## Posts

### Converting image to 3D molecule using VEGA ZZ OSRA

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

### Saving AutoDock Vina Docking Result to PDB using Chimera

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.

### RNA Secondary Structure Prediction using Nussinov Algorithm

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. \(

### Taking High Resolution Web-Page Screenshots on Chrome

Google Chrome (or simply Chrome) is a free and fast web browser developed by Google . The currently released Chrome web browser comes with built-in functionality to take a screenshot of webpages without any add-ons. It allows taking a high-quality screenshots at high resolutions. Types of Screenshots The Chrome browser support taking 4 types of screenshots of a web page. Capture area screenshot - taking screenshot on specific region Capture full size screenshot - taking scrolling screenshot from top to bottom Capture node screenshot - taking screenshot of a specific HTML element Capture screenshot - taking full screen screenshot The Capture full size screenshot / Capture screenshot options are accessible via Chrome's developer tools (Ctrl+Shift+I). Furthermore, Capture area screenshot / Capture node screenshot options are accessible via Run command (Ctrl+Shift+P) by entering command “ screenshot ”. The video tutorial below demonstrates various typ

### Protein-Ligand Binding Site Analysis using Chimera

Chimera (or UCSF Chimera ) is an interactive molecular visualization and analysis program developed by the Resource for Biocomputing, Visualization, and Informatics ( RBVI ) at the University of California, San Francisco ( UCSF ). ChimeraX (or UCSF ChimeraX ) is the next-generation molecular visualization program, which is a successor of Chimera. The Chimera/ChimeraX program supports analyzing various molecular structures and related data, including sequence alignments, docking results, molecular assemblies, electron density maps, trajectories, and conformational ensembles. It can be downloaded freely for academic, government, nonprofit, and personal use. Protein-Ligand Interaction Models In the protein-ligand interaction model, proteins or ligands are represented by a wire-frame model / stick model / ball-and-stick model / cartoon model / space-fill model / surface model, but not both. The interactions between protein and ligand atoms is represented by dotted or dashed lines. T

### PCA, PCoA, and Tree Plot using NTSYSpc

This tutorial explains how to perform P rincipal C omponent A nalysis (PCA) and P rincipal C oordinate A nalysis (PCoA) of multivariate data using the NTSYSpc tool. NTSYSpc ( N umerical T axonomy and Multivariate Analysis SYS tem for p ersonal c omputer) is a simple and efficient statistical tool used to find patterns and display structures in multivariate data. The tool used in this tutorial is NTSYSpc v2.11a . In this tutorial, I have used a sample allelic data matrix (shown below). The matrix file consists of molecular weight size marker (rows) and sample/loci (columns). \[M_{mw,s}=\begin{bmatrix}0&0&1&1&0&0\\0&0&1&0&0&0\\0&0&1&1&0&0\\0&0&1&1&1&1\\1&1&1&0&0&0\\0&1&1&1&0&0\\0&0&1&1&1&1\\0&0&0&0&1&1\\1&0&0&0&0&0\\1&1&0&0&0&0\\1&1&0&0&0&0\\0&1&0&0&a

### Benefits of Falling Lizard

பல்லி விழும் பலன்கள். Benefits of falling lizard in human body parts. பல்லி விழும் பலன்கள் உறுப்பு இடம் வலம் தலை கலகம் துன்பம் வயிறு தானியம் மகிழ்ச்சி கண் சுகம் சிறைபயம் பிருஷ்டம் சுகம் செல்வம் காது ஆயுள் லாபம் கணைக்கால் பிரயாணம் சுகம் மணிக்கட்டு பீடை கீர்த்தி நகம் செலவு நஷ்டம் மார்பு தனலாபம் சுகம் நெற்றி லட்சுமிகரம் காரியசித்தி முதுகு நஷ்டம் கவலை உதடு கஷ்டம் வரவு முழங்கால் நஷ்டம் பந்தயம் தோல் வெற்றி போகம் பாதவிரல் ராசபயம் நோய் கைவிரல் சன்மானம் சஞ்சலம்