Dr. Till Rudack, Project Group Leader "Biomolecular Simulations"

My general areas of interest are computational chemistry and molecular structural biology. I am especially interested in investigating protein structure and function in order to develop a fundamental understanding of their role for cellular processes. I enjoy working in the interdisciplinary field of biophysical protein science in international teams and collaborative projects. In my graduate work, I studied at the interface between physics, biology, and chemistry as well as at the interface between theory and experiment.

During my doctorate I studied enzymatic catalyzed reaction mechanism. In order to obtained structural insights into active sites of proteins with highest spatio-temporal resolution possible I developed methods to combine results from biomolecular simulations with results from time-resolved FTIR spectroscopic measurements. With these methods I proved that sub-Å resolution is needed to understand enzymatically catalyzed hydrolysis reaction mechanisms of small GTPases, which are crucial switches to regulate cellular processes. I gained experimentally validated dynamic atomic structural models of the different states of Ras during the signaling cascade of cell growth. From these atomic models I decoded the catalysis mechanism of GTP hydrolysis by Ras.

During my postdoc I resolved several atomic models of different states of cellualr protein recycling to elucidate structure, dynamics, and function of substrate recognition, translocation and degradation by the 26S proteasome at atomic detail. I adapted hybrid structure analysis strategies to fit models into high-resolution cryo-electron microscopy (cryo-EM) data by to combining structural data from experimetal sources with computational modeling approaches.

Currently, I employ and develope computational startegies to analyzing strucutre function relationships of proteins to understand molecular mechanism underlying diseases like cancer or neurodegenerative disease, as well as for targeted protein engineering and drug discovery.

Home Department: Center for Protein Diagnostics (PRODI), Biospectroscopy

Office Address: PRODI E3/265

Office Phone: (+49) 234 32 18132

Home Department II: Department of Biophysics, Ruhr University Bochum

Office Address II: NDEF 04/352

Office Phone II: (+49) 234 32 22236

Email Address: till.rudack@rub.de

Visit my Google Scholar profile or my profile on ResearchGate for more details.

Research Interests

Protein Structure Function Relationship
Protein Modeling
Protein Engineering
Molecular Dynamics Simulations
Theoretical Spectroscopy

Software Developments

Press Releases

Teaching

All Year

Seminars

Seminar Computersimulations of Proteins (2CP)
Every Friday 9am
Topics: protein modeling and simulation techniques, recent applications, literature presentations
Everybody is welcome just contact me by email
Seminar Schedule WiSe21/22

Practicals

Specialization Module: „Special Topics of Biophysics: Molecular Dynamics Simulations“ (15CP; B.Sc. and M.Sc. Biology)
six weeks all day practical course on recent research related biomolecular simulations projects
individual times upon request
Research Practical (4CP; Focal Point Biophysics for Physicists, Focal Point Biophysics for Medical Physicists)
four weeks all day practical course on computational methods to analyze structure and dynamics of proteins >
Focal Pont Practical (Focal Point "Proteins in Biomedicin" in M.Sc. Biochemistry)
individual times upon request
Advanced Practical Course for Physicist
Advance Practical 705 Protein Modeling (1 CP; Focal Point Biophysics for Medical Physicists)
Advance Practical 704 Molecular Dynamics Simulations (1 CP; Focal Point Biophysics for Medical Physicists)
one day hands-on practical (usually Wednesdays within the semester but individual times are possible upon request)

Winter Semester

Lectures

Introduction to Biophysics
(6CP; Focal Point Biophysics for Physicists, Focal Point Biophysics for Medical Physicists)
One guest lecture on current research topics using molecular mechanics and quantum mechanics simulations to study proteins.
One lecture on artificial intelligence in structural biophysics.
Introduction to Bioinformatics
(5CP; M.Sc. Biochemistry, M.Sc. Stem Cell Biology, Focal Point Biophysics for Physicists, Focal Point Biophysics for Medical Physicists)
One lecture on protein modeling.
One lecture on molecular dynamics simulations.
Eight hours hands-on practical course on protein modeling and structure analysis with PyMol

