BIOINFORMATICS

Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. At the beginning of the "genomic revolution", a bioinformatics concern was the creation and maintenance of a database to store biological information, such as nucleotide and amino acid sequences. Development of this type of database involved not only design issues but the development of complex interfaces whereby researchers could both access existing data as well as submit new or revised data.

Ultimately, however, all of this information must be combined to form a comprehensive picture of normal cellular activities so that researchers may study how these activities are altered in different disease states. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:

Drug Discovery process is an expensive and time consuming process that may be succeed or may not. Retrospective analysis of pharmaceutical industry during the 1990’s estimate that each new drug in the market takes an average 12-15 years to develop, costing in the region of $1.3 billion. In addition, one in nine compounds that enters clinical trials makes it to the market.

In the present era, the emerging new diseases are very much responsible for the advancement in the field of Computer Aided Drug Design (CADD). Drug Designing is the innovative boom in the field of Bioinformatics which is very cost and time effective. Hence, computers are playing a vital role in the Drug Designing.

Drug Discovery process have formed by four factors ; Scientific Knowledge, Available Technology, Human Resources and Diseases. The Scientific Knowledge, Available Technology, Human Resource provide the strategic assets by which the strategies were formed.

A pharmaceutical company conducts laboratory and animal studies to show biological activity of the compound against the target disease, and the compound is evaluated for safety.

II. INVESTIGATIONAL NEW DRUG APPLICATION (IND):

After completing preclinical testing, a company files an IND with the U.S. Food and Drug Administration (FDA) to begin to test the drug in people. The IND becomes effective if FDA does not disapprove it within 30days. The IND shows results of previous experiments; how, where and by whom the new studies will be conducted; the chemical structure of the compound; how it is thought to work in the body; any toxic effects found in the animal studies; and how the compound is manufactured. All clinical trials must be reviewed and approved by the Institutional Review Board (IRB) where the trials will be conducted.

III. CLINICAL TRIALS:

In this studies are primarily concerned with assessing the drug candidate’s safety. A small number of healthy volunteers are given the compound to test what happens to the drug in the human body – how it is absorbed, metabolized and excreted. About 70% of drug candidates pass this initial phase of testing.

The drug candidate is tested for efficacy. Usually, this is explored in a randomised trial where the compound or a drug is given to several hundred patients with the condition or disease to be treated. Depending on the condition the trial can last from several months to several number of years. The output is an increased understanding of the safety of the compound and clear information about effectiveness. If a drug passes this phase, then it can be considered that the drug can be considered truly a drug.

A drug is tested in several hundred to several thousand patients. This provides a more through understanding of the drug’s effectiveness, benefits and the range of possible adverse reactions. These trials typically last several years.

Once FDA approves an NDA, the new medicine becomes available for physicians to prescribe. A company must continue to submit periodic reports to FDA, including any cases of adverse reactions and appropriate quality control records.

Hence, in this way a drug is said to be passed through different trials and atlast to the market.

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.
Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.
Protein Databank (PDB) files can be downloaded for visualization from the Research Collaboratory for Structural Bioinformatics (RCSB) bank. These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography or NMR spectroscopy.

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2. SWISS PDB VIEWER:
Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

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3. CHEMSKETCH:
ACD/ChemSketch is an advanced chemical drawing tool and is the accepted interface for the industry's best NMR and molecular property predictions, nomenclature, and analytical data handling software. ACD/ChemSketch is also available as freeware, with functionalities that are highly competitive with other popular commercial software packages. The freeware contains tools for 2D structure cleaning, 3D optimization and viewing, InChI generation and conversion, drawing of polymers, organometallics, and Markush structures—capabilities that are not even included in some of the commercial packages from other software producers. Also included is an IUPAC systematic naming capability for molecules with fewer than 50 atoms and 3 rings. The capabilities of ACD/ChemSketch can be further extended and customized by programming.