CCD2: design constructs for protein expression, the easy way.

Studying the function or structure of proteins usually requires the generation of many protein-truncation constructs for recombinant expression, which is a tedious and error-prone job. CCD2 is a software tool designed to facilitate and automate this task. CCD2 helps scientists by aggregating the information necessary to design protein-expression constructs. This information includes sequence conservation, secondary structure prediction, domain(s) and disorder detection, post-translational modifications and information on similar (domain) structures that are available in the Protein Data Bank. CCD2 then allows users to easily choose the boundaries for protein constructs and automatically generates the primers necessary for construct amplification by polymerase chain reaction. Finally, CCD2 provides a quick analysis of the properties of the chosen constructs, together with their DNA vector maps for bookkeeping. The features of CCD2 are discussed step by step, showing that it can be a useful tool for laboratories that engage in recombinant protein production for any type of experiment, and in particular for structural biology studies.

LAHMA: structure analysis through local annotation of homology-matched amino acids.

Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays structural features in sequence space, allowing users to uncover differences between homologous structure models that can be analyzed for their relevance to chemistry or biology. LAHMA visualizes numerous structural features, also allowing one-click comparison of structure-quality plots (for example the Ramachandran plot) and `in-browser' structural visualization of 3D models.

West-Life: A Virtual Research Environment for structural biology.

The West-Life project (https://about.west-life.eu/) is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of structural biologists, and in particular to support integrative experimental approaches within the field of structural biology. It has developed enhancements to existing web services for structure solution and analysis, created new pipelines to link these services into more complex higher-level workflows, and added new data management facilities. Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.