Dr. rer. nat. Patrick Quoika
Dr. rer. nat. Patrick Quoika
Technical University of Munich
Chair of Theoretical Biophysics - Biomolecular Dynamics (Prof. Zacharias)
Postal address
Ernst-Otto-Fischer-Str. 8
85748 Garching b. München
- Phone: +49 (89) 289 - 13766
- 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 |