State-of-the-Art Neural Networks Applications in Biology

Abstract

Artificial neural networks (ANNs) are a well-established computational method inspired by the structure and function of biological central nervous systems. Since their conception, ANNs have been utilized in a vast variety of applications due to their impressive information processing abilities. A vibrant field, ANNs have been utilized in bioinformatics, a general term for describing the combination of informatics, biology and medicine. This article is an effort to investigate recent advances in the area of bioinformatical applications of ANNs, with emphasis in disease diagnosis, genetics, proteomics, and chemoinformatics. The combination of neural networks and game theory in some of these application is also discussed.

A Bioinformatics Method for the Production of Antibody-Drug Conjugates Through Site-Specific Cysteine Conjugation

“…Find the atoms that will determine the distance between the linker-drug complex and the cysteine residue, as specified in Eqs. (33)(34)(35). Briefly, the distance between the linker-drug complex and the cysteine has been specified as the distance between the atoms participating in the disulfide bond between the two molecules.…”

“…In cysteine conjugation, however, it has been defined as the distance between the sulfur (S) linker atom and the sulfur atom of the cysteine side chain [Eqs. (33)(34)(35); Figure 2, step S7c]. The translation of the drug in relation to the linker is performed for the values of the variables T x , T y , T z for which the distance between the two molecules takes the official length l Hb = 1.5-2.5 Å of the hydrogen bond (Eq.…”

“…JSDraw-Antibody-Drug Conjugates is an editor tool that can be used for ADCs, although it is drawing-oriented and uses 2D coordinates. In addition, a mathematical model was recently developed to describe mechanistically the pharmacokinetic behavior and preclinical efficacy of THIOMABdrug conjugates [32][33][34][35][36][37][38][39][40][41].…”

Computational Construction of Antibody–Drug Conjugates Using Surface Lysines as the Antibody Conjugation Site and a Non-cleavable Linker

“…However, even though a number of computational tools for drug design exist, the specialized field of ADC computational design has been explored to a much smaller degree. [38][39][40][41][42][43][44][45] The in silico study of biological molecules requires their computational representation, usually in the Protein Data Bank (PDB) format. The PDB format provides a standard representation for three-dimensional structures of biological macromolecules, derived experimentally with X-ray diffraction and NMR studies.…”

“…However, even though a number of computational tools for drug design exist, the specialized field of ADC computational design has been explored to a much smaller degree. 38–45…”