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Benchmark databases for multiple sequence alignment: An overview

in Algorithms/Sequence Analysis/Softwares by

Multiple sequence alignment (MSA) is a very crucial step in most of the molecular analyses and evolutionary studies. Many MSA programs have been developed so far based on different approaches which attempt to provide optimal alignment with high accuracy. Basic algorithms employed to develop MSA programs include progressive algorithm [1], iterative-based [2], and consistency-based algorithm [3]. Some of the programs incorporate several other methods into the process of creating an optimal alignment such as M-COFFEE [4] and PCMA [5]. Continue reading “Benchmark databases for multiple sequence alignment: An overview” »

How to perform protein structure modeling using I-Tasser stand-alone tool?

in Softwares/Structural Bioinformatics/Structure Prediction/Tools by

I-Tasser stands for the iterative threading assembly refinement is a well-known tool for ab-initio structure modeling of proteins [1]. It uses secondary-structure enhanced profile-profile threading alignment (PPA) [2] and iterative structure assembly simulations using a threading assembly refinement program [3]. I-Tasser is used for ab-initio prediction when the similarity of a protein is quite low (<=30%). Mostly, the I-Tasser server [4] is used for this purpose, which can be easily accessed by registering with a valid institutional mail ID.  In this article, we will learn how to predict a protein structure using the I-Tasser standalone version. Continue reading “How to perform protein structure modeling using I-Tasser stand-alone tool?” »

Intrinsically disordered proteins’ predictors and databases: An overview

in Algorithms/Softwares/Tools by

Intrinsically unstructured proteins (IUPs) are the natively unfolded proteins which must be unfolded or disordered in order to perform their functions.  They are commonly referred to as intrinsically disordered proteins (IDPs) and play significant roles in regulating and signaling biological networks [1]. IDPs are also involved in the assembly of signaling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles [1]. The disordered regions in a protein can be highly conserved among the species in respect of both the composition and the sequence [2]. Continue reading “Intrinsically disordered proteins’ predictors and databases: An overview” »

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