Practicals

Advanced Module: "Molecular Biology of Proteins" (M.Sc. and B.Sc. Biology)
One quarter of the practical including lectures and hands-on practical courses on protein modeling and biomolecular simulations
Advanced Module: "Biophotonics und Diagnostic Imaging" (M.Sc. and B.Sc. Biology)
Three days of hands-on practicals on bioinformatic tools to study protein function
Advanced Practical: "Computational Protein Modeling and Simulation Techniques" (M.Sc. Biochemistry, M.Sc. Stem Cell Biology)
Two weeks hands-on practical on the underlying techniques for protein modeling and simulation

Summer Semester

Lectures

Biophysics II
(4CP; Focal Point Biophysics for Physicists, Focal Point Biophysics for Medical Physicists)
One quarter of the lecture series on underlying technical principals and applications of molecular mechanics and quantum mechanics calculations to study protein dynamics.

Research Highlights

The 26S Proteasome - the recycling maschine of the cell

While waste recycling became popular in our daily life more recently, living cells have mastered recycling of their protein content since their very beginning. Recycling of unneeded protein molecules in cells is performed by a molecular machine called 26S proteasome, which cuts these proteins into smaller pieces for reuse as building blocks for new proteins. Proteins that need to be recycled are labeled by tags made of poly-ubiquitin protein chains. The 26S proteasome machine recognizes and binds to these tags, pulls the tagged protein close, then unwinds it, and finally cuts it into pieces. Despite its substantial role in the cell’s life cycle, the proteasome’s atomic structure and function remained elusive for decades. Employing a combination of computational modeling and simulation techniques along with cryo-electron microscopy data we obtained atomic structural models of the proteasome and related proeins in different functional states, elucidating the mechanism underlying substrate recruitment and unfolding during protein degradation. Our constructed 3D atomic structures will play a pivotal role to further develop the proteasome as crucial drug target.

More information is provided on our proteasome website

ModelMaker - An interactive, integrative easy-to-use, all-in-one modeling solution

Hybrid structure analysis combines structural data from sources such as X-ray crystallography and cryo-electron microscopy (cryo-EM) with computational modeling and has become a successful strategy for resolving protein structures. We developed an integrative modeling tool called ModelMaker, to interactively build complete models into cryo-EM densities guided by incomplete structural data from experiments, homology modeling, automated structure prediction, and molecular dynamics flexible fitting (MDFF). ModelMaker is an all-in-one modeling solution combining the strength of established but often complicated to use modeling suites like Rosetta and Modeller with MDFF in an easy-to-use manner in VMD. Integrative modeling approaches usually aim to automate the process of structure analysis to avoid human bias, yet the experience of structural biologists may be a desirable factor in structure refinement. Therefore, ModelMaker uniquely allows for incorporation of user expertise by taking advantage of interactive MDFF, allowing for manual manipulation of the structure.

QwikMD - Gateway to Easy MD Simulations

Everything that living things do can be understood in terms of jigglings and wigglings of atoms. Richard Feynman's remark in the early 1960's summarizes what is today widely accepted, namely, that molecular processes can be described by the dynamics of biological molecules, therefore connecting protein dynamics to biological function. Molecular dynamics (MD) is by far the best tool to investigate jigglings and wigglings of biological systems. Advances in both software and hardware have spread the use of MD, however the steepness of the learning curve of the methodology of MD remains high. To assist new users in overcoming the initial barrier to use MD software, and to help the more advanced users to speed up tedious steps, we have developed the QwikMD software, as decribed in a recent paper. By incorporating an easy-to-use point-and-click user interface that connects the widely used molecular graphics program VMD with the powerful MD program NAMD, QwikMD allows its users to prepare both basic and advanced MD simulations in just a few minutes. At the same time, QwikMD keeps track of every step performed during the preparation of the simulation, allowing easy reproducibility and shareability of protocols. More information about QwikMD, as well as introductory tutorials are available on our QwikMD webpage. QwikMD is available in VMD 1.9.3 or later versions.

