Topics covered Scope and applications of insilico modeling in modern biology. Comparative modeling Constructing an initial model refining the model manipulating the model Molecular superposition and structural alignment concept of energy minimization Different types of interactions and formulation of force fields. Basic MD algorithm, its limitations, treatment of long range forces.

Content of the class Structure Visualization and Graphical representation of molecular structures: Small molecules (low molecular weight – peptides, nucleotides, disaccharides, simple drugs molecules) Macromolecules (high molecular weight molecules - proteins, DNA, RNA, membranes).

Structure visualization

The best chemist develop a feel for how structural variation will change properties of interest While this may be rationalized in terms of steric, electronic and other effects Molecular graphic help us to know receptor- binding site or structure-activity pattern so that we can design active compound

The use of joystick, a mouse, or other interactive devices allows the user to interact with the structure and There by use hand-to-eye coordination to further analyze spatial characteristics of the molecule Different methods of representing structure and properties can enhance this learning experience 1). Stick models represent the bonding arrangements

Stick model Ball and stick model Spacefill

Stick models are popular modes of molecular display and are incorporated into most modeling programs 2). Ball and stick models combine the stick features of joining atoms by lines but the atoms are represented by spheres. This type of representation allows easy viewing of the skeleton with the advantage of a clear 3-D perspective 3). space filling representation join atoms by spheres whose radius depends on the atom type Vanderwaals radii of the atoms they represent so that bonded atoms intersect each other

The images obtained look like the Corey-Pauling-Koltun (CPK) models Such representations with shading can show three dimensionality as well as the steric environment of the molecule as a stick or a ball and stick These models can elucidate the steric environment, volumetric properties or electronic properties of the molecule

Graphical representation of molecular structure

Molecular graphics (MG) is the discipline of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device" Ever since Dalton's atoms and Kekule's benzene, there has been a rich history of hand-drawn atoms and molecules, and These representations have an important influence on modern molecular graphics.

The use of computers to create molecular graphics. However, that many molecular graphics programs and systems have close coupling between the graphics and editing commands or calculations such as in molecular modeling

Small molecule (low molecular weight – peptides, nucleotides, disaccharides, simple drugs molecules) Macromolecules (high molecular weight molecules - proteins, DNA, RNA, membranes)

A small molecule is a low molecular weight organic compound Small molecules are not a polymer. The term small molecule, in the field of pharmacology, is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or polysaccharide. In addition alters the activity or function of the biopolymer.

The maximum molecular weight limit for a small molecule is approximately 800 Daltons  Which allows for the possibility to rapidly diffuse across cell membranes and can reach intracellular sites of action. Small molecules can have a variety of biological functions, serving as cell signaling molecules, as tools in molecular biology, as drugs in medicine, as pesticides in farming, and in many other roles.

These compounds can be natural Biopolymers such as nucleic acids, proteins, and polysaccharides are macromolecules Their constituent monomers — ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively — are often considered to be very small oligomers are also usually considered small molecules Dinucleotides, peptides such as the antioxidant glutathione, and disaccharides such as sucrose are small molecules