Detailansicht

[Zurück]

Univ.-Prof. Mag. Dr. Stefan Boresch

T: +43-1-4277-52715

stefan.boresch@univie.ac.at

http://www.mdy.univie.ac.at

Sommersemester 2024

270004 UE Computer in der Biologischen Chemie

270006 SE ABC-SE Research Report: Algorithmsm, Biomolecules & Computers I

270020 PR Wahlfachpraktikum D (Bachelormodul) - Theoretische Chemie / Computergestützte Biologische Chemie

270021 SE Erstellen der Bachelorarbeit D - Theoretische Chemie / Computergestützte Biologische Chemie

270040 PR Praktikum zur Computersimulation von Biopolymeren

270128 PR Forschungsbeispiele aus Computergestützter Biologischer Chemie

270275 VO Computersimulation von Biopolymeren

301558 UE UE aus Biomolekularer Simulation

301577 VO Biomolekulare Simulation

530036 SE Modern aspects of molecular dynamics simulations

Wintersemester 2023

270004 UE Computer in der Biologischen Chemie

270020 PR Wahlfachpraktikum D (Bachelormodul) - Theoretische Chemie / Computergestützte Biologische Chemie

270021 SE Erstellen der Bachelorarbeit D - Theoretische Chemie / Computergestützte Biologische Chemie

270025 SE ABC-SE Research Report: Algorithmsm, Biomolecules & Computers I

270124 VO Computergrafik und Molekulare Modellierung

270128 PR Forschungsbeispiele aus Computergestützter Biologischer Chemie

270129 PR Praktikum zu Computergrafik und Molekulare Modellierung

301628 VO Mathematik in der Molekularbiologie

530036 SE Modern aspects of molecular dynamics simulations

Sommersemester 2023

270004 UE Computer in der Biologischen Chemie

270020 PR Wahlfachpraktikum D (Bachelormodul) - Theoretische Chemie / Computergestützte Biologische Chemie

270021 SE Erstellen der Bachelorarbeit D - Theoretische Chemie / Computergestützte Biologische Chemie

270040 PR Praktikum zur Computersimulation von Biopolymeren

270128 PR Forschungsbeispiele aus Computergestützter Biologischer Chemie

270275 VO Computersimulation von Biopolymeren

301126 SE ABC-SE Research Report: Algorithms, Biomolecules & Computers I

301558 UE UE aus Biomolekularer Simulation

301577 VO Biomolekulare Simulation

Karwounopoulos, J., Kaupang, Å., Wieder, M., & Boresch, S. (2023). Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field. Journal of Chemical Theory and Computation, 19(17), 5988–5998. https://doi.org/10.1021/acs.jctc.3c00691

Schöller, A., Woodcock, H. L., & Boresch, S. (2023). Exploring Routes to Enhance the Calculation of Free Energy Differences via Non-Equilibrium Work SQM/MM Switching Simulations Using Hybrid Charge Intermediates between MM and SQM Levels of Theory or Non-Linear Switching Schemes. Molecules, 28(10), [4006]. https://doi.org/10.3390/molecules28104006

Karwounopoulos, J., Wieder, M., & Boresch, S. (2022). Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool. Frontiers in Molecular Biosciences, 9, [954638]. https://doi.org/10.3389/fmolb.2022.954638

Wieder, M., Fleck, M., Braunsfeld, B., & Boresch, S. (2022). Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program. Journal of Computational Chemistry, 43(17), 1151-1160. https://doi.org/10.1002/jcc.26877

Schoeller, A., Kearns, F., Woodcock, H. L., & Boresch, S. (2022). Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations. Journal of Physical Chemistry B, 126(15), 2798-2811. https://doi.org/10.1021/acs.jpcb.2c00696

Fleck, M., Wieder, M., & Boresch, S. (2021). Dummy Atoms in Alchemical Free Energy Calculations. Journal of Chemical Theory and Computation, 17(7), 4403-4419. https://doi.org/10.1021/acs.jctc.0c01328

Heid, E., Boresch, S., & Schroeder, C. (2020). Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control. Journal of Chemical Physics, 152(9), [094105]. https://doi.org/10.1063/1.5143746

Hudson, P. S., Woodcock, H. L., & Boresch, S. (2019). Use of Interaction Energies in QM/MM Free Energy Simulations. Journal of Chemical Theory and Computation, 15(8), 4632-4645. https://doi.org/10.1021/acs.jctc.9b00084

Kearns, F. L., Warrensford, L., Boresch, S., & Woodcock, H. L. (2019). The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations. Molecules, 24(4), [681]. https://doi.org/10.3390/molecules24040681

Hudson, P. S., Boresch, S., Rogers, D. M., & Woodcock, H. L. (2018). Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching. Journal of Chemical Theory and Computation, 14(12), 6327-6335. https://doi.org/10.1021/acs.jctc.8b00517

Siebert, D. C. B., Wieder, M., Schlener, L., Scholze, P., Boresch, S., Langer, T., Schnürch, M., Mihovilovic, M. D., Richter, L., Ernst, M., & Ecker, G. (2018). SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2- Benzodiazepine Site. Journal of Chemical Information and Modeling, 58(8), 1682-1696. https://doi.org/10.1021/acs.jcim.8b00199

Hudson, P., Boresch, S., Rogers, D., & Woodcock, H. (2017). Enhancing QM/MM indirect free energy simulations with intramolecular force matching. American Chemical Society. Abstracts of Papers (at the National Meeting), 254.

