are able to study the stability and minimization of energy of proteins as well as protein bound complexes. It can be downloaded from http://www.gromacs.org.
1.2.10 ADME Prediction
It plays an important role in the process of drug discovery. Most drugs with poor pharmacokinetic and toxicity predictions fail in the clinical trials. The toxicity and the molecular property are important properties in a drug whose prediction will help in determining the positivity or negativity of the drug during clinical trials. This method of prediction follows Lipinski’s rule of five [45]. The Lipinski’s rule of five states that HBAs must be less than 10, HBDs must be less than 5, MW of the ligand must not be more than 500 Daltons; the number of rotatable bonds should be less than 10 and the milogP value must be less than five. The Lipinski’s rule accepts compounds with one violation and those satisfying these rules can be orally available for humans. Softwares like PreADMET, VolSurf, admet-SAR, QikProp, PASS, and Molinspiration are used for ADME prediction [46, 47].
MOLINSPIRATION: It provides a wide range of cheminformatic softwares and tools which supports manipulation and processing of molecules. It also includes SD file conversion, SMILES, fragmentation of molecules, creation of tautomers, and calculating molecular properties that are required in QSAR, modeling and designing of drugs, depiction of high quality molecule, and molecular database tools which supports substructure and similarity searches. Molinspiration is user friendly and can be easily accessed at https://www.molinspiration.com/.
1.3 Various Softwares Used in the Steps of Drug Designing
Bioinformatics tools provides information about potential targets that include nucleotide and protein sequencing information, protein and gene expression data, prediction of the function, information of the pathway, mapping information, disease associations, information of the structure, and taxonomic distribution, among others. This helps in reducing time, effort, and money in characterization of different targets. The field of bioinformatics has thus become a major component of the drug discovery pipeline, playing a vital role for validating drug targets. Table 1.4 illustrates some of the most commonly used software for drug design, along with their descriptions.
Table 1.4 The list of softwares used in the steps of drug designing is represented in tabular form.
| Sr. no. | Software name | Description |
| 1 | DDDPlus | It helps in dissolution and disintegration study. |
| 2 | GastroPlus | Correlation for various formulations in in vivo and in vitro. |
| 3 | MapCheck | It helps in comparing dose or fluency measurement. |
| 4 | AutoDock | They help in evaluating the ligand-protein interaction. |
| 5 | Schrodinger | They perform ligand-receptor docking. |
| 6 | GOLD | They perform protein-ligand docking. |
| 7 | BioSuite | It performs genome analyzing and sequence analyzing. |
| 8 | Maestro | It involves molecular modeling analysis. |
| 9 | ArgusLab | They perform Molecular docking calculations and provides molecular modeling package. |
| 10 | GRAMM | Protein-protein docking and protein-ligand docking. |
| 11 | SYBYL-X Suite | It involves molecular modeling and ligand-based designing. |
| 12 | Sanjeevini | It can predict protein-ligand binding affinity. |
| 13 | PASS | It can create and analysis of SAR models. |
| 14 | AMIDE (A Medical Image Data Examiner) | They provide medical image analysis in molecular imaging. |
| 15 | Discovery Studio® Visualizer | It helps in viewing and analyzing protein data. |
| 16 | Imaging Software SCGE-Pro | They perform cytogenetic and DNA damage analysis. |
| 17 | Xenogen Living Image Software | It involves in vivo imaging display and analysis. |
| 18 | GeneSpring | It can identify variation across set of sample and for correction method in samples. |
| 19 | QSARPro | It involves protein-protein interaction study. |
| 20 | REST 2009 Software | They perform analysis of gene expression data. |
| 21 | EthoWatcher | It performs behavior analysis. |
| 22 | MARS (Multimodal Animal Rotation System) | It can perform animal activity tracking, enzyme activity, and nanoparticle tracking and delivery study. |
1.4 Applications
Bioinformatics plays an important role in defining and classifying the nucleotide compositions of human genome sequence. This field helps in identifying and analyzing a large number of biological drug targets, thereby greatly increasing the possibility of potential drugs. This approach provides strategies and algorithm to predict new drug targets and also stores and control available drug target information. The annual expenditure of developing a new drug has been reduced due to the application of bioinformatics in drug discovery. They play a major role in determining the variation of species on the basis of similarity or dissimilarity of gene structure or amino acid sequence in protein. The level of sequence similarity can also be determined using bioinformatics analysis tools. Bioinformatics techniques are mainly applied in two different phases of drug discovery. First is extracting interesting information. Second is finding important genes and proteins, thereby speeding the process
