Eva Soriano | Instituto Politécnico Nacional (original) (raw)
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Papers by Eva Soriano
Two derivatives of 5-fluorouracil (5-FU) with similar structure were synthesised, and their inter... more Two derivatives of 5-fluorouracil (5-FU) with similar structure were synthesised, and their interactions with calf thymus-DNA (CT-DNA) have been studied using cyclic voltammetry (CV) at a DNA-modified gold electrode. The variations in the cyclic voltammetric behaviour of different concentrations of drugs with CT-DNA have been investigated. Molecular docking was used to predict the modes of interactions of the drugs with DNA. The molecular docking results indicated that the modes of interactions between two drugs and DNA helix can be considered as groove binding. To measure the binding ability of the two drugs with DNA, binding constants (K) were calculated from voltammetric data, i.e., and the binding free energies of the two drugs with DNA were calculated using the AMBER software package. For the binding strength, the computational results complemented the experimental results.
Assignment of structure and function to all genes and gene products (such as proteins) of all org... more Assignment of structure and function to all genes and gene products (such as proteins) of all organisms represents a major challenge in this postgenomic era. Here we present the I-TASSER Suite (http://zhanglab.ccmb.med.umich.edu/I-TASSER/download/), a stand-alone software package for protein structure and function modeling. The gap between the number of proteins with known sequences and the number of proteins with experimentally characterized structure and function keeps increasing. One way to narrow this gap is by developing advanced computational approaches for modeling structure and function from sequences, where progress has been recently witnessed in community-wide blind experiments 1,2. I-TASSER 3 was originally designed for protein structure modeling by iterative threading assembly simulations. It was recently extended for structure-based function annotation by matching structure predictions with known functional templates 4,5. Here we introduce the I-TASSER Suite, a stand-alone package implementing the I-TASSER–based protein structure and function modeling pipelines. Although the on-line I-TASSER server is established and widely used in the community, limited computing resources from a single laboratory have prevented large-scale applications of these algorithms. We expect that the development of the stand-alone package will remove the computing resource barriers and therefore enable benchmarking of new structure and function modeling methods. The I-TASSER Suite pipeline consists of four general steps: threading template identification, iterative structure assembly simulation, model selection and refinement, and structure-based function annotation (Fig. 1a). In the first step, the query is threaded by
Two derivatives of 5-fluorouracil (5-FU) with similar structure were synthesised, and their inter... more Two derivatives of 5-fluorouracil (5-FU) with similar structure were synthesised, and their interactions with calf thymus-DNA (CT-DNA) have been studied using cyclic voltammetry (CV) at a DNA-modified gold electrode. The variations in the cyclic voltammetric behaviour of different concentrations of drugs with CT-DNA have been investigated. Molecular docking was used to predict the modes of interactions of the drugs with DNA. The molecular docking results indicated that the modes of interactions between two drugs and DNA helix can be considered as groove binding. To measure the binding ability of the two drugs with DNA, binding constants (K) were calculated from voltammetric data, i.e., and the binding free energies of the two drugs with DNA were calculated using the AMBER software package. For the binding strength, the computational results complemented the experimental results.
Assignment of structure and function to all genes and gene products (such as proteins) of all org... more Assignment of structure and function to all genes and gene products (such as proteins) of all organisms represents a major challenge in this postgenomic era. Here we present the I-TASSER Suite (http://zhanglab.ccmb.med.umich.edu/I-TASSER/download/), a stand-alone software package for protein structure and function modeling. The gap between the number of proteins with known sequences and the number of proteins with experimentally characterized structure and function keeps increasing. One way to narrow this gap is by developing advanced computational approaches for modeling structure and function from sequences, where progress has been recently witnessed in community-wide blind experiments 1,2. I-TASSER 3 was originally designed for protein structure modeling by iterative threading assembly simulations. It was recently extended for structure-based function annotation by matching structure predictions with known functional templates 4,5. Here we introduce the I-TASSER Suite, a stand-alone package implementing the I-TASSER–based protein structure and function modeling pipelines. Although the on-line I-TASSER server is established and widely used in the community, limited computing resources from a single laboratory have prevented large-scale applications of these algorithms. We expect that the development of the stand-alone package will remove the computing resource barriers and therefore enable benchmarking of new structure and function modeling methods. The I-TASSER Suite pipeline consists of four general steps: threading template identification, iterative structure assembly simulation, model selection and refinement, and structure-based function annotation (Fig. 1a). In the first step, the query is threaded by