In this work the charge distribution of the tRNA acceptor stem is characterized, considering all ... more In this work the charge distribution of the tRNA acceptor stem is characterized, considering all the possible WatsonCrick base pair combinations. 256 RNA fragments modeled by 10 nucleotides were used in order to model the first three pairs of the acceptor stem, the discriminator base and the CCA end. We propose two local charge descriptors based on the charge distribution of the nitrogenated 31 REVISTA COLOMBIANA DE QUÍMICA, VOLUMEN 37, No. 1 DE 2008 O rg án ic a y B io q u ím ic a 1 Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, sede Bogotá, Bogotá, D. C., Colombia. eedazac@unal.edu.co base to characterize each nucleotide. These descriptors were computed from atomic partial charges derived from HF/6-31G calculations. From the characterization and classification of the stems according to the proposed descriptors, we found a special behavior for the discriminator base (in contrast to the other positions) and a strong effect of this position on the CC...
En este trabajo se caracteriza la distribucion de carga del tallo aceptor del tRNA, considerando ... more En este trabajo se caracteriza la distribucion de carga del tallo aceptor del tRNA, considerando todas las posibles combinaciones de pares Watson-Crick. El estudio se realizo con 256 fragmentos moleculares de 10 nucleotidos que modelan los tres primeros pares del tallo aceptor, la base diferenciadora y el extremo CCA. Para caracterizar los nucleotidos se proponen dos descriptores locales basados en la distribucion de carga de las base nitrogenada de cada nucleotido, los cuales se calculan a partir de las cargas parciales de Mulliken obtenidas de calculos HF/6-31G. La caracterizacion y clasificacion de los tallos segun estos descriptores mostro como la base diferenciadora tiene un comportamiento particular respecto a los demas nucleotidos del tallo y una fuerte influencia sobre el extremo CCA. La clasificacion de nueve variaciones del tallo aceptor del tRNA Ala mostro una buena relacion estructura-actividad que pone en evidencia la bondad de los descriptores propuestos para caracteri...
RNA representation is one of the most important issues in bioinformatics. A challenge, however, i... more RNA representation is one of the most important issues in bioinformatics. A challenge, however, is achieving a correct representation that is able to encode the directionality, secondary and primary structure. One possible solution is the RNA graph representation and its associate tree; however, it fails to encode the directionality of the RNA molecule. Therefore, a succession based on the tree representation is proposed as an alternative. From this novel succession, we have defined three metrics in order to compare the similarity between RNAs. Finally, we have used the properties of pretopological spaces which were generated from the metrics as a cluster tool. This methodology has allowed the classification of an RNA hairpin, which was mutated in two different positions.
Following several authors, we point out the importance of relations in the conceptual frame of ch... more Following several authors, we point out the importance of relations in the conceptual frame of chemistry. We propose that an important charac- teristic of chemistry is given by the epistemological challenge associated with selectively related entities. We also suggest that internal relation ontologies have been seen by chemists as better suited for assessing this challenge, and that this ontological perspective has played an important role in shaping chemical concepts.
We have classified a set of 250 benzimidazoles using a criterion of structural similarity. This c... more We have classified a set of 250 benzimidazoles using a criterion of structural similarity. This criterion has led us to several clusters, which keep a close relationship between the molecules belonging to each one of them and their pharmacological activity. To study the structural similarity we have built a mathematical space where chemical structures are pictured as vectors. A set of well-chosen descriptors was used as variables. These descriptors arise from graph theoretical studies and quantum mechanical calculations. Principal components analysis was employed to find the suitable dimension for the space. Finally, cluster analysis was performed to classify the set of molecules by similarity. A Euclidean metric was used as a similarity coefficient.
Journal of Chemical Information and …, Jan 1, 1994
Page 1. J. Chem. If. Comput. Sci. 1994,34, 309-313 Upper and Lower Bonds for Molecular Energies E... more Page 1. J. Chem. If. Comput. Sci. 1994,34, 309-313 Upper and Lower Bonds for Molecular Energies Edgar E. Daza' and Jose Luis Villaveces Grupo de Qufmica Tdrica, Universidad Nacional de Colombia, BogotPi DC, Colombia Received May 18, 19938 ...
