Cryo‐EM targets in CASP13: overview and evaluation of results

Structures of seven CASP13 targets were determined using cryo‐electron microscopy (cryo‐EM) technique with resolution between 3.0 and 4.0 å. We provide an overview of the experimentally derived structures and describe results of the numerical evaluation of the submitted models. The evaluation is carried out by comparing coordinates of models to those of reference structures (CASP‐style evaluation), as well as checking goodness‐of‐fit of modeled structures to the cryo‐EM density maps. The performance of contributing research groups in the CASP‐style evaluation is measured in terms of backbone accuracy, all‐atom local geometry and similarity of inter‐subunit interfaces. The results on the cryo‐EM targets are compared with those on the whole set of eighty CASP13 targets. A‐posteriori refinement of the best models in their corresponding cryo‐EM density maps resulted in structures that are very close to the reference structure, including some regions with better fit to the density

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

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

O zagadnieniu poprzecznie izotropowej półprzestrzeni osłabionej szczeliną kołową wypełnioną gazem

An axially-symmetric problem of a penny-shaped crack situated in a position parallel to the boundary of a semi-infinite transversely isotropic solid is formulated with due regard for the presence of an ideal gas in the crack. The method of the Hankel integral transforms is used to solve this problem. The dual integral equations obtained are reduced to a set of integral equations which are solved numerically. The graphs presented illustrate the influence of the gas on the stress intensity factors of Mode I and Mode II.W pracy rozważono osiowo-symetryczne zagadnienie kołowej szczeliny wypełnionej idealnym gazem i położonej równolegle do brzegu półprzestrzeni sprężystej poprzecznie izotropowej. Używając techniki transformacji całkowej Hankela, rozpatrywany problem został sprowadzony do złożonego układu równań całkowych. Na podstawie procedury numerycznej zbadano i zilustrowano wpływ gazu na współczynniki intensywności naprężeń

Contact strength of a system of two elastic half spaces with an axially symmetric recess under compression

Frictionless contact of two isotropic half spaces is considered one of which has a small smooth circular recess. A method of solving the corresponding boundary value problem of elasticity in axially symmetric case is presented via the function of gap height. The governing integral equation for this function is solved analytically by assuming a certain shape of the initial recess. On the basis of the closed-form solution obtained the strength analysis of a contact couple is performed and illustrated from the standpoint of fracture mechanics

O zagadnieniu pewnego defektu międzywarstwowego wypełnionego ściśliwym płynem w periodycznym ośrodku warstwowym

A periodic two-layered elastic containing an interface defect filled with a barotropic compressible fluid is considered. At infinity, the composite is subjected to a uniformly distributed load applied perpendicularly to the layering. Faces of the defect are under action of constant internal fluid pressure. An approximate solution to this problem is given within a certain homogenized model. The resulting singular integro-differential equation is obtained and solved for two types of defects by using an analogue of Dyson's theorem. The influence of the filler on the mechanical behaviour of the considered body is analysed and illustrated graphically.W pracy rozważono zagadnienie periodycznej dwuwarstwowej przestrzeni zawierającej defekt na granicy warstw, który wypełniony jest ściśliwym płynem. Zakłada się, że kompozyt jest pod działaniem stałego obciążenia w nieskończoności prostopadłego do uwarstwienia, a powierzchnie defektu są pod wpływem stałego i nieznanego wewnętrznego ciśnienia płynu. Analizowany problem sprowadza się w ramach pewnego zhomogenizowanego modelu do poszukiwania rozwiązania osobliwego równania całkowo-różniczkowego. Wyniki otrzymano dla dwóch typów defektu z użyciem analogu twierdzenia Dysona. Zbadano i zilustrowano wpływ wypełniacza defektu na mechaniczne zachowanie rozważanego ciała