Bio-Prodict has recently released a novel tool for automatic design of enzyme panels using protein family data. This tool ensures that the enzymes in a panel have maximum specificity diversity. This allows for rapid screening for enzymes that can convert (novel) substrates.
How it works
First hotspots related to specificity are defined using different parameters such as, structural distance to the substrate cave, availability of literature describing relations to specificity, correlated mutation data, etc. Than the tool divides a protein family into groups based on the different sequence motifs that are present at these specificity hotspots. Next, the user can select the number and the type of sequences (e.g. a published sequence, or a swiss-prot sequence, see fig 1) which are preferred in the panel from each group. The result is plotted on a phylogenic tree of the enzyme family to analyze how the groups are divided over the phylogenetic tree (see figure 2).
Fig 1. Panel design tool. At the top five selected hotspots are shown, (here based on correlating positions) which are used for generating motif groups (45 groups). In this example published sequences and sequences from the Swiss-prot and the TrEMBL databases are preferred in the panel. The bottom shows the different sequence motifs detected at the five hotspots.
Fig 2. Phylogenetic tree tool. The resulting sequence selection (fig 1) is plotted on a phylogenetic tree of the protein family. This enables the user to analyze the coverage and spread of sequences over the protein family. The colored sequences are the sequences selected for the enzyme panel.
In the summer of 2015, the project partners gathered in Nijmegen, the Netherlands for a three day course given by Bio-Prodict on 3DM protein super-family information systems. In this course the participants were taught to use 3DM for the design of smart but small mutant libraries to optimize enzymes. This course covered the use of protein structure visualization tools, the use of protein sequence alignments to discover evolutionary patterns and automated literature mining tools to assign function to protein residues.
The 3DM course will gave an overview of what 3DM information systems can and cannot do when applied to problems in Protein Engineering, Homology Modeling and Drug Design. The participants explored different kinds of protein super-family data and learned how to use and extract relations from the data. The structure visualization tool YASARA was used to deal with the data from a structural perspective, whereas Utopia Documents showed them how the data in the 3DM systems is integrated with full-text literature. The course contained a large practical component in which the participants learned to work with the tools using real-life protein engineering and drug design examples.
If you want to know more about 3DM technology visit BIOP website or watch the following video:
SUSMOM is a project partner specialized in Intellectual Property and in Industrial Sustainable Chemistry. A new product of the firm is being commercialized: a Competitive Intelligence analysis of Ezetimibe.
Ezetimibe is a commercially available anti-cholesterolemic drug whose IP rights will expire shortly. Tthis Competitive Intelligence dossier includes a patent analysis on Ezetimibe, in particular about its synthesis and pharmaceutical formulations.
See Dr. Pablo Domíngez and his team’s work and request a copy: http://sustainable-momentum.net/uploads/File/Ezetimibe_Patent_Analysis_Flyer.pdf
For more information about their expertise, services and products visit the Sustainable Momentum page.
The Netherlands' Catalysis and Chemistry Conference attracts about 500 participants, including around 100 scientists from industry. The meeting comprises plenary and keynote lectures from invited speakers and selected oral papers and posters. Scientists, and especially PhD-students, are encouraged to submit abstracts so they can present their work and discuss it with leading scientists and representatives from industry.
NCCC offers a unique, international forum to exchange innovative ideas between academic and industrial scientists in a broad area of catalysis and chemistry research and technology.
This event will be held in Noordwijkerhout, The Netherlands during 7th - 9th March 2017. Prof. Dr. G.J. Poelarends from RUG, a leading PI of the Carbazymes project will give a keynote lecture, about (Bio) Organic Synthesis and Catalysis.
For more information: http://www.n3c.nl/
On February 25th 2016 the IUCT Project Manager, Dr. Roberto Horcajada shared his experience in preparing H2020 proposals for Biotechnology.
The event was organized by the Spanish Association of Biocompanies (ASEBIO) and the Fundació Pons, was focused on Intellectual Property and took place in Madrid, Spain. The “How to prepare a successful proposal in H2020 Biotech?” event presented to the attendees the highlights about IPR, the opportunities in BIOTEC WP2016-2017 H2020 calls and the know-how of the experts.