Publications related to Cheminformatics

Related publications (27)

Towards high-throughput many-body perturbation theory: efficient algorithms and automated workflows

Giovanni Pizzi, Antimo Marrazzo, Junfeng Qiao

The automation of ab initio simulations is essential in view of performing high-throughput (HT) computational screenings oriented to the discovery of novel materials with desired physical properties. In this work, we propose algorithms and implementations ...

NATURE PORTFOLIO2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets

Christoph Merten, Vida Vafaizadeh

Droplet microfluidics is a powerful tool for a variety of biological applications including single-cell genetics, antibody discovery and directed evolution. All these applications make use of genetic libraries, illustrating the difficulty of generating che ...

NATURE PORTFOLIO2022

Identification of a Heteroleptic Pd6L6L′6 Coordination Cage by Screening of a Virtual Combinatorial Library

Rosario Scopelliti, Kay Severin, Farzaneh Fadaei Tirani, Suzanne Maria Jansze, Rujin Li, Sylvain Alexandre Marie Sudan

The design of structurally defined heteroleptic coordination cages is a challenging task, and only few examples are known to date. Here we describe a selection approach that allowed the identification of a novel hexanuclear Pd cage containing two types of ...

2021

Image- and Fluorescence-Based Test Shows Oxidant-Dependent Damages in Red Blood Cells and Enables Screening of Potential Protective Molecules

Gerardo Turcatti, Benjamin Rappaz, Michel Prudent, Manon Sandra Bardyn

An increase of oxygen saturation within blood bags and metabolic dysregulation occur during storage of red blood cells (RBCs). It leads to the gradual exhaustion of RBC antioxidant protective system and, consequently, to a deleterious state of oxidative st ...

2021

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Vassily Hatzimanikatis, Jasmin Maria Hafner

Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valua ...

Nature Research2021

Antiviral Screen against Canine Distemper Virus-Induced Membrane Fusion Activity

Gerardo Turcatti, Marc Chambon, Jonathan Patrice Vesin

Canine distemper virus (CDV), a close relative of the human pathogen measles virus (MeV), is an enveloped, negative sense RNA virus that belongs to the genus Morbillivirus and causes severe diseases in dogs and other carnivores. Although the vaccination is ...

2021

Macrocycle synthesis strategy based on step-wise “adding and reacting” three components enables screening of large combinatorial libraries

Christian Heinis, Gerardo Turcatti, Alessandro Angelini, Alessandro Zorzi, Jonathan Patrice Vesin, Kaycie Marie Butler, Julien Bortoli Chapalay, Sangram Shivdas Kale, Ganesh Kumar Mothukuri, Carl Leonard Stenbratt

Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three ...

2020

DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening

Guillaume André Jean Fraux

Benchmarking is a crucial step in evaluating virtual screening methods for drug discovery. One major issue that arises among benchmarking data sets is a lack of a standardized format for representing the protein and ligand structures used to benchmark the ...

2020

An optimized and validated 384-well plate assay to test platelet function in a high-throughput screening format

Nikolaos Stergiopoulos, Olivier Burri, Rodrigo Araujo Fraga Da Silva, Marc Chambon, Augusto Martins Lima, Maiia Bragina, Julien Bortoli Chapalay

Despite significant advances in the treatment of cardiovascular diseases, antiplatelet therapies are still associated with a high risk of hemorrhage. In order to develop new drugs, methods to measure platelet function must be adapted for the high-throughpu ...

TAYLOR & FRANCIS INC2019

Micropollutant Oxidation Studied by Quantum Chemical Computations: Methodology and Applications to Thermodynamics, Kinetics, and Reaction Mechanisms

Urs von Gunten, Peter Rudolf Tentscher, Minju Lee

The abatement of organic micropollutants during oxidation processes has become an emerging issue for various urban water systems such as drinking water, wastewater, and water reuse. Reaction kinetics and mechanisms play an important role in terms of effici ...

American Chemical Society2019

An ecotoxicological view on neurotoxicity assessment

The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts in ...

SPRINGEROPEN2018

A computer-based prediction platform for the reaction of ozone with organic compounds in aqueous solution: kinetics and mechanisms

Urs von Gunten, Minju Lee

Ozonation of secondary wastewater effluents can reduce the discharge of micropollutants by transforming their chemical structures. Therefore, a better understanding of the formation of transformation products during ozonation is important. In this study, a ...

Royal Soc Chemistry2017

On the functional group composition of organic aerosol

Giulia Ruggeri

Atmospheric aerosol is ubiquitous and its impact on climate and health has not been fully understood yet. Multiple diverse processes and sources lead to atmospheric aerosol formation and emission and this reflects on its heterogeneity in chemical compositi ...

EPFL2017

Computational design of environmental sensors for the potent opioid fentanyl

Kai Johnsson, Luc Reymond

We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to opt ...

Elife Sciences Publications Ltd2017

Technical Note: Development of chemoinformatic tools to enumerate functional groups in molecules for organic aerosol characterization

Satoshi Takahama, Giulia Ruggeri

Functional groups (FGs) can be used as a reduced representation of organic aerosol composition in both ambient and controlled chamber studies, as they retain a certain chemical specificity. Furthermore, FG composition has been informative for source apport ...

Copernicus GmbH2016

Thermal Stability Predictions for Inherently Safe Process Design Using Molecular-Based Modelling Approaches

Thierry Meyer, Nadia Baati, Francis Stoessel, Annik Nanchen

For efficient inherently safe design, awareness of all available options at the appropriate decision-making moment is key. Simulations offer both timely availability and large screening possibilities. Therefore computer-aided product design gained in popul ...

Aidic Servizi Srl2016

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

Vassily Hatzimanikatis, Noushin Hadadi, Adrian Shajkofci, Jasmin Maria Hafner, Aikaterini Zisaki

Because the complexity of metabolism cannot be intuitively understood or analyzed, computational methods are indispensable for studying biochemistry and deepening our understanding of cellular metabolism to promote new discoveries. We used the computationa ...

Amer Chemical Soc2016

In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis

Berend Smit, Kyriakos Stylianou, Samantha Lynn Anderson

In this work we present the in silico design of metal-organic frameworks (MOFs) exhibiting 1-dimensional rod topologies. We introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type ...

2016

Integrating Gene Synthesis and MITOMI for Rapid Protein Engineering

Matthew Christopher Blackburn

The research described within this thesis is primarily motivated by two fields of science with reversed, yet complementary, approaches to addressing the same essential objective: manipulating and understanding the complex program of life. Whereas synthetic ...

EPFL2016