Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Coreceptor usage prediction software tools | Protein sequence analysis

A coreceptor is a cell surface receptor that binds a signalling molecule in addition to a primary receptor in order to facilitate ligand recognition and initiate biological processes, such as entry of a pathogen into a host cell. Currently, the two…
AUTO–MUTE
Desktop
Web
CRUSH
Web

CRUSH CoReceptor USage prediction for HIV-1

An SVM model for the prediction of HIV-1 coreceptor usage based on the amino…

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. CRUSH utilizes inter-residue interaction energies derived…

CM Classifier
Web

CM Classifier

A web server for HIV coreceptor tropism determination. CM Classifier is…

A web server for HIV coreceptor tropism determination. CM Classifier is composed of two coreceptor-specific weight matrices (CMs) based on a full-scale dataset. Our classifier outperformed all other…

G T A T C G C T A
gCUP
Desktop

gCUP

A computional coreceptor usage prediction model. gCUP is based on our recently…

A computional coreceptor usage prediction model. gCUP is based on our recently developed method T-CUP, but was redeveloped, parallelized and optimized for the use on graphics processing units (GPUs).…

Geno2pheno
Web

Geno2pheno

A tool for predicting HIV-1 coreceptor usage from the V3 region of the HIV…

A tool for predicting HIV-1 coreceptor usage from the V3 region of the HIV envelope protein gp120. Geno2pheno analyzes the NGS data in a elaborate fashion and performs better than existing methods…

IDEPI
Desktop

IDEPI IDentify EPItopes

A software package for learning genotype-to-phenotype predictive models from…

A software package for learning genotype-to-phenotype predictive models from sequences with known phenotypes.

T-CUP
Desktop

T-CUP

A model for predicting co-receptor tropism. T-CUP 2.0 is based on our recently…

A model for predicting co-receptor tropism. T-CUP 2.0 is based on our recently published T-CUP model. T-CUP 2.0 models co-receptor tropism using information of the electrostatic potential and…

Segminator
Desktop

Segminator

Permits management and downstream analysis of pathogen sequence data.…

Permits management and downstream analysis of pathogen sequence data. Segminator quantifies the effects of divergence on the mapping of reads to a template sequence. It employs joint nucleotide…

PhenoSeq
Web

PhenoSeq

A suite of highly accurate in silico tests for all of the major HIV subtypes,…

A suite of highly accurate in silico tests for all of the major HIV subtypes, namely subtypes A, B, C, D, CRF01_AE and CRF02_AG, which together account for 95% of HIV-1 infections worldwide. PhenoSeq…

HIV-1…
Web

HIV-1 coreceptor usage prediction without sequence alignments

A string kernel (the distant segments kernel), a SVM predictor for HIV-1…

A string kernel (the distant segments kernel), a SVM predictor for HIV-1 coreceptor usage with the identification of the most relevant features and state-of-the-art results on accuracy, specificity,…

HIVcoPRED
Desktop
Web

HIVcoPRED

A web server developed for predicting the coreceptor usage by HIV-1. It takes…

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.…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.