0000000000441203

AUTHOR

Vicente Romero-zaldivar

showing 3 related works from this author

Protein linear indices of the ‘macromolecular pseudograph α-carbon atom adjacency matrix’ in bioinformatics. Part 1: Prediction of protein stability …

2005

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 …

Quantitative structure–activity relationshipClinical BiochemistryQuantitative Structure-Activity RelationshipPharmaceutical ScienceBiochemistryCombinatoricsViral ProteinsLinear formDrug DiscoveryLinear regressionViral Regulatory and Accessory ProteinsMolecular BiologyAlanineChemistryOrganic ChemistryTemperatureLinear modelComputational BiologyProteinsModels TheoreticalLinear discriminant analysisMatthews correlation coefficientRepressor ProteinsAmino Acid SubstitutionTopological indexMutationLinear algebraLinear ModelsMolecular MedicineSoftwareBioorganic & Medicinal Chemistry
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Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity.

2005

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…

Quantitative structure–activity relationshipStochastic ProcessesMolecular modelDatabases FactualChemistryOrganic ChemistryClinical BiochemistryMolecular ConformationPharmaceutical ScienceAtom (order theory)Quantitative Structure-Activity RelationshipModels TheoreticalLinear discriminant analysisBiochemistryAnti-Bacterial AgentsSet (abstract data type)Quadratic equationSimple (abstract algebra)Drug DiscoveryMolecular MedicineComputer SimulationBiological systemMolecular BiologyAntibacterial agentBioorganicmedicinal chemistry
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Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification

2008

The recently introduced non-stochastic and stochastic bond-based linear indices are been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. These improved modified descriptors are applied to several well-known data sets to validate each one of them. Particularly, Cramer's steroid data set has become a benchmark for the assessment of novel quantitative structure activity relationship methods. This data set has been used by several researchers using 3D-QSAR approaches such as Comparative Molecular Field Analysis, Molecular Quantum Similarity Measures, Comparative Molecular Moment Analysis, E-state, Mapping Prope…

Stochastic ProcessesQuantitative structure–activity relationshipIndolesProperty (programming)ChemistryComparabilityQuantitative Structure-Activity RelationshipAngiotensin-Converting Enzyme InhibitorsStereoisomerismGeneral ChemistrySet (abstract data type)Data setComputational MathematicsModels ChemicalPiperidinesComputational chemistryDrug DesignBenchmark (computing)Molecular symmetryCombinatorial Chemistry TechniquesReceptors sigmaThermodynamicsTrigonometryAlgorithmJournal of Computational Chemistry
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