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-Str. 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

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