A bibliometric analysis of the Journal of Molecular Graphics and Modelling

This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported

Dynamic and multi-pharmacophore modeling for designing polo-box domain inhibitors.

The polo-like kinase 1 (Plk1) is a critical regulator of cell division that is overexpressed in many types of tumors. Thus, a strategy in the treatment of cancer has been to target the kinase activity (ATPase domain) or substrate-binding domain (Polo-box Domain, PBD) of Plk1. However, only few synthetic small molecules have been identified that target the Plk1-PBD. Here, we have applied an integrative approach that combines pharmacophore modeling, molecular docking, virtual screening, and in vitro testing to discover novel Plk1-PBD inhibitors. Nine Plk1-PBD crystal structures were used to generate structure-based hypotheses. A common pharmacophore model (Hypo1) composed of five chemical features was selected from the 9 structure-based hypotheses and used for virtual screening of a drug-like database consisting of 159,757 compounds to identify novel Plk1-PBD inhibitors. The virtual screening technique revealed 9,327 compounds with a maximum fit value of 3 or greater, which were selected and subjected to molecular docking analyses. This approach yielded 93 compounds that made good interactions with critical residues within the Plk1-PBD active site. The testing of these 93 compounds in vitro for their ability to inhibit the Plk1-PBD, showed that many of these compounds had Plk1-PBD inhibitory activity and that compound Chemistry_28272 was the most potent Plk1-PBD inhibitor. Thus Chemistry_28272 and the other top compounds are novel Plk1-PBD inhibitors and could be used for the development of cancer therapeutics

The Journal of Computer-Aided Molecular Design: a bibliometric note

Summarizes the articles in, and the citations to, volumes 2-24 of the Journal of Computer-Aided Molecular Design. The citations to the journal come from almost 2000 different sources that span a very wide range of academic subjects, with the most heavily cited articles being descriptions of software systems and of computational methods

Modeling the vapor-liquid equilibrium and association of nitrogen dioxide/dinitrogen tetroxide and its mixtures with carbon dioxide

We have used in this work the crossover soft-SAFT equation of state to model nitrogen dioxide/dinitrogen tetraoxide (NO2/N2O4), carbon dioxide (CO2) and their mixtures. The prediction of the vapor – liquid equilibrium of this mixture is of utmost importance to correctly assess the NO2 monomer amount that is the oxidizing agent of vegetal macromolecules in the CO2 + NO2 / N2O4 reacting medium under supercritical conditions. The quadrupolar effect was explicitly considered when modeling carbon dioxide, enabling to obtain an excellent description of the vapor-liquid equilibria diagrams. NO2 was modeled as a self associating molecule with a single association site to account for the strong associating character of the NO2 molecule. Again, the vapor-liquid equilibrium of NO2 was correctly modeled. The molecular parameters were tested by accurately predicting the very few available experimental data outside the phase equilibrium. Soft-SAFT was also able to predict the degree of dimerization of NO2 (mimicking the real NO2/N2O4 situation), in good agreement with experimental data. Finally, CO2 and NO2 pure compound parameters were used to predict the vapor – liquid coexistence of the CO2 + NO2 / N2O4 mixture at different temperatures. Experimental pressure – CO2 mass fraction isotherms recently measured were well described using a unique binary parameter, independent of the temperature, proving that the soft-SAFT model is able to capture the non-ideal behavior of the mixture