Tag: Coreceptor

CRUSH – CoReceptor USage prediction for HIV-1

CRUSH

:: DESCRIPTION

CRUSH is an SVM model for the prediction of HIV-1 coreceptor usage based on the amino acid sequence of the V3-loop of envelope glycoprotein gp120.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.
Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA.
PLoS One. 2016 Feb 9;11(2):e0148974. doi: 10.1371/journal.pone.0148974.

WebPSSM – Analyze V3 Loop Coreceptor Motifs

WebPSSM

:: DESCRIPTION

WebPSSM (position-specific scoring matrices ) is a bioinformatic tool for predicting HIV-1 coreceptor usage from amino acid or nucleotide sequences of the third variable loop (V3) of the envelope gene. When a nucleotide sequence is entered, it will be translated to amino acid sequence first. If a nucleotide sequence contains ambiguous bases, it will be translated to all possible amino acid sequences.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences.
Jensen MA, Li FS, van ‘t Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI.
J Virol. 2003 Dec;77(24):13376-88.

HIVcoPRED – Prediction of HIV Coreceptor Usage

HIVcoPRED

:: DESCRIPTION

HIVcoPRED is a web server developed for predicting the coreceptor usage by HIV-1. It takes amino acid sequences of Variable loop (V3) of gp120 protein of HIV and predicts the coreceptor used by the HIV strain.

::DEVELOPER

HIVcoPRED team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013 Apr 15;8(4):e61437. doi: 10.1371/journal.pone.0061437. Print 2013.
Hybrid approach for predicting coreceptor used by HIV-1 from its V3 loop amino acid sequence.
Kumar R1, Raghava GP.