Puxano: matchmaking, mapping industry challenges to research

Puxano - biotech company

Optimizing the Procondor platform

PUXANO is a biotech company offering structure-based protein research services to pharma and biotech companies. The company differentiates from others by developing its own technologies to accelerate the process of obtaining protein structures. The procondor platform, a software platform for automated protein construct design, is one of these technologies. 

A protein construct is an optimized version of a native protein sequence that you use to express [1]  and purify [2]  a protein. The procondor platform helps to optimize the sequence in a semi-automated manner.

Wouter Van Putte (founder and CEO of Puxano): “We initially used the procondor platform internally, but we wanted to automate it further and make it available for others to use. Our intent was to accelerate how the data was collected, analyzed and transferred in a structured manner to our own data folder. This analyzed data is then used to design protein constructs. But after the first analysis, it became clear we first had to rethink how we would structure the data before accelerating the data retrieval and analysis.” 

Vlaams Supercomputer Centrum (VSC) as match-maker between Puxano and DSI 

With the ‘Call for extensive HPC support,’ the VSC Industrial Board invites applications from organizations in Flanders with an interesting idea that would benefit from using High-Performance Computing to increase their competitiveness. Puxano participated in the ‘Call for extensive HPC support.

Carl Mensch (VSC): “The services offered by Puxano are highly technology-driven. In protein structure determination, a lot of data is generated that needs to be processed. To meet this computational demand, Puxano has employed the high-performance computing services of VSC when their own computers were not up to the task. Furthermore, it was clear that the novel technologies that Puxano develops could benefit from further in-depth support of domain experts in data science.”

Matchmaking is one of the services offered by VSC: finding the right partner to help solve research questions of users. In this case, VSC introduced Puxano to the Data Science Institute of UHasselt (DSI). DSI brings together over 150 researchers working in the broad field of data science across faculties and research groups at Hasselt University. DSI's main objective is to facilitate a data-driven future. Apart from supporting & enhancing academic collaboration DSI also supports organizations and companies with consultancy. For Puxano, DSI redesigned the scope of the project of the Proconder platform. 

Wouter Van Putte (Puxano): “Our key objective was to rethink our current script for protein construct design into a software platform. This included redesigning the procondor dataset of protein features at the meta and sequence level. The idea was to find out which type of database structure served best to integrate protein information in different formats, to be updated quickly, have efficient data storage, easily updatable and easily searchable.” 

Design of a suitable database structure by DSI

Through a structured step-by-step approach, DSI helped Puxano design a suitable database structure 
Stijn Van Summeren (research professor DSI): “First, we jointly specified the concrete database requirements in terms of data to be stored, queries to be supported, and performance requirements. Based on this analysis, we proposed a corresponding database. Once the blueprint design was approved and the implementation system was selected, we implemented the initial database prototype.”  

Wouter Van Putte: “Thanks to DSI’s expertise in data analysis and structuring data, we got a better idea of how to make protein data in different formats accessible in the procondor platform and to perform certain analyses from drug target selection to protein engineering more efficiently.

The developed database is being incorporated into the Puxano analysis pipelines and serves as the core source of information for the Puxano (web-based) service platform.
A successful synergy between theory and practice  
The fresh outsider look from DSI gave Puxano new insights to approach their database. 

Wouter Van Putte: “People from various backgrounds look to problems from different perspectives. During the interactions with Stijn, new questions arose which really helped us to define how we would structure our data and platform in the future.” 

Stijn Van Summeren (UHasselt): “I aim for a successful synergy between theory and practice, where problems from practical applications and systems motivate the development of relevant theory. Conversely, the theoretical insights are applied to build more performant systems. This project is a perfect illustration of such a successful synergy.’ 

Academia understands and can respond to the needs of industry

Wouter Van Putte: “We are very positive about the collaboration with academia. The approach was very professional. Stijn took time to analyze the problem, and all results were delivered in a timely manner. He succeeded in understanding our needs by asking the right critical questions. That was very valuable for the success of the project.” 

This is also what the VSC strives to achieve, as Mia Vanstraelen, VSC Industrial Board’s chair, points out: “VSC is dedicated to driving innovation in Flanders. In addition to offering top-notch HPC infrastructure and consultancy services, we focus on bridging knowledge and experiences from academia to industry and vice versa.”

[1] Protein expression refers to the way in proteins are synthesized, modified and regulated in living organisms. In protein research, the term can apply to either the object of study or the laboratory techniques required to manufacture proteins. (Thermofisher scientific). 

[2] Protein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms      (Source: Wikipedia

Published on 27/04/2023

Wouter Van Putte

Wouter Van Putte 

Wouter Van Putte, PhD is the Director & co-Founder of PUXANO, a Belgian biotechnology company that provides structure-based R&D services to pharmaceutical and biotechnology companies. He has a licensed degree in Philosophy, a master’s degree in Biochemistry and a PhD in Structural Biology. Within PUXANO, he steers R&D teams that develop novel nano-, bio- and computational technologies that accelerate structural biology workflows. 

Stijn Vansummeren

Stijn Van Summeren 

Stijn Vansummeren is a research professor of Data Management and Data Wrangling at the Data Science Institute of Hasselt University, Belgium. His research focuses on large-scale data management, with as overarching theme the study, development, and application of formal approaches to wrangling, querying and analysing data at scale. As a guiding principle, prof. Vansummeren aims for a successful synergy between theory and practice, where problems from practical applications and systems motivate the development of relevant theory. Conversely, the theoretical insights are applied to build more performant systems.  
Prof. Vansummeren’s research has been awarded the ACM SIGMOD Research Highlights Award (2018), the best paper award at WebDB (2016), and the best paper nomination award at the World Wide Web (WWW) conference (2008).