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

Files from: The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State

<p>Atomic coordinates for the molecular systems studied in <a href="http://dx.doi.org/10.1021/ct200121f">The ethidium-UA/AU intercalation site: effect of model fragmentation and backbone charge state, <em>J. Chem. Theory Comp.</em>, <strong>2011</strong>, 7, pp 2600-2609</a>.</p

Nonempirical Energetic Analysis of Reactivity and Covalent Inhibition of Fatty Acid Amide Hydrolase

Fatty acid amide hydrolase (FAAH) is a member of the amidase signature family and is responsible for the hydrolytic deactivation of fatty acid amide neuromodulators, such as anandamide. FAAH carries an unusual catalytic triad consisting of Lys-Ser-Ser, which uniquely enables the enzyme to cleave amides and esters at similar rates. The acylation of 9<i>Z</i>-octadecenamide (oleamide, a FAAH reference substrate) has been widely investigated by computational methods, and those have shown that conformational fluctuations of the active site affect the reaction barrier. Empirical descriptors have been devised to provide a possible mechanistic explanation for such conformational effects, but a first-principles understanding is still missing. A comparison of FAAH acylation with a reference reaction in water suggests that transition-state stabilization is crucial for catalysis because the activation energy barrier falls by 6 kcal/mol in the presence of the active site. With this in mind, we have analyzed the enzymatic reaction using the differential transition-state stabilization (DTSS) approach to determine key active-site residues for lowering the barrier. We examined several QM/MM structures at the MP2 level of theory and analyzed catalytic effects with a variation–perturbation partitioning of the interaction energy into electrostatic multipole and penetration, exchange, delocalization, and correlation terms. Three residues – Thr236, Ser218, and one water molecule – appear to be essential for the stabilization of the transition state, a conclusion that is also reflected by catalytic fields and agrees with site-directed mutagenesis data. An analogous analysis for URB524, URB618, and URB694 (three potent representatives of covalent, carbamate-based FAAH inhibitors) confirms the importance of the residues involved in oleamide acylation, providing insight for future inhibitor design