BioGem Blog

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...

A hydrophobicity or lipophilicity plot is a 2D graphical display of the hydrophobic regions in the protein. The Kyte-Doolittle scale was widely used for identifying surface-exposed regions and transmembrane regions. The plot has the amino acid sequence of a protein on its x -axis and a degree of hydrophobicity on its y -axis. The graph regions with a positive value are hydrophobic. There are several hydrophobicity scales have been published for various uses. The commonly used hydrophobicity scales are Kyte-Doolittle scale, Engelman scale (GES scale), Eisenberg scale, Hopp-Woods scale, Cornette scale, Rose scale, and Janin scale. For further details, refer my previous article https://www.biob.in/2014/05/hydrophobicity-plot-using-biopython.html Program Implementation In this tutorial, I have used Google Colab Notebook for running the Python program. Click here for interactive demo. Python Program try: import google.colab !pip install biopython except ImportError: pa...

நீங்கள் வீட்டில் இருந்தபடியே உங்கள் மின் உபயோக கட்டணத் தொகை சுலபமாக அறிந்து கொள்ளலாம். TNEB Bill Calculator - 2024 ( Revised on July 01, 2024 ) For Domestic Usage Only Units Consumed: Units ( u ) Subsidy Unit Range Unit Cost From To ≤ 100 ₹ 4.80 × u 1 100 ₹ 0.00 ≤ 200 ₹ 4.80 × u 1 100 ₹ 0.00 ₹ 2.45 × u 101 200 ₹ 2.35 ≤ 400 ₹ 4.80 × u 1 100 ₹ 0.00 ₹ 2.45 × u 101 200 ₹ 2.35 ₹ 0.10 × u 201 400 ₹ 4.70 ≤ 500 ₹ 4.80 × u 1 100 ₹ 0.00 ₹ 2.45 × u 101 200 ₹ 2.35 ...

OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images, as they appear in journal articles, patent documents, textbooks, trade magazines etc., to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. The CACTUS OSRA tool parses the graphical input to a SMILES string and converts it to a 3D molecule. The video tutorial below demonstrates the conversion of a document in GIF format image to a 3D structure. Note that any software designed for optical recognition is unlikely to b...

VEGA ZZ is a free (for non-profit academic uses) molecular modelling suite. It consists of many third-party packages, which act as an interface to the VEGA ZZ software. OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. VEGA ZZ consists of an OSRA plug-in that acts as an interface to it. Moreover, it supports imaging devices such as cameras and image scanners for acquiring documents through the TWAIN interface. The VEG...

AutoDock is a free molecular modeling simulation suite mainly used for molecular docking. It consists of two programs, namely AutoGrid and AutoDock. The three variants of AutoDock are AutoDock 4.2.6 , AutoDock Vina 1.2.3 (a successor of AutoDock), and AutoDock GPU . AutoDock or Vina use PDBQT (Protein Data Bank (PDB), Partial Charge (Q), and Atom Type (T)) molecular structure file format for input and output. But, most molecular analysis and visualization tools accept the PDB file format. The video tutorial for converting AutoDock or Vina results in a complex PDBQT file format to PDB file format is below.

The Nussinov algorithm is an RNA secondary structure (folding) prediction method using a dynamic programming approach. Ruth Nussinov introduced this algorithm in the year 1978. It involves computing a two-dimensional (2D) diagonal matrix with the same sequence at both dimensions. The scores are given based on complementary ( 1 ) or non-complementary ( 0 ) matches of characters. Matrix solving consists of three stages ( i ) initialization , ( ii ) matrix-filling , and ( iii ) trace-back of arrows for structures. \(\style{ color: blue; } {\begin{array} \\ \text{RNA sequence, } S=a_1a_2a_3....a_{l-1}a_l \\ \begin{align*} \\ \!\!\!\!\! \text{where,} \\ & a=\text{characters (A, U, C, G)} \\ & l=\text{length of the sequence} \\ \end{align*} \end{array}} \) In this tutorial, I have taken a sample RNA sequence ( S ) as GGGAAAUCC for prediction. Initialization The initialization step is to preset the diagonal cells with zero ( 0 ) values to perform matrix filling. \(...