0000000000441202
AUTHOR
Eduardo A. Castro
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…
3D-Chiral quadratic indices of the ‘molecular pseudograph’s atom adjacency matrix’ and their application to central chirality codification: classification of ACE inhibitors and prediction of σ-receptor antagonist activities
Quadratic indices of the 'molecular pseudograph's atom adjacency matrix' have been generalized to codify chemical structure information for chiral drugs. These 3D-chiral quadratic indices make use of a trigonometric 3D-chirality correction factor. These indices are nonsymmetric and reduced to classical (2D) descriptors when symmetry is not codified. By this reason, it is expected that they will be useful to predict symmetry-dependent properties. 3D-Chirality quadratic indices are real numbers and thus, can be easily calculated in TOMOCOMD-CARDD software. These descriptors circumvent the inability of conventional 2D quadratic indices (Molecules 2003, 8, 687-726. http://www.mdpi.org) and othe…
QSAR Modeling ANTI-HIV-1 Activities by Optimization of Correlation Weights of Local Graph Invariants
Results of using descriptors calculated with the correlation weights (CWs) of local graph invariants for modeling of anti-HIV-1 potencies of two groups of reverse transcriptase (RT) inhibitors are reported. Presence of different chemical elements in molecular structure of the inhibitors and the presence of Morgan extended connectivity values of zeroth-, first- and second order have been examined as local graph invariants in the labeled hydrogen-filled graphs. By Monte Carlo method optimization procedure, values of the CWs which produce as large values as possible of correlation coefficient between the numerical data on the anti-HIV-1 potencies and values of the descriptors on the training s…
QSPR Modeling of Hydrocarbon Dipole Moments by Means of Correlation Weighting of Local Graph Invariants
Hydrocarbon dipole moments are calculated by means of correlation weighting of local graph invariants within the context of QSPR theory. This sort of flexible topological descriptor is used for several parameters: local invariants of k th vertex in the labeled hydrogen filled graph extended connectivity of zero-, first- and second-orders, number of paths of length 2 at k th vertex and valence shell of the k th vertex. The models predict hydrocarbon dipole moments in a quite sensible way. The best model is that one based upon numbers of path length 2 correlation weighting.
Atom, atom-type and total molecular linear indices as a promising approach for bioorganic and medicinal chemistry: theoretical and experimental assessment of a novel method for virtual screening and rational design of new lead anthelmintic.
Abstract Helminth infections are a medical problem in the world nowadays. In this paper a novel atom-level chemical descriptor has been applied to estimate the anthelmintic activity. Total and local linear indices and linear discriminant analysis were used to obtain a quantitative model that discriminates between anthelmintic and non-anthelmintic drug-like compounds. The discriminant model has an accuracy of 90.11% in the training set, with a high Matthews’ correlation coefficient (MCC = 0.80). To assess the robustness and predictive power of the obtained model, internal (leave-n-out) and external validation process was performed. The QSAR model correctly classified 88.55% of compounds in t…