Reviews, book chapters

Reviews

Recent Advances in First-Principles Based Molecular Dynamics

F. Mouvet; J. Villard; V. Bolnykh; U. Rothlisberger 

Accounts Of Chemical Research. 2022-01-13. Vol. 55, num. 3, p. 221–230. DOI : 10.1021/acs.accounts.1c00503.

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Expanding the boundaries of ligand-target modeling by exascale calculations

V. Bolnykh; G. Rossetti; U. Rothlisberger; P. Carloni 

Wiley Interdisciplinary Reviews-Computational Molecular Science. 2021-04-10.  p. e1535. DOI : 10.1002/wcms.1535.

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Organic Spacers in 2D Perovskites: General Trends and Structure-Property Relationships from Computational Studies

F. Jahanbakhshi; M. Mladenovic; M. Dankl; A. Boziki; P. Ahlawat et al. 

Helvetica Chimica Acta. 2021-04-07. Vol. 104, num. 4, p. e2000232. DOI : 10.1002/hlca.202000232.

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Allostery in Its Many Disguises: From Theory to Applications

S. J. Wodak; E. Paci; N. V. Dokholyan; I. N. Berezovsky; A. Horovitz et al. 

Structure. 2019-04-02. Vol. 27, num. 4, p. 566-578. DOI : 10.1016/j.str.2019.01.003.

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

G. Palermo; A. Magistrato; T. Riedel; T. Von Erlach; C. A. Davey et al. 

ChemMedChem. 2016. Vol. 11, num. 12, p. 1199-1210. DOI : 10.1002/cmdc.201500478.

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Computational insights into function and inhibition of fatty acid amide hydrolase

G. Palermo; U. Rothlisberger; A. Cavalli; M. De Vivo 

European Journal Of Medicinal Chemistry. 2015. Vol. 91, p. 15-26. DOI : 10.1016/j.ejmech.2014.09.037.

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Nonadiabatic ab initio molecular dynamics using linear-response time-dependent density functional theory

B. F. E. Curchod; T. J. Penfold; U. Rothlisberger; I. Tavernelli 

Central European Journal Of Physics. 2013. Vol. 11, num. 9, p. 1059-1065. DOI : 10.2478/s11534-013-0321-2.

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A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations

S. Vanni; U. Rothlisberger 

Current Medicinal Chemistry. 2012. Vol. 19, num. 8, p. 1135-1145. DOI : 10.2174/092986712799320493.

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Book chapters

Hybrid Car-Parrinello Molecular Dynamics/Molecular Mechanics Simulations: a Powerful Tool for the Investigation of Biological Systems

E. Ippoliti; J. Dreyer; P. Carloni; U. Röthlisberger 

Hierarchical Methods for Dynamics in Complex Molecular Systems; Forschungszentrum Jülich GmbH, 2012-03-09. p. 556.

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Hybrid QM/MM simulations of enzyme-catalyzed DNA repair reactions

D. Bucher; F. Masson; J. S. Arey; U. Rothlisberger 

Quantum Biochemistry; Wiley, 2010.

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Drug-target binding investigated by quantum mechanics/molecular mechanics methods

U. Rothlisberger; P. Carloni 

Computer simulations in condensed matter systems : from materials to chemical biology; Berlin: Springer, 2006. p. 447-479.

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Advances in density-functional-based modeling techniques – Recent extensions of the Car-Parrinello approach

D. Sebastiani; U. Roethlisberger 

Methods and Principles in Medicinal Chemistry; Weinheim: Wiley-VCH, 2003. p. 5-39.

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Time and length scales in ab initio molecular dynamics

U. Röthlisberger; M. Sprik; J. Hutter 

Bridging time scales : molecular simulations for the next decade; Berlin: Springer, 2002. p. 413-442.

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Enantioselective hydrosilylation by chiral Pd based homogeneous catalysts with first-principles and combined QM/MM molecular dynamics simulations

A. Magistrato; A. Togni; U. Roethlisberger; T. K. Woo 

Computational modeling of homogeneous catalysis; Dordrecht: Kluwer, 2002. p. 213-252.

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Magic and mysteries of modern molecular dynamics simulations: A basic introduction

U. Rothlisberger 

Strength from Weakness: Structural Consequences of Weak Interactions in Molecules, Supermolecules, and Crystals; Berlin: Springer, 2002. p. 121-141.

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Simulations of enzymatic systems: Perspectives from Car-Parrinello molecular dynamics simulations

P. Carloni; U. Rothlisberger 

Theoretical Biochemistry: Processes and Properties of Biological Systems; Amsterdam: Elsevier, 2001. p. 215-251.

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15 years of Car-Parrinello simulations in physics, chemistry and biology

U. Rothlisberger 

Computational Chemistry: Reviews of Current Trends; Singapore: World Scientific, 2001. p. 33-68.

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Ab initio and hybrid molecular dynamics simulations of the active site of human carbonic anhydrase II: a test case study

U. Rothlisberger 

Combined Quantum Mechanical and Molecular Mechanical Methods; 1998. p. 264-274.

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Simulation of self-assembled monolayers:microscopic structure of amino alkylthiols

U. Rothlisberger; M. L. Klein; M. Sprik 

Computational Approaches in Supramolecular Chemistry; Dordrecht: Kluwer, 1994. p. 399-409.

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Some considerations on “isoarithmic” and isoelectronic clusters

W. Andreoni; U. Roethlisberger 

Nuclear physics concepts in the study of atomic cluster physics; Berlin: Springer, 1992. p. 352-357.

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