Publications related to Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

Related publications (21)

OSCAR: an extensive repository of chemically and functionally diverse organocatalysts

Anne-Clémence Corminboeuf, Alberto Fabrizio, Rubén Laplaza Solanas, Sergio Vela Llausi, Simone Gallarati, Puck Elisabeth van Gerwen

The automated construction of datasets has become increasingly relevant in computational chemistry. While transition-metal catalysis has greatly benefitted from bottom-up or top-down strategies for the curation of organometallic complexes libraries, the fi ...

ROYAL SOC CHEMISTRY2022

New Vinylation and Alkynylation Strategies with Hypervalent Iodine Reagents and Diazo Compounds

Guillaume Dominique Pisella

The development of a sequential copper-catalyzed oxy-alkynylation/intramolecular [4+2] cycloaddition of allenes and arenes was investigated at first. This one-pot protocol allowed the construction of complex polycylic architectures with high efficiency fro ...

EPFL2021

Predicting involuntary hospitalization in psychiatry: A machine learning investigation

Mehdi Gholam

Background Coercion in psychiatry is a controversial issue. Identifying its predictors and their interaction using traditional statistical methods is difficult, given the large number of variables involved. The purpose of this study was to use machine-lear ...

CAMBRIDGE UNIV PRESS2021

Modeling, predicting and mining metabolism at atom-level resolution

Jasmin Maria Hafner

Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...

EPFL2020

Palladium Catalysed Intramolecular Carbo-oxygenation of Propargylic Amines to Access 1,2-Amino Alcohols and alpha-Amino Ketones via in situ Tether Formation

Phillip Gulliver Dominic Greenwood

a-Amino ketones and 1,2-amino alcohols are important structural motifs in organic chemistry, that can be observed in natural products, pharmaceutically and bioactive compounds. For these reasons, they constitute privileged targets for the development of ne ...

EPFL2020

Reactions of nitrogen-containing compounds with ozone: kinetics and mechanisms

Sung Eun Lim

Nitrogen-containing moieties are widespread in natural waters in dissolved organic nitrogen and micropollu-tants. They are often susceptible to an electrophilic attack of ozone because of the electron-rich nature of the neutral form of nitrogen in organic ...

EPFL2020

Organocatalysts in C-N Bond Forming Reactions of Amines with CO2

Martin Hulla

The thesis describes a simple approach for N-formylation of amines with CO2 and hydrosilane reducing agents, the use of organic salts as N-formylation catalysts, their physical properties required for high catalytic activity and their role in the catalytic ...

EPFL2019

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Vassily Hatzimanikatis, Ljubisa Miskovic, Noushin Hadadi, Marianne Seijo

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, l ...

National Academy of Sciences2019

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

Vassily Hatzimanikatis, Daniel Robert Weilandt

Many computational models for analyzing and predicting cell physiology rely on in vitro data collected in dilute and controlled buffer solutions. However, this can mislead models because up to 40% of the intracellular volume-depending on the organism, the ...

2019

Gas-Phase Ozone Reactions with a Structurally Diverse Set of Molecules: Barrier Heights and Reaction Energies Evaluated by Coupled Cluster and Density Functional Theory Calculations

Jeremy Samuel Arey, Peter Rudolf Tentscher, Daniela Trogolo

Reactions with ozone transform organic and inorganic molecules in water treatment systems as well as in atmospheric chemistry, either in the aqueous phase, at gas/particle interfaces, or in the gas phase. Computed thermokinetic data can be used to estimate ...

AMER CHEMICAL SOC2019

Pivotal Role of the Basic Character of Organic and Salt Catalysts in C-N Bond Forming Reactions of Amines with CO2

Paul Joseph Dyson, Martin Hulla

Organocatalysts promote a range of C-N bond forming reactions of amines with CO2. Herein, we review these reactions and attempt to identify the unifying features of the catalysts that allows them to promote a multitude of seemingly unrelated reactions. Ana ...

Wiley-VCH Verlag GmbH2020

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

Stereoselective synthesis of alkenes via base-metal-catalyzed addition reactions to alkynes and activation of hydrogen peroxide and carbon dioxide by iron complexes

Fedor Zhurkin

Alkene functionality can be found in the majority of natural products, drugs, catalysts and organic materials. Therefore, methods of C-C double bond formation constitute a cornerstone of organic synthesis. Selective formation of either (Z)- or (E)-isomer i ...

EPFL2017

Organocatalysis: Fundamentals and Comparisons to Metal and Enzyme Catalysis

Pierre Vogel

Catalysis fulfills the promise that high-yielding chemical transformations will require little energy and produce no toxic waste. This message is carried by the study of the evolution of molecular catalysis of some of the most important reactions in organi ...

2016

CO2 capture in amine solutions: modelling and simulations with non-empirical methods

Fabio Pietrucci, Wanda Andreoni

Absorption in aqueous amine solutions is the most advanced technology for the capture of CO2, although suffering from drawbacks that do not allow exploitation on large scale. The search for optimum solvents has been pursued with empirical methods and has a ...

Iop Publishing Ltd2016

Reversible supramolecular modification of surfaces

Negar Moridi

Enzymes are biocatalysts widely used in a large number of industrial biotech processes as they offer clear advantages over their chemical counterparts. Indeed, enzymes often show high substrate selectivity along with elevated turnover rates. Enzymatic cata ...

EPFL2015

Runtime Prediction for Scale-Out Data Analytics

Adrian Daniel Popescu

Many analytics applications generate mixed workloads, i.e., workloads comprised of analytical tasks with different processing characteristics including data pre-processing, SQL, and iterative machine learning algorithms. Examples of such mixed workloads ca ...

EPFL2015

Pd(0)-Catalyzed Alkene Oxy- and Aminoalkynylation with Aliphatic Bromoacetylenes

Jérôme Waser, Stefano Nicolai, Raha Sedigh-Zadeh

Tetrahydrofurans and pyrrolidines are among the most important heterocycles found in bioactive compounds. Cyclization-functionalization domino reactions of alcohols or amines onto olefins,constitute one of the most efficient methods to access them. In this ...

American Chemical Society2013

Predicting Concentrations of Organic Chemicals in Fish by Using Toxicokinetic Models

Kristin Schirmer, Julita Maria Stadnicka-Michalak

Quantification of chemical toxicity continues to be generally based on measured external concentrations. Yet, internal chemical concentrations have been suggested to be a more suitable parameter. To better understand the relationship between the external a ...

2012

Accurate Thermochemistry of Hydrocarbon Radicals via an Extended Generalized Bond Separation Reaction Scheme

Anne-Clémence Corminboeuf, Matthew Wodrich

Detailed knowledge of hydrocarbon radical thermochemistry is critical for understanding diverse chemical phenomena, ranging from combustion processes to organic reaction mechanisms. Unfortunately, experimental thermochemical data for many radical species t ...

2012