QwikMD offers:

Easy Setup of MD Simulations
Point Mutations
Changes in Protonation
Protocols for MD and SMD
Live View Simulations
Integrated Basic Analysis
Info Buttons to Guide Novices
Advanced Protocols
Membrane Environment
Advanced Analysis
Available on Amazon Cloud
Full log Capabilities
Easy Reproducibility

Enzymatic Catalyzed GTP Hydrolysis Reaction

Beside large macromolecular motors I also investigate the enzymatically catalyzed reaction mechanisms of small GTPases. Many cellular processes are regulated by members of the Ras superfamily. They are switched "on" by GDP-to-GTP exchange and "off" by a GTPase reaction. GTP hydrolysis is vitally important for the regulation of several signal-transduction processes in living cells. In the case of Ras, external growth signals are transduced to the nucleus. Site-specific oncogenic mutations inhibit the GTPase reaction and the growth signal can no longer be down-regulated. This contributes to uncontrolled cell growth, eventually leading to cancer. Common to all members of the Ras superfamily is the catalysis of GTP hydrolysis by the G domain. Ras-catalyzed GTP hydrolysis is five orders of magnitude faster than in water (30 min vs. 200 d). However, to control growth signals in the living cell, a further increase of five orders of magnitude in the reaction rate (30 min to 50 ms) is enabled. This is effected by GTPase-activating proteins (GAPs) that interact with Ras. This down-regulation of small GTPases by GAP-catalysis is crucial in the living cell and its interference causes several diseases.

I have developed a workflow to combine the advantages of biomolecular simulations with time-resolved Fourier-transformed infrared (FTIR) spectroscopy measurements and X-Ray crystallographic structural analysis. By this we elucidate the reaction mechanism of the by Ras enzymatically catalyzed GTP hydrolysis and resolve with highest spatio-temporal resolution possible, how this remarkable catalysis is brought about.

My developed workflow combines MM, QM and QM/MM simulations in order to gain detailed information about structure, dynamics and charge distribution of the active site of small GTPases. These computer models are validated by comparing the calculated IR spectra with the experimentally measured ones. This leads to an experimentally validated refinement of the X-ray structure with sub Ãngstroem resolution. Within my work I have proven that sub Ãngstroem resolution of the dynamic structural models is essential to elucidate the catalytic effect of the active site of the small GTPase Ras on GTP hydrolysis. Ras rotates the g-phosphate relative to the b-phosphate from a staggered into an eclipsed conformation and GAP binding further rotates the a- relative to the b-phosphate into an eclipsed conformation. Thereby the oxygen atoms repel each other and GTP is driven in an energetically unfavourable conformation. Furthermore, the protein induced charge shift at the g-phosphate prepares for an optimal nucleophilic attack of the water molecule. Protein binding induce a precatalytic GTP conformation by which the activation free energy is reduced as compared to GTP in water. Beyond, the magnesium ion provides temporary storage for electrons during hydrolysis. All in all, the protein environment drives the conformation and the charge distribution of GTP closer to that of its hydrolysis transition state and facilitates thereby hydrolysis. This result exemplified, that understanding protein catalysis deserves time-resolved studies at atomic details provided here by combining vibrational spectroscopy and biomolecular simulations.

Furthermore, I have been able to resolve the detailed structure and inclusion into the protein environment of the nucleotide during a transient intermediate state within a cooperation project with the Chines Academy of Science Max Planck Gesellschaft Partner Institue for Computational Biology (CAS MPG PICB) in Shanghai (China). In addition, I have been able to show that the clustering of Ras at a membrane is driven by dimerization. This was the result of a combination of MD simulations, attenuated total reflection fourier transform infrared (ATR FTIR) spectroscopic investigations and Foerster Resonance Energy Transfer (FRET) experiments.

