Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand—protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Garrett M. Morris and Marguerita Lim-Wilby, Molecular Docking, In Molecular Modeling of Proteins Methods in Molecular Biology, 2008, Volume 443 Virtual screening of compound libraries has become a standard technology in modern drug discovery pipelines [1]. If a suitable structure of the target is available molecular docking can be used to discriminate between putative binders and non-binders in large databases of chemicals and to reduce the number of compounds to be subjected to experimental testing substantially. Visual examination of predicted binding geometries (docking poses) thereby contributes crucially to the further development of a lead compound either towards enhanced binding affinity, towards reduced side effects or towards reduced susceptibility to drug resistance related mutations. …show more content…
2.6.1Introduction to molecular docking 2.6.1.1 Biological background Molecular docking is used to predict the structure of the intermolecular complex formed between two or more molecules. The most interesting case is the protein-ligand interaction, because of its applications in medicine. Ligand is a small molecule, which interacts with protein’s binding sites. Binding sites are areas of protein known to be active in forming of compounds. There are several possible mutual conformations in which binding may occur. These are commonly called binding modes. 2.6.1.2 Physical
Pang, A., Warren, M. J. and Pickersgill, R. W. (2011), Structure of PduT, a trimeric bacterial microcompartment protein with a 4Fe–4S cluster-binding site. Acta Crystallographica D, 67: 91–96. doi: 10.1107/S0907444910050201
Complex linkages are system of activities, business organization, resources, and information involved in transferring services and product from supplier of the product to customers. In complex linkage, the products and services from a single company interact in several ways. The complex linkage needed for a competitive business environment should focus on business management, connection with other countries, development of new markets, and technology.
The structures of liposomes are spherical and are usually between 15nm and 1000 nm in diameter. They are able to target the ligands that are attached to their surface to direct them to the appropriate sites wi...
Acknowledgements. Special thanks go to the Department of Chemistry and Chemical Biology at IUPUI, Dr. Ryan E. Denton, Professor and Dan Preston, TA.
Drug resistance in mycobacterium tuberculosis (TB) has become a severe global health threat. The fight against TB is now facing major challenges due to the appearance of Multi-Drug Resistant Tuberculosis (MDR-TB) and more recently, the virtually untreatable Extensively Drug Resistant Tuberculosis (XDR-TB). MDR-TB are strains that are resistant to both top first-line drugs, Isoniazid and Rifampin, while XDR-TB are MDR-TB strains that are also resistant to any fluoroquinolone and one or more of 3 injectable drugs. With this new resistance, there emerges a great need to find new drugs that are as effective, yet bypass the problem of resistance. One method of research is to find new vulnerabilities of tuberculosis to use as new target sites of drugs. This method is highly expensive (Scheffler, Colmer, Tynan, Demain, & Gullo, 2013), and requires intense and lengthy research just to implicate the new target site. An alternative is to develop new drugs that work on the same already known target as the first-line drugs, but by a different mechanism, thereby bypassing the resistance of the TB to the drug.
...Coauthor, ChemBioChem 2006, 7, 1-10; b) A. Author, B. Coauthor, Angew. Chem. 2006, 118, 1-5; Angew. Chem. Int. Ed. 2006, 45, 1-5.))
middle of paper ... ... Chemistry, the Central Science 11th Edition (p. 1072). (2009). The 'Standard' of the 'Standard'. 25.
“This knowledge will help us design drugs that mimic the viral effects on these proteins to either activate a host’s immune response or shut it down,” said Dr. Michael Gale, associate ...
Wood, A. (2005, August 10). Chemtura: Making a merger work. Chemical Week, 167, pp. 17-19.
To examine the interaction between two molecules in solution without isolating the compound Jobfs method is used. Although unstable compounds tend to be generated, this is not a reflection of weak interactions. In some cases, the transition metal species cannot be crystallized from the solution and separated from the other species present. Without Jobfs Method this composition can be very difficult to deduce.
I have always been fascinated by Biology and Computer Science which propelled me to take up my undergraduate studies in the field of Bioinformatics. As a part of my undergraduate curriculum, I have been exposed to a variety of subjects such as “Introduction to Algorithms”, “System Biology”, “PERL for Bioinformatics”, “Python”, “Structure and Molecular Modeling” and “Genomics and Proteomics” which had invoked my interest in areas such as docking algorithms, protein structure prediction, practical aspects of setting and running simulation, gene expression prediction through computational analysis. These fields have both a strong computational flavour as well as the potential for research which is what attracts me towards them.
More than 45 million chemical compounds are known and the number may increase in million every year, without cheminformatics, the access of these huge amounts of information is very difficult.
"Within a single subunit [polypeptide chain], contiguous portions of the polypeptide chain frequently fold into compact, local semi-independent units called domains." - Richardson, 1981
Plontke, R. (2003, March 13). Chemnitz UT. TU Chemnitz: - Technische Universität Chemnitz. Retrieved April 1, 2014, from http://www.tu-chemnitz.de/en/
Ionic compounds, when in the solid state, can be described as ionic lattices whose shapes are dictated by the need to place oppositely charged ions close to each other and similarly charged ions as far apart as possible. Though there is some structural diversity in ionic compounds, covalent compounds present us with a world of structural possibilities. From simple linear molecules like H2 to complex chains of atoms like butane (CH3CH2CH2CH3), covalent molecules can take on many shapes. To help decide which shape a polyatomic molecule might prefer we will use Valence Shell Electron Pair Repulsion theory (VSEPR). VSEPR states that electrons like to stay as far away from one another as possible to provide the lowest energy (i.e. most stable) structure for any bonding arrangement. In this way, VSEPR is a powerful tool for predicting the geometries of covalent molecules.