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Installing and executing ProtTest3 on Ubuntu

in Phylogenetics/Softwares/Tools by

Prottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criterions: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu. Continue reading “Installing and executing ProtTest3 on Ubuntu” »

Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions

in Docking/Softwares/Tools by

Molecular docking is the most widely used technique which is used to predict the binding affinities and bound conformations of a ligand and protein complex. Autodock Vina [1] is one of the most widely used docking software for structure-based drug designing.  Continue reading “Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions” »

How to blast against a particular set of local sequences (local database)?

in Softwares/Tools by

BLAST [1,2] is a local alignment tool widely used as a preliminary step for the identification of gene or protein functions. The command-line package of NCBI-Blast offers several useful features. These features include making a BLAST database of a set of nucleotide or protein sequences, blast a query sequence against them or all-against-all blast. In this article, these commands are explained.  Continue reading “How to blast against a particular set of local sequences (local database)?” »

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