1,721,524 research outputs found
Protein-ligand binding affinities from large-scale quantum mechanical simulations
No full textThe accurate prediction of protein-drug binding affinities is a major aim of computational drug optimisation and development. A quantitative measure of binding affinity is provided by the free energy of binding, and such calculations typically require extensive configurational sampling of entities such as proteins with thousands of atoms. Current binding free energy methods use force fields to perform the configurational sampling and to compute interaction energies. Due to the empirical nature of force fields and the neglect of electrons, electron polarisation and charge transfer are not accounted for explicitly. This can limit the accuracy with which interactions are calculated and consequently the free energies obtained. Ideally ab initio quantum chemistry approaches should be used as these explicitly include the electrons. However, conventional ab initio approaches are not suitable due to their prohibitively high computational cost and unfavourable scaling.In this thesis we use large-scale ab initio quantum chemistry calculations within the Density Functional Theory (DFT) method to address the above mentioned limitations of force fields. To obtain quantitative results with ab initio approaches it is important to converge the calculations with the size of the basis set. For this reason we have used the ONETEP program, which is capable of linear-scaling DFT with near-complete basis set accuracy.A well known binding free energy approach is the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA), which obtains free energies from evaluation of the energy of configurations in an implicit solvent model. We present the first application of a “QM-PBSA” approach to a protein-ligand system containing over 2600 atoms. In this QM-PBSA approach the energies of the configurations in vacuum are evaluated with ONETEP. The solvation energies were also obtained with ONETEP using a minimal parameter implicit solvent model within the self-consistent calculation. Large-scale DFT calculations were also applied within a more theoretically rigorous free energy approach which can, in principle, obtain the full entropic contributions to free energy change. The method performs a mutation from a molecular mechanical (MM) description to an quantum mechanical (QM) description of a system. As a result a QM correction is added to the relative binding free energy obtained from a thermodynamic integration calculation within the MM description.This approach was combined with an electrostatic embedding model within ONETEP and used to calculate the hydration energies of small molecules. As well as the computation of more accurate energies, large-scale DFT calculation compute the electron density of the entire system. Using electron density analysis approaches, such as the Hirshfeld density analysis, in combination with energy decomposition approaches, such as a second order perturbation estimate of natural bond orbital interactions, both qualitative and quantitative understandings can be gained into the contributions of particular chemical functional groups that define protein-ligand interactions. These two approaches where applied to study complexes of the Phosphodiesterase type 5 protein and used to rank ligand binding affinities that agree well with then experimentally observed trends
Targeting fibroblast growth factor receptor in breast cancer: a promise or a pitfall?
No full textFibroblast growth factors (FGFs) along with their receptors (FGFRs) are involved in several cellular functions, from embryogenesis to metabolism. Because of the ability of FGFR signalling to induce cell proliferation, migration and survival in cancer, these have been found to become overactivated by several mechanisms, including gene amplification, chromosomal translocation and mutations. New evidences indicate that FGFs and FGFRs may act in an oncogenic fashion to promote multiple steps of cancer progression by inducing mitogenic and survival signals, as well as promoting epithelial-to-mesenchymal transition, invasion and tumour angiogenesis. This review focuses on the predictive and prognostic role of FGFRs, the role of FGFR signalling and how it may be most appropriately therapeutically targeted in breast cancer
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
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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