Breaking the Fourth Wall: Modulating Quaternary Associations for Protein Regulation and Drug Discovery

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Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities

Guido Van Mierlo

Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emer ...

AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC2021

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

Vassily Hatzimanikatis, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Noushin Hadadi, Anush Chiappino-Pepe

The discovery of a drug requires over a decade of intensive research and financial investments – and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied ...

2021

Can Precision Electrophile Signaling Make a Meaningful and Lasting Impression in Drug Design?

Yimon Aye, Amogh Kulkarni

For several years, drugs with reactive electrophilic appendages have been developed. These units typically confer prolonged residence time of the drugs on their protein targets, and may assist targeting shallow binding sites and/or improving the drug-prote ...

WILEY-V C H VERLAG GMBH2022

An Oculus to Profile and Probe Target Engagement In Vivo: How T-REX Was Born and Its Evolution into G-REX

Yimon Aye, Chloé Rogg

Here we provide a personal account of innovation and design principles underpinning a method to interrogate precision electrophile signaling that has come to be known as "REX technologies". This Account is framed in the context of trying to improve methods ...

AMER CHEMICAL SOC2021

Methods for the generation of large combinatorial macrocycle libraries

Sevan Mleh Habeshian

Macrocycles are an attractive class of molecules due to their good binding properties and yet rather small size that allows, in many cases, crossing membranes to reach intracellular targets. In comparison to classical small molecule drugs, macrocycles are ...

EPFL2021

SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions

Jaume Bonet Martinez

BackgroundStatistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we deco ...

2021

Fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Freyr Sverrisson

Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...

IEEE COMPUTER SOC2021

The functional proteome landscape of Escherichia coli

Camille Véronique Bernadette Goemans

Recent developments in high-throughput reverse genetics1,2 have revolutionized our ability to map gene function and interactions3,4,5,6. The power of these approaches depends on their ability to identify functionally associated genes, which elicit similar ...

2020

Development of Photocatalysts towards the Visible-Light driven C-Terminal Bioconjugation of Peptides and Proteins

Marion Marie-Agnès Garreau

If small molecules have led to tremendous progress in curing diseases, new therapeutic agents such as peptides or antibody-drugs conjugates have emerged as a highly promising next generation of pharmaceuticals. As for small molecules, their derivatization ...

EPFL2020

MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

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