Explore the insights from industry experts on how to manage vast 3D protein structures to facilitate new design ideas in SBDD
Gain valuable insights into the selectivity of CLK kinase inhibitors with 3decision®. In this use case, we will show you the data sets preparation and binding mode analysis of the CLK kinase inhibitors’ using some of the 3decision’s cool features adapted to this specific scientific use case.
Following our Discngine Labs event and discussion with scientists in early drug discovery, we have summarized insights and experiences of the community on how they use AlphaFold technology to make it more suitable for drug discovery projects.
Discngine Labs: Protein structure prediction
What’s next after AlphaFold?
The introduction of machine learning (ML) approaches for protein structure prediction has been a game changer in the life science industry. The breakthrough with DeepMind’s technology AlphaFold immediately impacted drug discovery research by providing access to thousands of unprecedented protein structures.
However, the structure alone doesn’t tell the whole story. The scientific community is now building up on the foundation of this technology to introduce the functional context of AlphaFold predicted structures, accounting for non-protein molecules, interactions, and dynamics.
In our fourth Discngine Labs, the experts from both pharma and academia will present how they use AlphaFold and other machine-learning-based technologies to develop methods that predict protein structures even more suitable for drug discovery applications.
Hear from our speakers…
Event chair:
Seth Harris
Director of Computational Structural Biology
Genentech
Presenters:
Robbie Joosten
Research associate
Netherlands Cancer Institute
Christian Tyrchan
Team leader of Computational Chemistry
AstraZeneca
Jola Kopec
Senior Scientist I
Evotec
Andy Dore
Head of Structural Sciences
CharmTherapeutics
Sergey Bartunov
Heads of AI
Charm Therapeutics
… and discover:
What has happened since the release of AlphaFold, and where is its current biggest impact on drug discovery projects?
How can you adjust the AlphaFold algorithm toward drug discovery applications?
The limitations of ML-based protein structure predictions that persist and future perspectives
Where are we with Cryo-EM in Pharma?
Read the key takeaway messages from the Discngine Labs roundtable discussion with the domain experts from ThermoFisher Scientific, Sanofi, Boehringer Ingelheim and Nanoimaging Services, hosted by Gabriella Jonasson, PhD.
Discngine Labs: Virtual Reality for Structure-Based Drug Discovery
Ever wondered how Virtual Reality for Drug Design looks like in practice?
In the second session of our Discngine Labs we hosted industry experts Wilian Cortopassi and Dr. Rishi Gupta from Novartis Institutes for BioMedical Research (NIBR) that presented the “NIBR”Verse: the multidimensional space that brings together data and peers from all over the world in a single (virtual) place for effective collaborations in structure-based drug design.
The presentation was followed by the panel discussion on the current and future opportunities of Virtual Reality for Drug Discovery. Steve McCloskey, from the leading VR software company Nanome, chaired the discussion where industry experts and early adopters , Carmine Talarico, Dompe and Marc Baaden, The French National Centre for Scientific Research, shared their thoughts and experiences on the topic. Panelists were:
In this on-demand content you will learn:
What is the concept behind “NIBR”verse for drug discovery
How Virtual Reality can dramatically increase the productivity and efficiency of your research projects
A case study of successful project outcome with Discngine, Nanome and Novartis integrated technologies
The future trends for collaborative drug design
![The future of Cryo-EM in Pharma [event highlights]](https://images.squarespace-cdn.com/content/v1/5874c065e6f2e14222c3aa73/1664381641236-BME2BI6A4BW54VS6GGBM/Discngine+Labs+promo+ARTICLE.png)
Industry experts shared their experience with the application of the Cryo-EM structures in their drug discovery projects in our Discngine Labs event. Have a look at the key take-aways and access the recording
In this use case, we will show you the structural differences between Helios and its family members that aided the design of molecular glue. We used some of 3decision’s cool features adapted to this specific scientific use case.
Quick, Flexible and Secure are just some of the advantages of 3decision AWS Quick Start for pharma and biotech. Learn more about how you can benefit from streamlined deployment of 3decision on Amazon Web Services (AWS) cloud from our cloud expert Alexandre Gillet.
Discngine and Confo Therapeutics are starting strategic collaboration to enhance GPCR drug discovery. Companies aim to further collaborate on the future development of 3decision®.
![Efficient biomolecular structural data handling and analysis [Event highlights]](https://images.squarespace-cdn.com/content/v1/5874c065e6f2e14222c3aa73/1649178707347-8ONZWAJD9LKM95UD5Y30/maxresdefault.jpg)
After officially announcing the partnership, Discngine and Chemaxon organized a joint event to elaborate on technical and scientific opportunities coming from joint efforts.
Integrating several of ChemAxon’s cheminformatics and biologics software components into 3decision will expand its capabilities to work on larger biological entities, in addition to the already available features for proteins and small molecules. The registration and visualization of biological entries, like antibodies or peptides, efficient data mining, and advanced analytical capabilities will be accessible.
Get to know the latest advances of five structural biology techniques and how how they impact structure-based drug discovery
How can you be more efficient in deciding what compound to make next?
Read the key takeaway messages from the BAGIM panel discussion with experts from AstraZeneca and Novartis, hosted by Gabriella Jonasson, PhD.
Through this usecase you will get to know how to find novel chemical entities in early drug discovery using 3decision protein-ligand interaction-based search. As an example, we performed a scaffold optimization of an active compound co-crystallized with the malaria target DHODH.
In early drug discovery, coming up with rational ideas for chemically novel and biologically active compounds is no easy task. To assist the project team in this crucial ideation process, we introduce a new tool that allows you to quickly collect new starting points and alternative scaffolds by scanning the PDB for similar interaction patterns.
In this webinar, Gabriella Jonasson will present one of 3decision's latest features - the protein-ligand interaction search. During the presentation, she will show you how to mine the entire protein-ligand interaction structural knowledge base for systems containing a specific 3D interaction pattern. She will then overlay and compare the results to our query structure in order to design new ideas on the fly.
The purpose of this article is to illustrate how to apply some of 3decision’s features in scientific research. For this use case, the 3decision Subpocket Similarity Search is used to suggest modifications for the optimization of a small- molecule PROTAC. The Protein-Ligand interaction coloring by statistics is then used to evaluate docking poses of new compounds. The bromodomain-containing protein 4 – cereblon complex (BRD4-CBRN) and its degrader dBET23 are used as an example.
Discngine’s 3decision team is partnering up with Nanome to bring a new dimension to structural analysis. With 3decision in VR, users will be able to entirely exploit the structural knowledge stored in 3decision in a new and advanced way to accelerate drug-design processes.
![An innovative way of organizing data: How can 3decision® improve decision-making process? [Customer Success Story]](https://images.squarespace-cdn.com/content/v1/5874c065e6f2e14222c3aa73/1619614689736-618AAU5KTNNE3M4MZQN0/thumbnail+2.png)
Manuel Cases Thomas, a Medicinal chemistry consultant and director at Senechaem was looking for a solution to help him use the full potential of data at hand and generate new design ideas. In this interview, he shares how 3decision® makes a difference in his daily work: from a scientific need to the impact on design ideas and successful project outcomes.
I found my way to quickly learn new software: by validating its features. In this article, I am presenting the retrospective analysis of the detection of BCR-ABL1 allosteric binding site using the 3decision Pocket Explorer feature.