Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.Peer Reviewe

Experimental and simulated phase separation in a PS-b-PMMA/Au-PEO thin film

<p>Comparison of experimental (left, SEM images) and simulation (right, DDFT/BD) phase separation dynamics in an ultra thin film (20-30 nm) comprising a 1000 kDa PS-PMMA block copolymer and gold nanoparticles coated with PEO (5kDa). The system starts from a homogeneous dispersion and evolves towards microphase separated BCP domains with hexagonal NP structures selectively locating in PMMA-rich areas.</p> <p>This work is part of a published article: Hierarchical structuring in block copolymer nanocomposites through two phase separation processes operating on different time scales, E. Ploshnik, K. M. Langner, A. Halevi, M. Ben-Lulu, A. H. E. Müller, J. G. E. M. Fraaije, G. J. A. Sevink, R. Shenhar, Adv. Funct. Mater. 2013, http://dx.doi.org/10.1002/adfm.201300091.</p> <p>Available under the terms of the Creative Commons Attribution 3.0 license: http://creativecommons.org/licenses/by/3.0/.</p

Release of cclib version 1.4

This is an archive of the source code for cclib version 1.4, orginally released on github (https://github.com/cclib/cclib/releases/tag/v1.4)

Robust Predictive Power of the Electrostatic Term at Shortened Intermolecular Distances

At distances shorter than equilibrium, electrostatic interactions seem to be a more robust indicator of relative molecular dimer stability than more accurate electronic structure approaches. We arrive at this conclusion by investigating the nonparametric correlation between reference interaction energies at equilibrium geometries (coupled cluster with singles, doubles, and perturbative triples at the complete basis set limit, Δ<i>E</i>_CCSD(T)^CBS,ref) and its various approximate values obtained at a range of distances for a training set of 22 biologically relevant dimers. The reference and other costly methods start to fail to reproduce the equilibrium ranking of dimer stabilities when the intermolecular distance is shortened by more than 0.2 Å, but the full electrostatic component (includes penetration) maintains a high success rate. Such trends provide a new perspective for any applications where inaccurate structures are used out of necessity, such as the scoring of ligands docked to enzyme active sites

Robust Predictive Power of the Electrostatic Term at Shortened Intermolecular Distances

At distances shorter than equilibrium, electrostatic interactions seem to be a more robust indicator of relative molecular dimer stability than more accurate electronic structure approaches. We arrive at this conclusion by investigating the nonparametric correlation between reference interaction energies at equilibrium geometries (coupled cluster with singles, doubles, and perturbative triples at the complete basis set limit, Δ<i>E</i>_CCSD(T)^CBS,ref) and its various approximate values obtained at a range of distances for a training set of 22 biologically relevant dimers. The reference and other costly methods start to fail to reproduce the equilibrium ranking of dimer stabilities when the intermolecular distance is shortened by more than 0.2 Å, but the full electrostatic component (includes penetration) maintains a high success rate. Such trends provide a new perspective for any applications where inaccurate structures are used out of necessity, such as the scoring of ligands docked to enzyme active sites

Files from: Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane

<p>Atomic coordinates for the four molecular systems studied in <a href="http://dx.doi.org/10.1021/jp056836b">Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane, <em>J. Phys. Chem. B</em>,<em> </em><strong>2006</strong>, 110 (19), pp 9720–9727</a>.</p

Release of cclib version 1.5

<p>This is an archive of the source code for cclib version 1.5, orginally released on github (https://github.com/cclib/cclib/releases/tag/v1.5).</p