Education

Doctoral Degree in Physics (2013) - Ruhr University of Bochum - Germany

Advisor: Prof. Dr. Klaus Gerwert

Thesis Title: Decoding of the enzymatic catalysis of small GTPases by quantam mechanics and molecular mechanics simulations of time resolved FTIR spectra

Diploma Degree in Physics (2007) - Ruhr University of Bochum - Germany

Advisor: PD Dr. Jürgen Schlitter

Thesis Title: Development of force field parameter for guanosine triphosphate for molecular dynamics simulations

Collaborators

Harvard Medical School - Finley Lab (Daniel Finley) - Boston, US

NIH Center for Macromolecular Modeling and Bioinformatics - University of Illinois at Urbana-Champaign - US

Upapsla University - Department of Cell and Molecular Biology (Lynn Kamerlin)- Sweden

Max Planck Institute of Biochemistry - Molecular Structural Biology (Wolfgang Baumeister) - Germany

Max Planck Institute for Coal Research - Molecular Theory and Spectroscopy (Frank Neese) - Germany

Helmholz Zentrum München - Cell Architecture Lab (Ben Engel) - Munich, Germany

Philipps University of Marburg - SYNMIKRO Research Center - CryoEM of Molecular Machines (Jan Schuller) - Marburg, Germany

Georg August University Göttingen - Institute for Auditory Neuroscience - Sakata Group (Eri Sakata) - Göttingen, Germany

Ruhr University Bochum - Department of General Zoology and Neurobiology (Stefan Herlitze) - Bochum, Germany

Ruhr University Bochum - Department of Plant Biochemistry - Molecular Mechanisms of Photosynthesis (Marc Nowaczyk) - Bochum, Germany

FACCTS - Fast and Accurate Computational Chemistry Tools

CHEOPS - Chemistry Oriented Program System

Journal Covers

Cell 184(14) (2021)

ChemBioChem 21 (2020)

ChemBioChem 20 (2019)

Biophys.J. 114(3) (2018)

J.Biol.Chem. 290(40) (2015)

Biophys.J. 103(7) (2012)

Awards

2018 Massenberg Fellowship to attend the Keystone Symposia on Molecular and Cellular Biology, Tahoe City, CA, US
2014-2016 Feodor-Lynen Postdoctoral Fellowship of the Alexander von Humboldt Foundation
2016 Attendance Fellowship of the German Accademic International Network (GAIN) to the 16th Annual GAIN Meeting 2016, Washington, D.C., US
2015 Travel Award of the German Biophysical Society to the European Biophysical Society Meeting 2015, Dreseden, Germany
2015 Best Image Award of the German Biophysical Society
2014 Nominated for the best interdisciplinary doctoral thesis of the Ruhr-University Bochum
2012 Cold Spring Habor Asia Fellowship: Best Poster Award
Ras and GAP drive the geometry and charge of GTP into a precatalytic state as revealed by combining FTIR and QM/MM simulations,
2012 Cold Spring Harbor Asia Conference: Small GTPases at Different Scales: Proteins, Membranes, Cells, Suzhou, China.
2011 Best Poster Award of the European Biophysical Society Mg²⁺ is a temporary electron storage during the GTP Hydrolysis Mechanism, 8th EBSA European Biophysics Congress, Budapest, Hungary.
2009 Travel Award of the German Biophysical Society to the European Biophysical Society Meeting 2009, Genua, Italy

Publications

29 peer reviewed publications
total number of citations: 1777
h-index: 18
i10-index: 22
As of November 2021.
For current figures and more details, please visit my Google Scholar Profile

