to improve accuracy and efficiency of the threading process, this paper investigates the effectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure, we formulate the protein threading problem as a large scale integer programming problem, then relax to a linear programming problem, and finally solve the integer program by a branch-and-bound method. The final solution is optimal with respect to energy functions incorporating pairwise interaction and allowing variable gaps. The algorithm has been implemented as software package RAPTOR--RApid Protein Threading predictOR. Experimental results for fold recognition show that RAPTOR significantly outperforms other programs at the fold similarity level. The RAPTOR webserver is at http://www.cs.uwaterloo.ca/-j3xu/RAPTOR_form.htm.

Algorithms↗

PubMed2002

An anti-CD45RO immunotoxin kills latently infected human immunodeficiency virus (HIV) CD4 T cells in the blood of HIV-positive persons.

Highly active antiretroviral therapy has decreased the morbidity and mortality of human immunodeficiency virus (HIV) infection, but latently infected cells remain for prolonged periods. CD4(+) CD45RO(+) T cells are a major latent virus reservoir in HIV-infected persons. Replication-competent, latently HIV-infected T cells can be generated in vitro by infecting peripheral blood mononuclear cells with HIV and then eliminating the HIV-producing cells with an anti-CD25 immunotoxin (IT). The CD25(-) latently infected cells then can be eliminated with an anti-CD45RO IT. This study determined whether this IT also could kill latently infected CD4 T cells from HIV-infected persons with or without detectable plasma viremia. The results show that ex vivo treatment of cells from HIV-positive persons by anti-CD45RO IT reduces the frequency of both productively and latently infected cells. In contrast, CD4(+) CD45RA(+) naive T cells and a proportion of CD4(+) CD45RO(lo) memory T cells are spared.

Antiretroviral Therapy, Highly Active↗