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Molecular docking is an in silico method used to predict how and how strongly a ligand binds to the binding site of a target protein. It is widely used in drug discovery and drug design.

The genome is the fundamental structure underlying heredity in organisms. Genomic information serves as a kind of library about the organism. In addition to directing essential biological functions of cells such as growth, development, and metabolism, the genome also contains non-coding DNA regions, regulatory regions, and repetitive sequences. The definition of a genome is not limited to DNA alone. In some organisms, genetic material exists in the form of RNA for example, in

In molecular modeling, the factors that determine the energy of a system are not limited to bonded interactions such as bonds, angles, and torsions. Even when atoms are not directly connected through covalent bonds, they can still influence each other via non-bonded interactions. These interactions form the basis of many physical and biological processes, including molecular folding, stability, binding affinity, and phase behavior.

Moleküler modelleme, atomlar arası etkileşimleri sayısal olarak tanımlayarak doğadaki fiziksel süreçleri bilgisayar ortamında canlandırmayı amaçlamaktadır. Bu sürecin temel yapı taşlarından biri olan kuvvet alanları (force fields), atomların birbirleriyle nasıl etkileştiğini belirleyen matematiksel fonksiyonlar ve parametrik sabitler bütünüdür. Kuvvet alanları sayesinde moleküllerin geometrisi optimize edilir.

DNA and protein sequences undergo changes over time due to mutations. To investigate these evolutionary or environmental mutations or to identify biologically meaningful regions such as evolutionary relationships or functional similarities two or more biological sequences are compared. In these comparisons, individual bases or specific patterns are searched for.