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity.
Gupta T K, Klumpe S, Gries K, Heinz S, Wietrzynski W, Ohnishi N, Niemeyer J, Spaniol B, Schaffer M, Rast A, Ostermeier M, Strauss M, Plitzko J M, Baumeister W, Rudack T, Sakamoto W, Nickelsen J, Schuller J M^#, Schroda M^#, Engel B^#
Cell 2021 184(14):3643-3659.e23 (Cover)
The Ras dimer structure.
Rudack T*^,#, Teuber C*, Scherlo M, Güldenhaupt J, Schartner J, Lübben M, Klare J, Gerwert K#, Kötting C#
Chemical Science 2021 12:8178-8189
Time-resolved spectroscopic and electrophysiological data reveal insights in the gating mechanism of anion channelrhodopsin.
Dreier M-A, Althoff P, Norahan M, Tennigkeit S, El-Mashtoly S, Lübben M, Kötting C, Rudack T^#, Gerwert K^#
Communications Biology 2021 4:578
Structural insights into photosystem II assembly.
Zabret J*, Bohn S*, Schuller SK, Arnolds O, Möller M, Meier-Credo J, Liauw P, Chan A, Tajkhorshid E, Langer JD, Stoll R., Krieger-Liszkay A, Engel BD, Rudack T^#, Schuller JM^#, Nowaczyk MM^#
Nature Plants 2021 7:524-538
The Effect of epigallocatechin-3-gallate on the Amyloid-β Secondary Structure.
Acharya A, Stockmann J, Beyer L, Rudack T, Nabers A^#, Gumbart JC, Gerwert K^#, and Batista VS^#
Biophysical Journal 2020, 119(2):349-350
Insights into the assembly and activation of the microtubule nucleator γ-TuRC.
Liu P, Zupa E, Neuner A, Böhler A, Loerke J, Flemming D, Ruppert T, Rudack T, Peter C, Spahn C, Gruss OJ, Pfeffer S^#, Schiebel E^#
Nature 2020, 578(7795):467-471
Lamprey Parapinopsin (“UVLamP”): a bistable UV-sensitive optogenetic switch for ultrafast control of GPCR pathways.
Eickelbeck D, Rudack T, Tennigkeit SA, Surdin T, Karapinar R, Schwitalla J, Mücher B, Shulmann M, Scherlo M, Althoff P, Mark MD, Gerwert K^#, Herlitze S^#
ChemBioChem 2020, 21:612-617 (Cover)
GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases.
Calixto AR*, Moreira C*, Pabis A, Kötting C, Gerwert K, Rudack T^#, Kamerlin SCL^#
JACS 2019, 141(27):10684-10701
Design of an ultra‐fast G protein switch based on a mouse melanopsin variant.
Tennigkeit SA*, Karapinar, R*, Rudack T*, Dreier MA, Althoff P, Eickelbeck D, Surdin T, Grömmke M, Mark MD, Spoida K, Herlitze S^#, Gerwert K^#
ChemBioChem 2019 20:1766–1771 (Cover Feature)
Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle.
Majumder P, Rudack T, Beck F, Danev R, Pfeifer G, Nagy I, Baumeister W^#
PNAS 2019 116(2):534-539
Monitoring transient events in IR‐spectra using Local Mode Analysis.
Massarczyk M, Schlitter J, Kötting C, Rudack T^#, Gerwert K^#
Proteins: Structure, Function, and Bioinformatics 2018 86(10):1013-1019
Expanded coverage of the 26S proteasome conformational landscape reveals mechanisms of peptidase gating.
Eisele MR*, Reed RG*, Rudack T*, Schweitzer A, Beck F, Nagy I, Pfeifer G, Plitzko JM, Baumeister W^#, Tomko RJ^#, Sakata E^#
Cell Reports 2018 24(5):1301-1315
NAMD goes quantum: an integrative suite for hybrid simulations.
Melo* MCR, Bernardi* RC, Rudack T, Scheurer M, Riplinger C, Phillips JC, Maia JDC, Rocha GD, Ribeiro JV, Stone JE, Neese F, Schulten K, Luthey-Schulten Z^#
Nature Methods 2018 15(5):351-354
In Situ Structural Studies of Neuronal C9ORF72 Poly-GA Aggregates Reveal Proteasome Accumulation and Impairment.
Guo Q, Lehmer C*, Martínez-Sánchez A*, Rudack T*, Beck F, Hartmann H, Pérez Berlanga M, Frottin F, Hipp M, Hart FU, Edbauer D^#, Baumeister W^#, Fernández-Busnadiego R^#
