BioGem Blog

Homology or comparative protein structure modeling is a complex process, but with the help of tools like Modeller , it becomes more accessible and efficient. It's fascinating how the program can automatically calculate a model with all non-hydrogen atoms based on an alignment of a sequence to be modeled with known related structures. The input to Modeller are restraints on the spatial structure of the amino acid sequence(s) and ligands to be modeled, and the output is a 3D structure that satisfies these restraints as well as possible. It's amazing how the program can derive restraints from various sources such as related protein structures, NMR experiments, rules of secondary structure packing, cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, residue-residue and atom-atom potentials of mean force, and even intuition. The program can operate on various spatial features defined by atoms or pseudo at

BioEdit is a free biological sequence alignment editor. It has an intuitive multiple document interface and offers convenient features that make alignment and manipulation of sequences relatively easy on windows desktop computers. Additionally, there are several sequence manipulation and analysis options and links to external analysis programs that facilitate a working environment, allowing users to view and manipulate sequences with simple point-and-click operations. The BioEdit software provides automated local and web BLAST ( B asic L ocal A lignment S earch T ool) searches with a simple graphical user interface (GUI) to the command-line BLAST program. This is a simple video tutorial on how to construct a custom nucleotide/protein database using BioEdit software to support NCBI BLAST . The tutorial also covers how to perform a query search, specifically pairwise sequence alignment, against the database.

A phylogenetic tree ( a.k.a. , cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. Phylogenetic tree helps to find the common ancestor. The i nteractive T ree O f L ife ( iTOL ) is an online tool to display and manipulate phylogenetic trees. iTOL offers free access (limited access), standard subscription (unlimited access), and iTOL annotation editor subscription (unlimited and versatile access). It supports user-interactive customizable tree layouts, manual drawing, and annotation. iTOL can visualize trees with 50,000 or more nodes. This is a simple video tutorial for user interactive visualization of phylogenetic trees using the iTOL tool. The iTOL tool produces phylogenetic trees in various formats, such as rectangular, slanting, curved, radial, and curved. It accepts input in Newick, Nexus, or PhyloXML file format.

A phylogenetic tree ( a.k.a. , cladogram or dendrogram) is a diagrammatic/graphical representation of the genetical/evolutionary relationship of species/organisms/genes. It helps to find the common ancestor. Construction of a phylogenetic tree consists of two phases, multiple sequence alignment and computing distance matrix. This is a simple video tutorial for constructing a phylogenetic tree using Molecular Evolutionary Genetics Analysis ( MEGA ) software. The MEGA software produces phylogenetic trees from multiple sequences in various formats: rectangular, slanting, curved, radial, and curved.

Network marketing (a.k.a. direct selling) is a trending business model which replaces the traditional sales and advertising system. It relies on person-to-person sales (chain system) through work from home. Digital marketing (or online marketing) is a way to expand the marketing network through the internet and digital platforms such as PC/laptops and smartphones using digital media and platforms to promote the products. Social media applications place a significant role in sharing product or service details and communicating with persons. Many local and global network marketing companies are emerging rapidly. Some of the most popular network marketing firms are Altos, Amway, Asclepius Wellness, Atomy India, Avon, Biosash, Forever, Future Maker, Galway, Happy Health India, Herbalife India, Highrich, IMC, Indusviva, Keva Industries, Mary Kay, MI Lifestyle, Modicare, Naswiz Retails, Netsurf Network, OK Life Care, Oriflame, RCM, Renatus Wellness, Rodan+Fields, Safe Shop India, Tuppe

JME/JSME is a free and open-source molecule editor developed by Peter Ertl and Bruno Bienfait. JSME (JavaScript Molecule Editor) is the successor of JME (Java Molecule Editor). JME is a Java applet application converted to JavaScript due to security and portability issues in Java. JSME is a popular lightweight molecule editor application developed so far. Jmol/JSmol is a free and open-source molecule visualization tool developed by Bob Hanson . JSmol (JavaScript Molecule Viewer) is the successor of Jmol (Java Molecule Viewer). Jmol is a JAR (Java ARchive) application converted to JavaScript due to security and portability issues in Java. Jmol is the most popular molecule visualization tool implemented in many bioinformatics or cheminformatics web applications. JSmol in collaboration with JSME, has implemented a 2D ( SMILES string) to 3D structure conversion method by integrating the API of the CACTUS server. The link to an interactive demo of JSME and JSmol is here . B

This is a simple and valuable tip for YouTube video uploaders to share the internal and external URLs in the video description. While entering the URLs in the video description, we must type the whole URL. For example, https://www.biob.in ( Not www.biob.in or biob.in ). Moreover, for YouTube channel names/handles, it must be with full URL (including valid handle name prefix by @). For example, https://youtube.com/@AKBIT ( Not /@AKBIT or @AKBIT ). YouTube automatically parses the URLs and replaces the YouTube URLs with a YouTube icon. Instead, the handle name can be hyperlinked by typing the at the rate of symbol ( @ ) followed by the handle name @AKBIT . Meanwhile, you have to select the exact handle from the dropdown list box. YouTube Video Description A sample YouTube video description with URLs are below, A simple video tutorial to convert chemical structures in the image to a 3D molecule using online OSRA (Optical Structure Recognition Application) tool. The resour