Literature DB >> 22026176

Pushing the frontiers of first-principles based computer simulations of chemical and biological systems.

Elizabeth Brunk1, Negar Ashari, Prashanth Athri, Pablo Campomanes, F Franco de Carvalho, Basile F E Curchod, Polydefkis Diamantis, Manuel Doemer, Julian Garrec, Andrey Laktionov, Marco Micciarelli, Marilisa Neri, Giulia Palermo, Thomas J Penfold, Stefano Vanni, Ivano Tavernelli, Ursula Rothlisberger.   

Abstract

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these methods to larger systems, longer time scales and increased accuracies. Their versatility is illustrated with a diverse range of applications, ranging from the determination of the gas phase structure of the cyclic decapeptide gramicidin S, to the study of G protein coupled receptors, the interaction of transition metal based anti-cancer agents with protein targets, the mechanism of action of DNA repair enzymes, the role of metal ions in neurodegenerative diseases and the computational design of dye-sensitized solar cells. Many of these projects are done in collaboration with experimental groups from the Institute of Chemical Sciences and Engineering (ISIC) at the EPFL.

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Year:  2011        PMID: 22026176     DOI: 10.2533/chimia.2011.667

Source DB:  PubMed          Journal:  Chimia (Aarau)        ISSN: 0009-4293            Impact factor:   1.509


  5 in total

Review 1.  Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations.

Authors:  Giulia Palermo; Lorenzo Casalino; Alessandra Magistrato; J Andrew McCammon
Journal:  J Struct Biol       Date:  2019-03-15       Impact factor: 2.867

Review 2.  Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.

Authors:  Pablo R Arantes; Amun C Patel; Giulia Palermo
Journal:  J Mol Biol       Date:  2022-02-28       Impact factor: 6.151

3.  Concerted hydrogen atom and electron transfer mechanism for catalysis by lysine-specific demethylase.

Authors:  Tao Yu; Masahiro Higashi; Alessandro Cembran; Jiali Gao; Donald G Truhlar
Journal:  J Phys Chem B       Date:  2013-06-14       Impact factor: 2.991

4.  The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition.

Authors:  Giulia Palermo; Angelo D Favia; Marino Convertino; Marco De Vivo
Journal:  ChemMedChem       Date:  2015-11-23       Impact factor: 3.466

Review 5.  Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies.

Authors:  Giulia Palermo; Alessandra Magistrato; Tina Riedel; Thibaud von Erlach; Curt A Davey; Paul J Dyson; Ursula Rothlisberger
Journal:  ChemMedChem       Date:  2015-12-04       Impact factor: 3.466

  5 in total

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