In this work the charge distribution of the tRNA acceptor stem is characterized, considering all ... more In this work the charge distribution of the tRNA acceptor stem is characterized, considering all the possible WatsonCrick base pair combinations. 256 RNA fragments modeled by 10 nucleotides were used in order to model the first three pairs of the acceptor stem, the discriminator base and the CCA end. We propose two local charge descriptors based on the charge distribution of the nitrogenated 31 REVISTA COLOMBIANA DE QUÍMICA, VOLUMEN 37, No. 1 DE 2008 O rg án ic a y B io q u ím ic a 1 Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, sede Bogotá, Bogotá, D. C., Colombia. eedazac@unal.edu.co base to characterize each nucleotide. These descriptors were computed from atomic partial charges derived from HF/6-31G calculations. From the characterization and classification of the stems according to the proposed descriptors, we found a special behavior for the discriminator base (in contrast to the other positions) and a strong effect of this position on the CC...
En este trabajo se caracteriza la distribucion de carga del tallo aceptor del tRNA, considerando ... more En este trabajo se caracteriza la distribucion de carga del tallo aceptor del tRNA, considerando todas las posibles combinaciones de pares Watson-Crick. El estudio se realizo con 256 fragmentos moleculares de 10 nucleotidos que modelan los tres primeros pares del tallo aceptor, la base diferenciadora y el extremo CCA. Para caracterizar los nucleotidos se proponen dos descriptores locales basados en la distribucion de carga de las base nitrogenada de cada nucleotido, los cuales se calculan a partir de las cargas parciales de Mulliken obtenidas de calculos HF/6-31G. La caracterizacion y clasificacion de los tallos segun estos descriptores mostro como la base diferenciadora tiene un comportamiento particular respecto a los demas nucleotidos del tallo y una fuerte influencia sobre el extremo CCA. La clasificacion de nueve variaciones del tallo aceptor del tRNA Ala mostro una buena relacion estructura-actividad que pone en evidencia la bondad de los descriptores propuestos para caracteri...
RNA representation is one of the most important issues in bioinformatics. A challenge, however, i... more RNA representation is one of the most important issues in bioinformatics. A challenge, however, is achieving a correct representation that is able to encode the directionality, secondary and primary structure. One possible solution is the RNA graph representation and its associate tree; however, it fails to encode the directionality of the RNA molecule. Therefore, a succession based on the tree representation is proposed as an alternative. From this novel succession, we have defined three metrics in order to compare the similarity between RNAs. Finally, we have used the properties of pretopological spaces which were generated from the metrics as a cluster tool. This methodology has allowed the classification of an RNA hairpin, which was mutated in two different positions.
Following several authors, we point out the importance of relations in the conceptual frame of ch... more Following several authors, we point out the importance of relations in the conceptual frame of chemistry. We propose that an important charac- teristic of chemistry is given by the epistemological challenge associated with selectively related entities. We also suggest that internal relation ontologies have been seen by chemists as better suited for assessing this challenge, and that this ontological perspective has played an important role in shaping chemical concepts.
We have classified a set of 250 benzimidazoles using a criterion of structural similarity. This c... more We have classified a set of 250 benzimidazoles using a criterion of structural similarity. This criterion has led us to several clusters, which keep a close relationship between the molecules belonging to each one of them and their pharmacological activity. To study the structural similarity we have built a mathematical space where chemical structures are pictured as vectors. A set of well-chosen descriptors was used as variables. These descriptors arise from graph theoretical studies and quantum mechanical calculations. Principal components analysis was employed to find the suitable dimension for the space. Finally, cluster analysis was performed to classify the set of molecules by similarity. A Euclidean metric was used as a similarity coefficient.
Journal of Chemical Information and …, Jan 1, 1994
Page 1. J. Chem. If. Comput. Sci. 1994,34, 309-313 Upper and Lower Bonds for Molecular Energies E... more Page 1. J. Chem. If. Comput. Sci. 1994,34, 309-313 Upper and Lower Bonds for Molecular Energies Edgar E. Daza' and Jose Luis Villaveces Grupo de Qufmica Tdrica, Universidad Nacional de Colombia, BogotPi DC, Colombia Received May 18, 19938 ...
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