| 1. |
- Joosten, Robbie P., et al.
(författare)
-
PDB_REDO : automated re-refinement of X-ray structure models in the PDB
- 2009
-
Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 42, s. 376-384
-
Tidskriftsartikel (refereegranskat)abstract
- Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
|
|
| 2. |
- Blanchet, Guillaume, et al.
(författare)
-
Impacts of regional climatic fluctuations on radial growth of Siberian and Scots pine at Mukhrino mire (central-western Siberia)
- 2017
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 1879-1026 .- 0048-9697. ; 574, s. 1209-1216
-
Tidskriftsartikel (refereegranskat)abstract
- Ring width (TRW) chronologies from Siberian (Pinus sibirica) and Scots (Pinus sylvestris) pine trees were sampled at Mukhrino - a large mire complex in central-western Siberia - to evaluate the impacts of hydroclimatic variability on tree growth over the last three centuries. For this purpose, we compared climate-growth correlation profiles from trees growing on peat soils with those growing on adjacent mineral soils. Tree growth at both peat and mineral soils was positively correlated to air temperature during the vegetation period. This finding can be explained by (i) the positive influence of temperature on plant physiological processes (i.e. growth control) during the growing season and (ii) the indirect impact of air temperatures on water table fluctuations. We observe also a strong link between TRW and the winter Palmer Drought Severity Index (PDSI), especially in Siberian pine, reflecting the isolating effect of snow and limited freezing damage in roots. Significant negative relations were, by contrast, observed between bog TRW chronologies and hydroclimatic indices during spring and summer; they are considered an expression of the negative impacts of high water levels and moist peat soils on root development. Some unusually old bog pines - exhibiting >500 growth rings - apparently colonized the site at the beginning of the Little Ice Age, and therefore seem to confirm that (i) peat conditions may have been drier in Siberia than in most other regions of western Europe during this period. At the same time, the bog trees also point to (ii) their strong dependence on surface conditions.
|
|
| 3. |
- Ison, Jon, et al.
(författare)
-
The bio.tools registry of software tools and data resources for the life sciences
- 2019
-
Ingår i: Genome Biology. - : BMC. - 1465-6906 .- 1474-760X. ; 20:1
-
Tidskriftsartikel (refereegranskat)abstract
- Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue () of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.
|
|
| 4. |
- Pettifer, Steve, et al.
(författare)
-
The EMBRACE web service collection
- 2010
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 38, s. W683-W688
-
Tidskriftsartikel (refereegranskat)abstract
- The EMBRACE ( European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.
|
|
