Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density

Innovative Strategies for Treating Retinal Diseases

Objective: The aim of this comprehensive paper is to acquaint the readers with innovative approaches in the treatment of retinal diseases, which could in the coming years to get into clinical practice. Retinal prostheses, retinal pigment epithelial (RPE) transplantation, gene therapy and optogenetics will be described in this paper. Methodology: Describing the basic characteristics and mechanisms of different types of therapy and subsequently literary minireview clarifying the current state of knowledge in the area. Results: Retinal prostheses, RPE transplantation, gene therapy and optogenetics offer yet unexplored possibilities and are considered as the future of treatment of retinal diseases where classical pharmacotherapy or surgical treatment are no longer sufficient. However, all these methods challenge not only in the innovative technical implementation itself, but also for the ethical, administrative and economic demands. Conclusion: There will be certainly interesting development in the treatment of retinal diseases, but it is not possible to fully estimate which modality of treatment will be dominant in the future.</jats:p

Ligand-forced dimerization of copper(I)–olefin complexes bearing a 1,3,4-thiadiazole core

As an important class of heterocyclic compounds, 1,3,4-thiadiazoles have a broad range of potential applications in medicine, agriculture and materials chemistry, and were found to be excellent precursors for the crystal engineering of organometallic materials. The coordinating behaviour of allyl derivatives of 1,3,4-thiadiazoles with respect to transition metal ions has been little studied. Five new crystalline copper(I) π-complexes have been obtained by means of an alternating current electrochemical technique and have been characterized by single-crystal X-ray diffraction and IR spectroscopy. The compounds are bis[μ-5-methyl-N-(prop-2-en-1-yl)-1,3,4-thiadiazol-2-amine]bis[nitratocopper(I)], [Cu2(NO3)2(C6H9N3S)2], (1), bis[μ-5-methyl-N-(prop-2-en-1-yl)-1,3,4-thiadiazol-2-amine]bis[(tetrafluoroborato)copper(I)], [Cu2(BF4)2(C6H9N3S)2], (2), μ-aqua-bis{μ-5-[(prop-2-en-1-yl)sulfanyl]-1,3,4-thiadiazol-2-amine}bis[nitratocopper(I)], [Cu2(NO3)2(C5H7N3S2)2(H2O)], (3), μ-aqua-(hexafluorosilicato)bis{μ-5-[(prop-2-en-1-yl)sulfanyl]-1,3,4-thiadiazol-2-amine}dicopper(I)–acetonitrile–water (2/1/4), [Cu2(SiF6)(C5H7N3S2)2(H2O)]·0.5CH3CN·2H2O, (4), and μ-benzenesulfonato-bis{μ-5-[(prop-2-en-1-yl)sulfanyl]-1,3,4-thiadiazol-2-amine}dicopper(I) benzenesulfonate–methanol–water (1/1/1), [Cu2(C6H5O3S)(C5H7N3S2)2](C6H5O3S)·CH3OH·H2O, (5). The structure of the ligand 5-methyl-N-(prop-2-en-1-yl)-1,3,4-thiadiazol-2-amine (Mepeta), C6H9N3S, was also structurally characterized. BothMepetaand 5-[(prop-2-en-1-yl)sulfanyl]-1,3,4-thiadiazol-2-amine (Pesta) (denotedL) reveal a strong tendency to form dimeric {Cu2L2}2+fragments, being attached to the metal atom in a chelating–bridging modeviatwo thiadiazole N atoms and an allylic C=C bond. Flexibility of the {Cu2(Pesta)2}2+unit allows the CuIatom site to be split into two positions with different metal-coordination environments, thus enabling the competitive participation of different molecules in bonding to the metal centre. ThePestaligand in (4) allows the CuIatom to vary between water O-atom and hexafluorosilicate F-atom coordination, resulting in the rare case of a direct CuI...FSiF52−interaction. Extensive three-dimensional hydrogen-bonding patterns are formed in the reported crystal structures. Complex (5) should be considered as the first known example of a CuI(C6H5SO3) coordination compound. To determine the hydrogen-bond interactions in the structures of (1) and (2), a Hirshfeld surface analysis has been performed.</jats:p

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

AbstractThis paper describes outcomes of the 2019 Cryo-EM Map-based Model Metrics Challenge sponsored by EMDataResource (www.emdataresource.org). The goals of this challenge were (1) to assess the quality of models that can be produced using current modeling software, (2) to check the reproducibility of modeling results from different software developers and users, and (3) compare the performance of current metrics used for evaluation of models. The focus was on near-atomic resolution maps with an innovative twist: three of four target maps formed a resolution series (1.8 to 3.1 Å) from the same specimen and imaging experiment. Tools developed in previous challenges were expanded for managing, visualizing and analyzing the 63 submitted coordinate models, and several novel metrics were introduced. The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual laboratory experiments and holdings of structure data archives such as the Protein Data Bank. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived from these benchmark maps by 13 participating teams, representing both widely used and novel modeling approaches. We also evaluate the pros and cons of the commonly used metrics to assess model quality and recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed density in the cryo-EM map.</jats:p

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

AbstractThis paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.</jats:p

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density