Andrea C Vaiana

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Helmut GrubmullerTheoretical and Computational Biophysics Department, Max Planck Institute for MultidisciplinaryVerified email at gwdg.de
Christian BlauMax-Planck-Institute for Biophysical ChemsitryVerified email at kth.se
Marina RodninaMax Planck Institute for Biophysical ChemistryVerified email at mpibpc.mpg.de
Gunnar F. SchröderForschungszentrum Jülich, GermanyVerified email at fz-juelich.de
Jeremy C SmithUniversity of Tennessee KnoxvilleVerified email at ornl.gov
Lars V. BockProject Leader, Theoretical and Computational Biophysics, MPI for Multidisciplinary SciencesVerified email at mpibpc.mpg.de
Pascal AuffingerIBMC/CNRS - UPR 9002 - University of StrasbourgVerified email at unistra.fr
Markus SauerUniversität WürzburgVerified email at uni-wuerzburg.de
Daniel WilsonUniversity of HamburgVerified email at chemie.uni-hamburg.de
Stefan ArenzPostdoc, Gene Center MunichVerified email at genzentrum.lmu.de
Carsten KutznerMax Planck Institute for Multidisciplinary SciencesVerified email at gwdg.de
Karissa SanbonmatsuPrincipal Investigator, Los Alamos National LaboratoryVerified email at lanl.gov
Iakov DavydovF. Hoffmann-La Roche AGVerified email at roche.com
Hannes NeuweilerUniversity of Würzburg, GermanyVerified email at uni-wuerzburg.de
Michael J. GrafBoston CollegeVerified email at bc.edu
Maxim IgaevProject Group Leader, Max Planck Institute for Biophysical ChemistryVerified email at gwdg.de
Zoe CourniaSenior Researcher - Associate Professor level, Biomedical Research Foundation, Academy of AthensVerified email at bioacademy.gr
Paul HuterPostDoc LMU, Munich, GenecenterVerified email at genzentrum.lmu.de
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
Niels FischerMolecular Machines in Motion - MPI for Multidisciplinary Sciences, GöttingenVerified email at mpinat.mpg.de

Andrea C Vaiana

Project Group Leader, Max Planck Institute for Multidisciplinary Sciences

Verified email at mpinat.mpg.de

Molecular biophysics Molecular dynamics simulations Ribosome tRNA translocation Antibiotics


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Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue? P Auffinger, TE Cheatham, AC Vaiana Journal of Chemical Theory and Computation 3 (5), 1851-1859, 2007	194	2007
Energy barriers and driving forces in tRNA translocation through the ribosome LV Bock, C Blau, GF Schröder, II Davydov, N Fischer, H Stark, ... Nature structural & molecular biology 20 (12), 1390-1396, 2013	182	2013
Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation AC Vaiana, H Neuweiler, A Schulz, J Wolfrum, M Sauer, JC Smith Journal of the American Chemical Society 125 (47), 14564-14572, 2003	181	2003
Structural basis for polyproline-mediated ribosome stalling and rescue by the translation elongation factor EF-P P Huter, S Arenz, LV Bock, M Graf, JO Frister, A Heuer, L Peil, AL Starosta, ... Molecular cell 68 (3), 515-527. e6, 2017	143	2017
A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest S Arenz, LV Bock, M Graf, CA Innis, R Beckmann, H Grubmüller, ... Nature communications 7 (1), 12026, 2016	111	2016
A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns AC Vaiana, E Westhof, P Auffinger Biochimie 88 (8), 1061-1073, 2006	95	2006
Automated cryo-EM structure refinement using correlation-driven molecular dynamics M Igaev, C Kutzner, LV Bock, AC Vaiana, H Grubmüller Elife 8, e43542, 2019	87	2019
Detection of individual p53‐autoantibodies by using quenched peptide‐based molecular probes H Neuweiler, A Schulz, AC Vaiana, JC Smith, S Kaul, J Wolfrum, M Sauer Angewandte Chemie International Edition 41 (24), 4769-4773, 2002	81	2002
Stochastic gating and drug–ribosome interactions AC Vaiana, KY Sanbonmatsu Journal of molecular biology 386 (3), 648-661, 2009	79	2009
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge CL Lawson, A Kryshtafovych, PD Adams, PV Afonine, ML Baker, ... Nature methods 18 (2), 156-164, 2021	72	2021
Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor A Simonetti, S Marzi, IML Billas, A Tsai, A Fabbretti, AG Myasnikov, ... Proceedings of the National Academy of Sciences 110 (39), 15656-15661, 2013	64	2013
A new view of protein synthesis: Mapping the free energy landscape of the ribosome using single‐molecule FRET JB Munro, A Vaiana, KY Sanbonmatsu, SC Blanchard Biopolymers: Original Research on Biomolecules 89 (7), 565-577, 2008	61	2008
AFMM: A molecular mechanics force field vibrational parametrization program AC Vaiana, Z Cournia, IB Costescu, JC Smith Computer Physics Communications 167 (1), 34-42, 2005	52	2005
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching AC Vaiana, A Schulz, J Wolfrum, M Sauer, JC Smith Journal of computational chemistry 24 (5), 632-639, 2003	45	2003
Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation LV Bock, C Blau, AC Vaiana, H Grubmüller Nucleic acids research 43 (14), 6747-6760, 2015	36	2015
Derivation of a molecular mechanics force field for cholesterol Z Cournia, AC Vaiana, GM Ullmann, JC Smith Pure and applied chemistry 76 (1), 189-196, 2004	31	2004
Detektion einzelner p53‐Autoantikörper mit fluoreszenzgelöschten Peptid‐Sonden H Neuweiler, A Schulz, AC Vaiana, JC Smith, S Kaul, J Wolfrum, M Sauer Angewandte Chemie 114 (24), 4964-4968, 2002	18	2002
Molecular dynamics simulations of RNA systems P Auffinger, AC Vaiana Handbook of RNA biochemistry, 2005	16	2005
Outcomes of the 2019 EMDataResource model challenge: Validation of cryo-EM models at near-atomic resolution CL Lawson, A Kryshtafovych, PD Adams, PV Afonine, ML Baker, ... BioRxiv, 2020.06. 12.147033, 2020	8	2020
Peptide-based molecular beacons for the detection of p53-autoantibodies in human sera H Neuweiler, A Schulz, A Vaiana, J Smith, S Kaul, J Wolfrum, M Sauer Angew. Chemie, 2002	4	2002

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