Iris: Interactive all-in-one graphical validation of 3D protein model iterations

Iris validation is a Python package created to represent comprehensive per-residue validation metrics for entire protein chains in a compact, readable and interactive view. These metrics can either be calculated by Iris, or by a third-party program such as MolProbity. We show that those parts of a protein model requiring attention may generate ripples across the metrics on the diagram, immediately catching the modeler's attention. Iris can run as a standalone tool, or be plugged into existing structural biology software to display per-chain model quality at a glance, with a particular emphasis on evaluating incremental changes resulting from the iterative nature of model building and refinement. Finally, the integration of Iris into the CCP4i2 graphical user interface is provided as a showcase of its pluggable design

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: the full-length glycan composition, including linkage details for the glycosidic bonds. The developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures

Diagnóstico y propuestas estratégicas en economía circular para una industria de máquina herramienta en el área de medioambiente

[EN] During this Master's Thesis (TFM), a diagnosis and proposals for improvement in circular economy and sustainability in a machine-tool company such as SHUTON have been carried out. This project has been carried out within the context of the Circular Berrindartzea programme; where the Basque Government, through the public company IHOBE, under an agreement with the company, has financed and guided this project. In order to carry out the diagnosis of the current situation of SHUTON in circular economy, an initial training has been carried out. Using various tools offered by IHOBE, the context in which the company finds itself was assessed. Then, several opportunities were identified in which the company could make progress in terms of circular economy. Once the opportunities have been evaluated, two of them have been selected for development, the packaging process and transport logistics.[ES] En este Trabajo de Fin de Máster (TFM) se han realizado un diagnóstico y unas propuestas de mejora en economía circular y sostenibilidad en una empresa de máquina – herramienta como es SHUTON (Legutio, Araba). Este proyecto se ha llevado a cabo bajo el contexto del programa Circular Berrindartzea; donde el Gobierno Vasco, mediante la sociedad pública IHOBE, bajo convenio con la empresa mencionada ha financiado y guiado este proyecto. Para llevar a cabo el diagnóstico de la situación actual de SHUTON en economía circular, se ha realizado una formación inicial. Mediante varias herramientas ofrecidas por IHOBE, se ha evaluado el contexto en el que se encuentra la empresa. Después se han identificado varias oportunidades en las que la empresa podría avanzar en términos de economía circular. Una vez evaluados las oportunidades, se han seleccionado dos de ellas para desarrollar; el procedimiento de embalajes y la logística de los transportes.[EU] Master Amaierako Lan honetan (TFM), SHUTON bezalako makina-erremintako enpresa batean ekonomia zirkularra eta iraunkortasuna hobetzeko diagnosia eta proposamenak egin dira. Proiektu hau Circular Berrindartzea programaren testuinguruan gauzatu da; bertan, Eusko Jaurlaritzak, IHOBE sozietate publikoaren bitartez, aipatutako enpresarekin sinatutako hitzarmenean, proiektu hau finantzatu eta gidatu du. SHUTONek ekonomia zirkularrean egun duen egoeraren diagnostikoa egiteko, hasierako prestakuntza egin da. Ihobek eskainitako hainbat tresnaren bidez, enpresaren testuingurua ebaluatu da. Ondoren, enpresak ekonomia zirkularrari dagokionez aurrera egin dezakeen hainbat aukera identifikatu dira. Aukerak ebaluatu ondoren, horietako bi hautatu dira garatzeko; bilgarrien prozedura eta garraioen logistika

Loyola'tar Iñaki Deuna'ren bederatziurruna

Dialecto : texto en euskera occidental -- vizcaínoS. XX -- Periodo : últimno euskera modernoEuskalkia : mendebalekoa -- bizkaieraXX. md. -- Aroa : azken euskara modernoaDigitalización. Vitoria-Gasteiz : Fundación Sancho el Sabio, 2008Rústic

Eleiz ama deunaren ikurtonak edo sakramentuak

Dialecto : texto en euskera occidental -- vizcaínoS. XX -- Periodo : último euskera modernopEuskalkia : mendebalekoa -- bizkaieraXX. md. -- Aroa : azken euskara modernoaDigitalización. Vitoria-Gasteiz : Fundación Sancho el Sabio, 2008Carton

Whole-proteome structures shed new light on posttranslational modifications

Accurate but protein-only AlphaFold models may show structural fingerprints of likely posttranslational modifications (PTMs). In this issue of PLOS Biology, Bludau and colleagues add a functional context to models by combining them with readily available proteomics results

Carbohydrate structure: : the rocky road to automation

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to ‘protein standards’ will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most

Structural glycobiology in the age of electron cryo-microscopy

The methodology underpinning the construction, refinement, validation and analysis of atomic models of glycoproteins and protein-carbohydrate complexes has received a long-overdue boost in the last five years. This is a very timely development, as the resolution revolution in electron cryo-microscopy is now routinely delivering structures of key glycomedical importance, with a three-dimensional precision where X-ray crystallographic methods have traditionally floundered. This review will focus on the new software developments that have been introduced in the past two years, and their impact on the field of structural glycobiology in terms of published structures

Edesti Deuna

Dialecto : texto en euskera occidental -- vizcaínoS. XX -- Periodo . último euskera modernoEuskalkia : mendebalekoa -- bizkaieraXX. md. -- Aroa : azken euskara modernoaDigitalización. Vitoria-Gasteiz : Fundación Sancho el Sabio, 2008Carton