1,720,960 research outputs found
A Three- Dimensional Quantitative Structure Activity Relationship (3D-QSAR) Model for Predicting the Enantioselectivity for Candida Antarctica Lipase B
No full textComputational techniques involving molecular modeling coupled with multivariate statistical analysis were used to evaluate and predict quantitatively the enantioselectivity of lipase B from Candida antarctica (CALB). In order to allow the mathematical and statistical processing of the experimental data largely available in the literature (namely enantiomeric ratio E), a novel class of GRID-based molecular descriptors was developed (differential molecular interaction fields or DMIFs). These descriptors proved to be efficient in providing the structural information needed for computing the regression model. Multivariate statistical methods based on PLS (partial least square – projection to latent structures), were used for the analysis of data available from the literature and for the construction of the first three-dimensional quanititative structure-activity relationship (3D-QSAR) model able to predict the enantioselectivity of CALB. Our results indicate that the model is statisticall
3D analysis of catalytic differences of hydrolases by integrating modelling and mutivariate statistics
No full text
Elucidating the structural and conformational factors responsible for the activity and substrate specificity of alkanesulfonate monooxygenase
No full textThe mechanism and substrate specificity of alkanesulfonate monooxygenase (SsuD) was investigated by combining
molecular dynamics simulations, docking, and a comprehensive quantitative structure activity relationships (QSAR)
analysis. The FMNH2 dependent monooxygenase undergoes a dynamic conformational change of the active site, passing
from a closed to an open state. As a consequence, substrates have access to the active site and the cofactor is then regenerated
by the associated oxidoreductase FMN reductase SsuE. Computational analysis of the interaction of SsuD with
FMNH2 based on molecular docking and multiple 20 ns molecular dynamics simulations pointed out that the conformational
change is mainly driven by salt bridge formation between Arg297 and Glu20 or Asp111. A set of substrates
accepted by SsuD were described by means of ALMOND chemical descriptors and a partial least square (PLS) mathematical
model was constructed. The PLS model correlates the structure of substrates and enzyme activity, namely kinetic
properties (kcat/KM). Therefore, information coming from the PLS analysis goes beyond the simple ability of the enzyme
to recognize the substrate, but includes the factors that affect the capacity of the enzyme to reduce the activation energy
of the rate determining step of the reaction. The two principal components of the model are able to describe both steric
and electronic factors and, more importantly, their interactions. Indeed, interactions of factors appear to affect significantly
the ability of SsuD of transforming efficiently a substrate
Conformational changes of lipases in aqueous media: A comparative computational study and experimental implications
No full textConformational changes occurring to the open form of five different lipases were studied by means of molecular dynamic simulations in explicit water. The conformational changes indicate remarkable differences among the lipases considered, not only in terms of accessibility of the active site but also of modification of the geometry of the catalytic machinery. Lipase B from Candida antarctica undergoes minor conformational change at either level, so that it appears to be the most suitable lipase for being applied and formulated in aqueous environments or other hydrophilic media. On the other side, lipase from Pseudomonas cepacia undergoes the most relevant conformational variations both at the level of the catalytic triad and the residues involved in the oxyanion stabilization, suggesting that its “interfacial activation” is not simply related to a variation of the accessibility of the active site. Indeed, preliminary experimental data here reported indicate that covalent immobilization of lipase from Pseudomonas cepacia performed in the presence of hydrophobic solvent allows one to achieve a more than 10-fold increase in immobilization yield as compared to similar protocols performed in simple aqueous buffer. On the contrary, the benefit coming from immobilizing lipase B from Candida antarctica in hydrophobic solvent appears more limited (two-fold higher immobilization yield)
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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