Dr. rer. nat. Patrick Quoika


Picture of Patrick Quoika

Technical University of Munich

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

Postal address

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

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

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?
T
he Journal of Physical Chemistry A, 126(19), 2966–2975.(https://doi.org/10.1021/acs.jpca.2c00857)

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. (https://dx.doi.org/10.3389%2Ffmolb.2022.812750)

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. (https://doi.org/10.1021/acs.jcim.0c01375)

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. (https://doi.org/10.3389/fchem.2021.641610)

2021

Fernández-Quintero, M. L., Seidler, C. A., Quoika, P. K., & Liedl, K. R.
Shark Antibody Variable Domains Rigidify Upon Affinity MaturationUnderstanding the Potential of Shark Immunoglobulins as Therapeutics
Frontiers in Molecular Biosciences, 8. (https://doi.org/10.3389/fmolb.2021.639166)

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. (https://doi.org/10.1021/acs.jcim.0c01438)

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 (https://doi.org/10.1021/acs.jpcb.1c01946)

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. (https://doi.org/10.3389/fimmu.2021.675655)

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. (https://doi.org/10.1021/acs.jpcb.9b11802)

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. (https://doi.org/10.1021/acs.jcim.0c00280)

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. (https://doi.org/10.1021/acs.jpcb.0c07232)

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. (https://doi.org/10.3389/fmolb.2020.609088)

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. (https://doi.org/10.1021/acs.jpcb.9b06125)