0000000001314964
AUTHOR
Ricardo Medina-marrero
Protein linear indices of the ‘macromolecular pseudograph α-carbon atom adjacency matrix’ in bioinformatics. Part 1: Prediction of protein stability effects of a complete set of alanine substitutions in Arc repressor
Abstract A novel approach to bio-macromolecular design from a linear algebra point of view is introduced. A protein’s total (whole protein) and local (one or more amino acid) linear indices are a new set of bio-macromolecular descriptors of relevance to protein QSAR/QSPR studies. These amino-acid level biochemical descriptors are based on the calculation of linear maps on R n [ f k ( x m i ) : R n → R n ] in canonical basis. These bio-macromolecular indices are calculated from the kth power of the macromolecular pseudograph α-carbon atom adjacency matrix. Total linear indices are linear functional on R n . That is, the kth total linear indices are linear maps from R n to the scalar R [ f k …
Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity.
The TOpological MOlecular COMputer Design (TOMOCOMD-CARDD) approach has been introduced for the classification and design of antimicrobial agents using computer-aided molecular design. For this propose, atom, atom-type, and total quadratic indices have been generalized to codify chemical structure information. In this sense, stochastic quadratic indices have been introduced for the description of the molecular structure. These stochastic fingerprints are based on a simple model for the intramolecular movement of all valence-bond electrons. In this work, a complete data set containing 1006 antimicrobial agents is collected and presented. Two structure-based antibacterial activity classificat…
In silicoAntibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach
In the recent times, the race to cope with the increasing multidrug resistance of pathogenic bacteria has lost much of its momentum and health professionals are grasping for solutions to deal with the unprecedented resistance levels. As a result, there is an urgent need for a concerted effort towards the development of new antimicrobial drugs to stay ahead in the fight against the ever adapting bacteria. In the present report, antibacterial classification functions (models) based on the topological molecular computational design-computer aided >rational> drug design (TOMOCOMD-CARDD) atom-based non-stochastic and stochastic bilinear indices are presented. These models were built using the li…
In silico Antibacterial Activity Modeling Based on the TOMOCOMD-CARDD Approach
In the recent times, the race to cope with the increasing multidrug resistance of pathogenic bacteria has lost much of its momentum and health professionals are grasping for solutions to deal with the unprecedented resistance levels. As a result, there is an urgent need for a concerted effort towards the development of new antimicrobial drugs to stay ahead in the fight against the ever adapting bacteria. In the present report, antibacterial classification functions (models) based on the topological molecular computational design-computer aided ‘‘rational’’ drug design (TOMOCOMD-CARDD) atom-based non-stochastic and stochastic bilinear indices are presented. These models were built using the …