The super-fast automated next-generation sequencing (NGS) technology
allows parallel sequencing of millions of genomics molecules with higher accuracy at
low cost and less time consumption. However, the three-dimensional structure needs to
be determined for experimental purposes, and solving the three-dimensional structure
of a biomolecule via the alternative experimental approaches requires special skills and
equipment, which is time-consuming, labor demanding and expensive. This situation
resulted in the widening of the space between solved biological molecules and known
sequences. Recently, bioinformaticians and computer scientists have developed
computer-based algorithms and protocols to solve these issues. The developed
computational approaches and algorithms allow researchers to 1) perform prediction
and refinement of models close to their native molecule structure based on the data
from other molecules possessing similar homology, 2) predict potential interaction and
possible reactions between two biomolecules and 3) gain meaningful insight when it is
impractical to be obtained via theoretical or experimental analysis. The development of
these computational algorithms allows scientists to discover, predict and study
important molecules at a faster pace. This chapter will introduce readers to the basic
computational algorithms used to develop advanced bioinformatic protocols and tools.
Keywords: Protein refinement, Assessment of model quality, Prediction of protein tertiary structure, Molecular docking, DNA, RNA, Genome, Protein, Receptor, Ligand, Algorithm.