Kearns, F. L., Hudson, P. S., Woodcock, H. L., & Boresch, S. (2017). Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities. Journal of Computational Chemistry, 38(16), 1376-1388. https://doi.org/10.1002/jcc.24706

Wieder, M., Garon, A., Perricone, U., Boresch, S., Seidel, T., Almerico, A. M., & Langer, T. (2017). Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 57(2), 365-385. https://doi.org/10.1021/acs.jcim.6b00674

Boresch, S., & Woodcock, H. L. (2017). Convergence of single-step free energy perturbation. Molecular Physics: an international journal in the field of chemical physics, 115(9-12), 1200-1213. https://doi.org/10.1080/00268976.2016.1269960

Wieder, M., Perricone, U., Seidel, T., Boresch, S., & Langer, T. (2016). Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations. Monatshefte für Chemie, 147(3), 553-563. https://doi.org/10.1007/s00706-016-1674-1

Wieder, M., Perricone, U., Boresch, S., Seidel, T., & Langer, T. (2016). Evaluating the stability of pharmacophore features using molecular dynamics simulations. Biochemical and Biophysical Research Communications, 470(3), 685-689. https://doi.org/10.1016/j.bbrc.2016.01.081

Kearns, F. L., Hudson, P. S., Boresch, S., & Woodcock, H. L. (2016). Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis. in G. A. Voth (Hrsg.), Computational Approaches for Studying Enzyme Mechanism Part A (S. 75-104). Elsevier Academic Press. Methods in Enzymology Band 577 https://doi.org/10.1016/bs.mie.2016.05.053

Hudson, P. S., Woodcock, H. L., & Boresch, S. (2015). Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems. The Journal of Physical Chemistry Letters, 6(23), 4850-4856. https://doi.org/10.1021/acs.jpclett.5b02164

Hudson, P. S., White, J. K., Kearns, F. L., Hodoscek, M., Boresch, S., & Woodcock, H. L. (2015). Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes. Biochimica et Biophysica Acta - General Subjects, 1850(5), 944-953. https://doi.org/10.1016/j.bbagen.2014.09.016

Setting up MD Simulations of Biomolecules

Stefan Boresch (Invited speaker)

10 Sep. 2023

Aktivität: Vorträge › Vortrag › Science to Science

Free Energy Update from Vienna

Stefan Boresch (Invited speaker)

21 Juli 2023

Aktivität: Vorträge › Vortrag › Science to Science

Applying the Common-Core Serial-Atom-Insertionapproach to large-scale calculations of relative binding free energies

Stefan Boresch (Invited speaker)

22 Juli 2022

Aktivität: Vorträge › Vortrag › Science to Science

Alchemical Free Energy Simulations --- What we can and cannot (yet) do

Stefan Boresch (Invited speaker)

21 Juli 2022

Aktivität: Vorträge › Vortrag › Science to Science

Relative Binding Free Energy calculations using TRANSFORMATO

Johannes Karwounopoulos (Vortragende*r) & Stefan Boresch (Autor*in)

31 Mai 2022

Aktivität: Vorträge › Vortrag › Science to Science

Recent results in free energy methodology, both MM and (S)QM/MM based

Stefan Boresch (Invited speaker)

16 Juli 2021

Aktivität: Vorträge › Vortrag › Science to Science

Alchemical FES - automated setup for the Common Core / Serial Atom Insertion approach

Stefan Boresch (Vortragende*r)

17 Juli 2020

Aktivität: Vorträge › Vortrag › Science to Science

A crash course in alchemical free energy simulations byways

Stefan Boresch (Invited speaker)

30 Sep. 2019

Aktivität: Vorträge › Vortrag › Science to Science

Setting up MD Simulations of Biomolecules

Stefan Boresch (Invited speaker)

19 Sep. 2019

Aktivität: Vorträge › Vortrag › Science to Science

Alchemical Free Energy Simulations without Speed-bumps

Stefan Boresch (Vortragende*r)

17 Juli 2019

Aktivität: Vorträge › Vortrag › Science to Science

MD Simulations of Proteins: Practical Hints and Pitfalls to Avoid

Stefan Boresch (Invited speaker)

19 Sep. 2017

Aktivität: Vorträge › Vortrag › Science to Science

Musings on alchemical (QM/MM) free energy simulations

Stefan Boresch (Invited speaker)

15 Juli 2017

Aktivität: Vorträge › Vortrag › Science to Science