Dr. rer. nat. Patrick Quoika

Technical University of Munich

Chair of Theoretical Biophysics - Biomolecular Dynamics (Prof. Zacharias)

Postal address

Postal:
Ernst-Otto-Fischer-Str. 8
85748 Garching b. München

Phone: +49 (89) 289 - 13766
Fax: fax +49 (89) 289 - 12444
Room: 5415.EG.048
Homepage: https://www.groups.ph.tum.de/t38/home/
patrick.quoika@tum.de

Research Interests

Molecular Dynamics and Monte Carlo simulations
Conformational transitions of thermosensitive polymers
Enhanced sampling techniques
Statistical analysis and Machine Learning
Biomolecular interfaces: Protein-protein, protein-RNA

Publications

Year	Authors, Title, Journal
2024	Quoika, P. K., Zacharias, M. Liquid–Vapor Coexistence and Spontaneous Evaporation at Atmospheric Pressure of Common Rigid Three-Point Water Models in Molecular Simulations J. Phys. Chem. B , 128 (10), 2457–2468
2024	Fischer, A.-L. M., Tichy, A., Kokot, J., Hoerschinger, V. J., Wild, R. F., Riccabona, J. R., Loeffler, J. R., Waibl, F., Quoika, P. K., Gschwandtner, P., Forli, S., Ward, A. B., Liedl, K. R., Zacharias, M., Fernández-Quintero, M. L. The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics. J. Chem. Theory Comput. 20 (5), 2321–2333
2023	Fernández-Quintero, M. L., Kokot, J., Waibl, F., Fischer, A.-L. M., Quoika, P. K., Deane, C. M. & Liedl, K. R. Challenges in Antibody Structure Prediction Mabs, 15 (1), 2175319
2023	Pomarici, N. D., Waibl, F., Quoika, P. K., Bujotzek, A., Georges, G., Fernández-Quintero, M. L. & Liedl, K. R. Structural Mechanism of Fab Domain Dissociation as a Measure of Interface Stability Journal of Computer-Aided Molecular Design, 37 (4), 201–215
2023	Quoika, P. K.; Kamenik, A. S.; Fernández-Quintero, M. L.; Zacharias, M. & Liedl, K. R. Water Model Determines Thermosensitive and Physicochemical Properties of Poly(N-Isopropylacrylamide) in Molecular Simulations Frontiers in Materials, 10
2022	Linke, M., Quoika, P. K.; Bramas, B., Köfinger, J., & Hummer, G. Complexes++: Efficient and Versatile Coarse-Grained Simulations of Protein Complexes and Their Dense Solutions The Journal of Chemical Physics, 157 (20), 204802
2022	Dinu, D. F., Bartl, P., Quoika, P. K., Podewitz, M., Liedl, K. R., Grothe, H., & Loerting, T. Increase of Radiative Forcing through Midinfrared Absorption by Stable CO2 Dimers? The Journal of Physical Chemistry A, 126(19), 2966–2975
2022	Fernández-Quintero, M. L., Quoika, P. K., Wedl, F. S., Seidler, C. A., Kroell, K. B., Loeffler, J. R., Liedl, K. R. Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats Frontiers in Molecular Biosciences, 9
2021	Kraml, J., Hofer, F., Quoika, P. K., Kamenik, A. S., & Liedl, K. R. X-Entropy: A Parallelized Kernel Density Estimator with Automated Bandwidth Selection to Calculate Entropy Journal of Chemical Information and Modeling, 61(4), 1533–1538
2021	Loeffler, J. R., Fernández-Quintero, M. L., Waibl, F., Quoika, P. K., Hofer, F., Schauperl, M., & Liedl, K. R. Conformational Shifts of Stacked Heteroaromatics: Vacuum vs. Water Studied by Machine Learning Frontiers in Chemistry, 9, 179
2021	Fernández-Quintero, M. L., Seidler, C. A., Quoika, P. K., & Liedl, K. R. Shark Antibody Variable Domains Rigidify Upon Affinity Maturation—Understanding the Potential of Shark Immunoglobulins as Therapeutics Frontiers in Molecular Biosciences, 8
2021	Ramos, M. C., Quoika, P. K., Horta, V. A. C., Dias, D. M., Costa, E. G., Do Amaral, J. L. M., … Horta, B. A. C. PyPolyBuilder: Automated Preparation of Molecular Topologies and Initial Configurations for Molecular Dynamics Simulations of Arbitrary Supramolecules Journal of Chemical Information and Modeling, 61(4), 1539–1544
2021	Quoika, P. K., Fernández-Quintero, M. L., Podewitz, M., Hofer, F., & Liedl, K. R. Implementation of the Freely Jointed Chain Model to Assess Kinetics and Thermodynamics of Thermosensitive Coil-Globule Transition by Markov States Journal of Physical Chemistry B, 125(18), 4898–4909
2021	Fernández-Quintero, M. L., Kroell, K. B., Bacher, L. M., Loeffler, J. R., Quoika, P. K., Georges, G., … Liedl, K. R. Germline-Dependent Antibody Paratope States and Pairing Specific VH-VL Interface Dynamics. Frontiers in Immunology, 12, 2741
2020	Jost Lopez, A., Quoika, P. K., Linke, M., Hummer, G., & Köfinger, J. Quantifying Protein-Protein Interactions in Molecular Simulations Journal of Physical Chemistry B, 124(23), 4673–4685
2020	Kamenik, A. S., Kraml, J., Hofer, F., Waibl, F., Quoika, P. K., Kahler, U., … Liedl, K. R. Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments Journal of Chemical Information and Modeling, 60(7), 3508–3517
2020	Quoika, P. K., Podewitz, M., Wang, Y., Kamenik, A. S., Loeffler, J. R., & Liedl, K. R. Thermosensitive Hydration of Four Acrylamide-Based Polymers in Coil and Globule Conformations Journal of Physical Chemistry B, 124(43), 9745–9756
2020	Fernández-Quintero, M. L., Kroell, K. B., Heiss, M. C., Loeffler, J. R., Quoika, P. K., Waibl, F., … Liedl, K. R. Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments Frontiers in Molecular Biosciences, 7, 339
2019	Podewitz, M., Wang, Y., Quoika, P. K., Loeffler, J. R., Schauperl, M., & Liedl, K. R. Coil-Globule Transition Thermodynamics of Poly(N-isopropylacrylamide) Journal of Physical Chemistry B, 123(41), 8838–8847