Computation in BioInformatics. Группа авторов
Чтение книги онлайн.

Читать онлайн книгу Computation in BioInformatics - Группа авторов страница 11

Название: Computation in BioInformatics

Автор: Группа авторов

Издательство: John Wiley & Sons Limited

Жанр: Базы данных

Серия:

isbn: 9781119654766

isbn:

СКАЧАТЬ homology-modeling server which is fully automated. One can easily obtain it through ExPASy web server or from Swiss PDB Viewer. Their main aim is to model protein and make it easier to all researchers of life sciences [29]. It can be accessed at https://swissmodel.expasy.org.

      1.2.4 Virtual Screening

       MTiOpenScreen: This approach involves docking of small molecules and virtual screening. The screening can be done in one run which can be up to 5,000 small molecules in different databases. The run can also be up to 10,000 molecules selected among 15,000 compounds that are prepared to be docked which is provided at MTiOpenScreen. The web server can be obtained from http://bioserv.rpbs.univ-parisdiderot.fr/services/MTiOpenScreen/.

       ICM-VLS: ICM Virtual Ligand Screening (VLS) is a combination of internal coordinate docking methodology with a sophisticated global optimization scheme. Its accuracy and fast potentials have led to an efficient virtual screening methodology in which ligands are fully and continuously flexible. It can be accessed at http://www.molsoft.com/vls.html.

      1.2.5 Molecular Docking

       AutoDock: It is an automated program to predict ligand and protein (bio-macromolecular targets) interactions. With recent advancement in bimolecular, X-ray crystallography is helping to provide structural information of complex bio-molecules such as protein and nucleic acids. The structures can be taken/downloaded and can be used as targets for new drug molecules in controlling diseases and disorders of human, animal, and plant and understanding of fundamental aspects of biology [41]. It can be downloaded from http://www.scripps.edu/olson/forli/autodock_flex_rings.html (accessed 12.12.16).

       GOLD: Genetic Optimization for Ligand Docking is a genetic algorithm which provides docking of flexible ligand and a protein with flexible hydroxyl groups. The software uses a scoring function that is based on favorable conformations found in Cambridge Structural Database. The speed of GOLD and the reliability of its predictions depend on the control of different values of the genetic algorithm parameters. It provides reliable results both protein and ligand (http://www.ccdc.cam.ac.uk/Solutions/GoldSuite/Pages/GOLD.aspx) (accessed 20.12.16).

S. no. Name of software Description Reference
1 AutoDock It performs automated docking of flexible ligands to macromolecules. [34]
2 DockVision It performs Monte Carlo, Genetic Algorithm, and database screening docking algorithms. [35, 36]
3 GOLD It helps in identifying correct binding modes of the active target molecules. [37]
4 Docking Server It provides a web-based interface for the molecular docking of protein and ligand. [38]
5 SwissDock It is a protein ligand server that is accessed through ExPASy. [39]
6 CombiBUILD It is a structure-based drug design program which helps in designing of combinatorial libraries. [37]
7 QM Polarized Ligand Docking It performs the function of both Glide and Q-Site applications of Schrodinger Suit. [40]
8 Docking Server It provides a web-based, easy to use interface for the molecular docking of protein and ligand. [34]
10 Click2Drug It is a protein ligand server that is accessed through ExPASy. http://www.click2drug.org/
Tool Brief description with uses
BLAST Basic local alignment search СКАЧАТЬ