• Biology

  What is computational biology?

  Posted by Encyclios on April 4, 2023 at 12:54 PM

  In some ways a synonym of bioinformatics itself, as it assimilates the general assumptions that coincide with the use of algorithms to solve certain problems of biological matrix.

  As we have seen, one of the first disciplinary areas in which biology and computer science have benefited from their collaboration is given to the alignment of sequences, to understand, for example, if their similarity is the effect of a common ancestor.

  The concept behind alignment algorithms is relatively simple, given the complexity of the operations they must solve: given a given scoring system, the algorithm must align two sequences with the highest possible score. Thus, there are different types of algorithms.

  The exact algorithms, such as the aforementioned Needleman-Wunsch (global gapped alignments) and Smith-Waterman (local gapped alignments), are very precise, but at the same time require very high computational resources to achieve their goal. The more recent heuristic algorithms do not guarantee the best alignment, but they are characterized by a remarkable speed of execution. This is the case of the BLAST algorithm (ungapped local alingments).

  The scenario varies significantly depending on the type of sequences analyzed, so it is necessary to identify from time to time the computational model based on algorithms and matrices of substitution suitable to solve in an optimal way the alignment.

  This brief introduction to mathematics does not give any idea of the complexity of the whole issue, but it is useful to focus on the considerable variety of computational aspects that concern molecular biology in order to understand the need for multidisciplinary research teams.

  Today’s computational resources allow, for example, very complex simulations to solve molecular sequences and structures, thanks to the most advanced techniques of artificial intelligence, including deep learning.

  An extraordinary example is AlphaFold, an open source project developed by DeepMind to solve the problem of protein folding, the 3D simulation of protein structures. Triumphant in the last edition of the aforementioned CASP, the famous London-based AI Lab, financially supported by Google, has achieved a result that opens a new era in molecular biology, thanks to its ability to progressively reduce the cost of research, making it extremely faster and more functional to respond to the growing needs in the medical and pharmacological fields.

  Encyclios replied 2 months ago 1 Member · 0 Replies
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