Jocelyne Vreede

Affiliations

Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands.

Publications (13)

Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models.

Physical review. E

Avec: Enrico Skoruppa , Aderik Voorspoels , Enrico Carlon

The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions.

Methods in molecular biology (Clifton, N.J.)

Avec: Alberto Pérez de Alba Ortíz , Bernd Ensing

Sequence dependence of transient Hoogsteen base pairing in DNA.

PLoS computational biology

Avec: Alberto Pérez de Alba Ortíz , Bernd Ensing

Binding dynamics of a stapled peptide targeting the transcription factor NF-Y.

Chembiochem : a European journal of chemical biology

Avec: Canan Durukan , Federica Arbore , Rasmus Klintrot , Carlo Bigiotti , Ioana M Ilie , Tom N Grossmann , Sven Hennig

Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins.

Nucleic acids research

Avec: Liang Qin , Fredj Ben Bdira , Yann G J Sterckx , Alexander N Volkov , Gabriele Giachin , Peter van Schaik , Marcellus Ubbink , Remus T Dame

Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations.

Nucleic acids research

Avec: Thor van Heesch , Peter G Bolhuis ,

Allostery in Its Many Disguises: From Theory to Applications.

Structure (London, England : 1993)

Avec: Shoshana J Wodak , Emanuele Paci , Nikolay V Dokholyan , Igor N Berezovsky , Amnon Horovitz , Jing Li , Vincent J Hilser , Ivet Bahar , John Karanicolas , Gerhard Stock , Peter Hamm , Roland H Stote , Jerome Eberhardt , Yassmine Chebaro , Annick Dejaegere , Marco Cecchini , Jean-Pierre Changeux , Peter G Bolhuis , Pietro Faccioli , Simone Orioli , Riccardo Ravasio , Le Yan , Carolina Brito , Matthieu Wyart , Paraskevi Gkeka , Ivan Rivalta , Giulia Palermo , J Andrew McCammon , Joanna Panecka-Hofman , Rebecca C Wade , Antonella Di Pizio , Masha Y Niv , Ruth Nussinov , Chung-Jung Tsai , Hyunbum Jang , Dzmitry Padhorny , Dima Kozakov , Tom McLeish

Deciphering Sequence-Specific DNA Binding by H-NS Using Molecular Simulation.

Methods in molecular biology (Clifton, N.J.)

Avec: Thor van Heesch , Eline M van de Lagemaat ,

Predicting the mechanism and rate of H-NS binding to AT-rich DNA.

PLoS computational biology

Avec: Enrico Riccardi , Eva C van Mastbergen , William Wiley Navarre ,

Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas.

The journal of physical chemistry. B

Avec: Sander Roet , Ferry Hooft , Peter G Bolhuis , David W H Swenson ,

Rigid Base Biasing in Molecular Dynamics Enables Enhanced Sampling of DNA Conformations.

Journal of chemical theory and computation

Avec: Aderik Voorspoels , Enrico Carlon

Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending.

Nucleic acids research

Avec: Yimin Hu , Samuel Schwab , Silvia Deiss , Pedro Escudeiro , Thor van Heesch , Joe D Joiner , Marcus D Hartmann , Andrei N Lupas , Birte Hernandez Alvarez , Vikram Alva , Remus T Dame

Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.

Nucleic acids research

Avec: Alberto Pérez de Alba Ortíz , Peter G Bolhuis , David W H Swenson

Réseau de co-auteurs

Peter G Bolhuis 4 collaborations

Alberto Pérez de Alba Ortíz 3 collaborations

Thor van Heesch 3 collaborations

Aderik Voorspoels 2 collaborations

Enrico Carlon 2 collaborations

Bernd Ensing 2 collaborations

Remus T Dame 2 collaborations

David W H Swenson 2 collaborations

Enrico Skoruppa 1 collaboration

Canan Durukan 1 collaboration

Federica Arbore 1 collaboration

Rasmus Klintrot 1 collaboration

Carlo Bigiotti 1 collaboration

Ioana M Ilie 1 collaboration

Tom N Grossmann 1 collaboration

Sven Hennig 1 collaboration

Liang Qin 1 collaboration

Fredj Ben Bdira 1 collaboration

Yann G J Sterckx 1 collaboration

Alexander N Volkov 1 collaboration

Gabriele Giachin 1 collaboration

Peter van Schaik 1 collaboration

Marcellus Ubbink 1 collaboration

Shoshana J Wodak 1 collaboration

Emanuele Paci 1 collaboration

Nikolay V Dokholyan 1 collaboration

Igor N Berezovsky 1 collaboration

Amnon Horovitz 1 collaboration

Jing Li 1 collaboration

Vincent J Hilser 1 collaboration

Ivet Bahar 1 collaboration

John Karanicolas 1 collaboration

Gerhard Stock 1 collaboration

Peter Hamm 1 collaboration

Roland H Stote 1 collaboration

Jerome Eberhardt 1 collaboration

Yassmine Chebaro 1 collaboration

Annick Dejaegere 1 collaboration

Marco Cecchini 1 collaboration

Jean-Pierre Changeux 1 collaboration

Pietro Faccioli 1 collaboration

Simone Orioli 1 collaboration

Riccardo Ravasio 1 collaboration

Le Yan 1 collaboration

Carolina Brito 1 collaboration

Matthieu Wyart 1 collaboration

Paraskevi Gkeka 1 collaboration

Ivan Rivalta 1 collaboration

Giulia Palermo 1 collaboration

J Andrew McCammon 1 collaboration

Joanna Panecka-Hofman 1 collaboration

Rebecca C Wade 1 collaboration

Antonella Di Pizio 1 collaboration

Masha Y Niv 1 collaboration

Ruth Nussinov 1 collaboration

Chung-Jung Tsai 1 collaboration

Hyunbum Jang 1 collaboration

Dzmitry Padhorny 1 collaboration

Dima Kozakov 1 collaboration

Tom McLeish 1 collaboration

Eline M van de Lagemaat 1 collaboration

Enrico Riccardi 1 collaboration

Eva C van Mastbergen 1 collaboration

William Wiley Navarre 1 collaboration

Sander Roet 1 collaboration

Ferry Hooft 1 collaboration

Yimin Hu 1 collaboration

Samuel Schwab 1 collaboration

Silvia Deiss 1 collaboration

Pedro Escudeiro 1 collaboration

Joe D Joiner 1 collaboration

Marcus D Hartmann 1 collaboration

Andrei N Lupas 1 collaboration

Birte Hernandez Alvarez 1 collaboration

Vikram Alva 1 collaboration