Cell 2018 172(4):696-705.
PyContact: Rapid, Customizable and Visual Analysis of Non-Covalent Interactions in MD Simulations.
Scheurer, M, Rodenkirch, P, Siggel, M, Bernardi, RC, Schulten, K, Tajkhorshid E^#, Rudack T^# Biophysical Journal 2018 114(3):577-583 (Cover)
Structural insights into the functional cycle of the ATPase module of the 26S proteasome.
Wehmer M*, Rudack T*, Beck F*, Aufderheide A, Pfeifer G, Plitzko JM, Förster F, Schulten K, Baumeister W^#, Sakata E^#
PNAS 2017 114(4):1305-1310.
Local Mode Analysis: Decoding IR spectra by visualizing molecular details.
Massarczyk M*, Rudack T*, Schlitter J, Kuhne J, Kötting C, Gerwert K^#
The Journal of Physical Chemistry B, Klaus Schulten Memorial Issue 2017 121(15):3483–3492
The structure of the 26S proteasome at a resolution of 3.9 A.
Schweitzer A*, Aufderheide A*, Rudack T*, Beck F, Pfeifer G, Plitzko JM, Sakata E, Schulten K, Förster F^#, Baumeister W^#
PNAS 2016 113(28):7816-7821.
QwikMD Integrative Molecular Dynamics Toolkit for Novices and Experts.
Ribeiro JV*, Bernardi RC*, Rudack T*, Stone JE, Phillips JC, Freddolino PL, Schulten K^#
Nature Scientific Reports 2016 6:26536
Recognition of poly-ubiquitins by the proteasome through protein re-folding guided by electrostatic and hydrophobic interactions.
Zhang Y*, Vukovic L*, Rudack T*, Han W, and Schulten K^#
The Journal of Physical Chemistry B, McCammon Festschrift 2016 120(33):8137-8146.
Computational methodologies for real-space structural refinement of large macromolecular complexes.
Goh BC*, Hadden JA*, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, and Schulten K^#
Annual Review Biophysics 2016 45:253-278.
Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental and theoretical IR spectroscopy.
Rudack T*, Jenrich S*, Brucker S, Vetter IR, Gerwert K^#, Kötting C^#
Journal of Biological Chemistry 2015 290(40):24079-24090(Cover)
Molecular dynamics simulations of large macromolecular complexes.
Perilla JR, Goh BC, Cassidy CK, Liu B, Bernardi RC, Rudack T, Yu H, Wu Z, Schulten K^#
Current Opinion in Structural Biology 2015 31:64-74.
Die Geheimnisse des Lebens berechnen.
Rudack T, Perilla JR, Schulten K
Spektrum der Wissenschaften 2014 11:86-95.
Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations.
Rudack T, Xia F, Schlitter J, Kötting C, Gerwert K^#
PNAS 2012 109(38):15295-15300.
Detailed Structure of the H2PO4 Guanosine Diphosphate Intermediate in RasGAP Decoded from FTIR Experiments by Biomolecular Simulations.
Xia F*, Rudack T*, Cui Q, Kötting C, Gerwert K^#
JACS 2012 136:20041-20044.
The Role of Magnesium for Geometry and Charge in GTP Hydrolysis, Revealed by Quantum Mechanics/Molecular Mechanics Simulations.
Rudack T, Xia F, Schlitter J, Kötting C, Gerwert K^#
Biophysical Journal 2012 103:293-302.
N-Ras forms dimers at POPC membranes.
Güldenhaupt J*, Rudack T*, Bachler P, Mann D, Triola G, Waldmann H, Kötting C, Gerwert K#
Biophysical Journal 2012 103(7):1585-1593 (Cover).
Exploring the Multidimensional Free Energy Surface of Phosphoester Hydrolysis with Constrained QM/MM Dynamics.
Li W, Rudack T, Gerwert K, Gräter F^#, Schlitter J^#
Journal of Chemical Theory and Computation 2012 8 (10):3596-3604.
The specific vibrational modes of GTP in solution and bound to Ras: a detailed theoretical analysis by QM/MM simulations.
Xia F, Rudack T*, Kötting C, Schlitter J, Gerwert K^#
Physical Chemistry Chemical Physics 2011 13:21451-21460.

