Prediction, expertise, and validation: An integrated approach to advancing SBDD
ScienceBlog, Events Maria Demou ScienceBlog, Events Maria Demou

Prediction, expertise, and validation: An integrated approach to advancing SBDD

Discover thoughts, practical examples, and perspectives of structural biologist and computational chemists on how integrating prediction, expertise, and experimental validation can enhance Structure-Based Drug Discovery (SBDD). In our latest blog, we summarized the key highlights from the Discngine Labs Live event in Cambridge, UK and included an event recording to fully benefit from the event insights.

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What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference
ScienceBlog, Events Elisa Martino ScienceBlog, Events Elisa Martino

What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference

The rapid advancements in structural biology techniques are revolutionizing drug discovery. We had the opportunity of exploring these breakthroughs at the PSDI Conference in Paris, November 2024.

Curious about the highlights? Check out our latest blog post by Elisa Martino, where she shares key insights from the event »

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Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study
ScienceBlog Elisa Martino ScienceBlog Elisa Martino

Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study

Can protein-protein complex models generated by AF3 effectively serve as starting points for predicting protein-protein interactions and identifying binding hotspots, thus facilitating drug design?

Using our software, 3decision®, we evaluated the accuracy of the AF3 models using Programmed cell death protein 1 (PD-1) complexes as a case study.

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What are the challenges for medicinal chemists when working with 3D structures? - Interview
ScienceBlog Marija Martini ScienceBlog Marija Martini

What are the challenges for medicinal chemists when working with 3D structures? - Interview

The continuous increase in the available 3D structural data brings along changes in the medicinal chemistry field. Dr. George Sheppard, Senior Principal Research Scientist at AbbVie, shared his thoughts on the benefits for medicinal chemists using 3D information, current challenges and limitations, and proposed potential ways for improvement, in the following interview.

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Getting ready for AlphaFold with 3decision®
ScienceBlog Marija Martini ScienceBlog Marija Martini

Getting ready for AlphaFold with 3decision®

Google-owned company DeepMind has achieved to predict 3D protein shapes with high accuracy and speed using the AI program AlphaFold. Although still in the early phase, this method can have a significant impact on drug discovery, accelerating the development of new drugs. In this article, we are discussing the importance of getting ready for the new source of structural data and how to gain the most of structural knowledge.

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Should medicinal chemists use 3D molecular modeling tools?
ScienceBlog Valentin Beuchillot ScienceBlog Valentin Beuchillot

Should medicinal chemists use 3D molecular modeling tools?

We sat down with Dr. Alexis Denis, Ph.D. Medicinal Chemistry Director at Galapagos to collect his thoughts on the question: Should medicinal chemists use 3D molecular modeling tools?
We were able to understand how he manages the collaboration in SBDD teams, but also to understand his vision of how these positions/roles could evolve in the future.

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Discngine & UserStudio: Uplifting User Experience in life science research applications
Products, ScienceBlog, TechBlog Valentin Beuchillot Products, ScienceBlog, TechBlog Valentin Beuchillot

Discngine & UserStudio: Uplifting User Experience in life science research applications

Recently, our collaborative platform, 3decision, just saw itself complemented with two new features (subpocket search & interaction search) and a radically different User Experience (UX). This new UX, with an updated User Interface (UI), is the result of months of collaborative work between UserStudio and the 3decision team.
In order to tell the story of this project, we gathered people from both companies to answer a few questions.

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SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur
ScienceBlog Peter Schmidtke ScienceBlog Peter Schmidtke

SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur

My German cartesian mind (here we go with stereotypes) asks me to start with the first protein expressed by the viral genome of SARS-Cov-2, nsp1. That is, by far, not the low hanging fruit. But it is interesting to learn more about the roles of the different constituents of the virus. Nsp1 actually has also a few very interesting roles to facilitate the viral lifecycle in its host environment.

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SARS-CoV-2 - part 2 - From the viral genome to protein structures
ScienceBlog Peter Schmidtke ScienceBlog Peter Schmidtke

SARS-CoV-2 - part 2 - From the viral genome to protein structures

The bread and butter of every structure based drug design or drug ID effort is the need for 3D structural information of a target of interest related to the phenotypic outcome we want to alter. In the case of SARS-Cov-2 several experimental structures are already available in the RCSB PDB. Other a large scale fragment screens from the Diamond Light Source are slowly becoming available (available in the 3decision protease project for now) on public resources likes the RCSB PDB. Popular homology modelling services also already started to provide several high quality models for some of the yet not resolved structures of the viral proteome.

But let’s first have a look what the viral genome actually contains and what are currently pursued efforts.

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