* equal contribution; ^# corresponding author

Talks

15/10/2021, Computational Protein Structure Prediction - The AI Revolution
Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
24/11/2020, Die Geheimnisse des Lebens berechnen - Struktur, Dynamik und Funktion lebenswichtiger molekularer Maschinen
Ringvorlesung Biochemie der juniorGBM (Gesellschaft für Biochemie und Molekularbiologie) Bochum, Ruhr University Bochum, Bochum, Germany
11/01/2020, Calculating the Secret of Life - Integrating classical and quantum mechanical simulations with experimental data
Physics Colloquium of the Faculty of Physics and Astronomy, Ruhr University Bochum, Bochum, Germany
10/04/2019, Molecular Modeling and Design of Retinal Proteins - Tools to Think
DFG Roundtable Discussion Meeting: Conformational Dynamics of Photoreceptors at Different Time Scales, Ringberg, Germany
09/24/2018 Integrative Modeling - A Journey through the Scales
Symposium “Integrated structural biology and functional genomics of genome transcription” of the Department of Molecular Biology MPI for Biophysical Chemistry, Altmorschen, Germany
05/07/2018 ModelMaker: An interactive integrative modeling tool to build complete macromolecular machines
Ringberg Meeting of the Department of Molecular Structural Biology MPI of Biochemistry, Ringberg, Germany
02/07/2018, ModelMaker: An Interactive Integrative Modeling Tool to Build Complete Macromolecular Machines.
Keystone Symposia on Molecular and Cellular Biology: Cryo-EM from Cells to Molecules: Multi-Scale Visualization of Biological Systems, Lake Taho, CA, US
11/29/2017 From Atom to Cell: MD Simulation Techniques to Bridge Computation and Experiment.
Theoretisch-Chemisches Kolloqium, Department of Theoretical Chemistry, Ruhr University Bochum, Germany
11/13/2017 Reduce-Reuse-Recycle: Insights into the Cellular Protein Recycling Machine by Integrative Modeling.
University of Illinois at Urbana Champaign, US
03/25/2017 ModelMaker: A Tool for Interactive Modeling of Complete Proteins Guided by Cryo‐EM, Structure Prediction, and Molecular Dynamics.
Computer Simulation and Theory of Macromolecules 2017. Huenfeld, Germany
03/08/2017 The story of a "precise" proteasome model: Integrating experimental results and user expertise into computational modeling.
Ringberg Meeting of the Department of Molecular Structural Biology MPI of Biochemistry, Ringberg, Germany
02/25/2017 From atom to cell: Integrating experimental results and user expertise into computational modeling.
Structural Transitions of Biomolecules in Experiment and Theory, Joint meeting of the Czech and German Biophysics Societies, Huenfeld, Germany
02/25/2017 From atom to cell: Integrating experimental results and user expertise into computational modeling.
Structural Transitions of Biomolecules in Experiment and Theory, Joint meeting of the Czech and German Biophysics Societies, Huenfeld, Germany
08/31/2016, How is chemical energy converted into motor action? Integrating experimental methods into computational modeling can provide answers.
Quantum Biology and Computational Physics Group, University of Southern Denmark, Denmark
07/14/2016, How is chemical energy converted into motor action? Integrating experimental methods into computational modeling can provide answers.
Max Planck Institute for Chemical Energy Conversion, Department of Frank Neese, Germany
07/12/2016, Integrating experimental results and computational modeling unravels functional details about catalytic centers of large macromolecular complexes.
SFB TR83, SFB TR186 Guest Seminar, Biochemistry Center of the University Heidelberg (BZH), Germany
06/15/2016, Molecular Dynamics Simulations of Large Macromolecular Complexes.
NCSA Blue Waters Symposium for Petascale Science and Beyond, Sunriver, US
05/06/2016, Molecular Dynamics Simulations for Everyone From iPad to Supercomputers From Atom to Cell.
Collaborative Research Center (SFB) 642 seminar, Ruhr-University Bochum, Germany
05/04/2016, How the Ras protein became a wind-up car.
Anniversary Symposium for Klaus Gerwert, Ruhr-University Bochum, Germany
03/04/2016, Integrating experimental results and user expertise into computational model building.
Amaro group, UCSD, San Diego, US
03/03/2016, Integrating experimental results and user expertise into computational model building.
Lander group, Scripps Research Institute, San Diego, US
03/01/2016, A tool to integrate user expertise into building atomic level models for large bimolecular systems.
60th Biophysical Society meeting, LA convention Center, US
09/10/2015, Exploring GTPase catalysis at atomic structure level by combining biomolecular simulations with FTIR spectroscopy.
2015 European Conference on the Spectroscopy of Biological Molecules (ECSMB), Bochum, Germany
02/09/2015, Integrating experimental results and user expertise into computational model building.
Pande Group, U Stanford, San Francisco, US
01/09/2015, Integrating experimental results and user expertise into computational model building.
Martin Group, UC Berkeley, San Francisco, US
08/31/2015, Integrating experimental results and user expertise into computational model building.
Sali Group, UCSF, San Francisco, US
07/27/2015, Rosetta/MDFF: A tool to integrate userÕs expertise into cryo-EM model building applied to the 26S proteasome.
Baumeister group, Max Plank Institute for Biochemistry, Munich, Germany
07/20/2015, Ubiquitin recruitment and transport through the 26S proteasome unraveled by an orchestra of MD simulation algorithms.
2015 European Biophysical Society Meeting, Dresden, Germany
09/28/2012, Decoding structural information from FTIR spectra by biomolecular simulations.
Cold Spring Harbor Asia Conference: Small GTPases at Different Scales: Proteins, Membranes, Cells, Suzhou, China
05/18/2012, Ras and GAP drive GTP into a precatalytic state: a combined FTIR and QM/MM simulation study.
CAS-MPG Partner Institute for Compuational Biology (PICB), Shanghai, China
04/20/2012, Catalysis of GTP Hydrolysis by 10 Orders of magnitude by Ras-Ras$\cdot$GAP Revealed at Atomic Detail by Combining QM/MM Simulations and FTIR Spectroscopy.
Computer Simulation and Theory of Macromolecules 2012, Hunfeld, Germany
09/08/2011, Mg²⁺ is a temporary electron storage at GTP Hydrolysis.
2nd summer school of the graduate college of the SFB 642, Wenden, Germany
05/20/2011, The Ras Protein: Theoretical IR Spectroscopy of Different States of GTP Hydrolysis.
Spectroscopy Symposium, CAS-MPG Partner Institute for Compuational Biology (PICB), Shanghai, China
08/16/2010, Biomolecular Simulations on the Ras Protein.
Symposium on Biomolecular Simulations, CAS-MPG Partner Institute for Compuational Biology (PICB), Shanghai, China
04/16/2010 Hydrolysis Mechanism of Ras Investigated by QM/MM Simulations, Computer Simulation and Theory of Macromolecules 2010. Huenfeld, Germany
01/25/2010, QM/MM Simulations on the Hydrolysis Mechanism of Ras.
B-IT/PICB Workshop: Computational Life Science, Bonner-IT, Bonn, Germany
05/23/2009 Interaction of N-Ras-GTP and N-Ras-GDP with a POPC Bilayer.
Protein-Protein-Interaction: Experiment and Theory, Joint meeting of the Danish and German Biophysics Societies, Huenfeld, Germany
03/02/2009 Interaction of N-Ras-GTP and N-Ras-GDP with a POPC Bilayer.
Bioquant, University Heidelberg, Heidelberg, Germany