Research output per year
Research output per year
Search results
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2024
Advanced sampling simulations of coupled folding and binding of phage P22 N-peptide to boxB RNA
Vollmers, L. & Zacharias, M., 1 Oct 2024, In: Biophysical Journal. 123, 19, p. 3463-3477 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Characterizing ATP processing by the AAA+ protein p97 at the atomic level
Shein, M., Hitzenberger, M., Cheng, T. C., Rout, S. R., Leitl, K. D., Sato, Y., Zacharias, M., Sakata, E. & Schütz, A. K., Mar 2024, In: Nature Chemistry. 16, 3, p. 363-372 10 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations
Kienlein, M., Zacharias, M. & Reif, M. M., 26 Mar 2024, In: Journal of Chemical Theory and Computation. 20, 6, p. 2643-2654 12 p.Research output: Contribution to journal › Article › peer-review
Open Access -
cPEPmatch Webserver: A comprehensive tool and database to aid rational design of cyclic peptides for drug discovery
Santini, B. L., Wendel, S., Halbwedl, N., Knipp, A. & Zacharias, M., Dec 2024, In: Computational and Structural Biotechnology Journal. 23, p. 3155-3162 8 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction
Abdel‐Rahman, S. A., Santini, B. L., Calvo-Barreiro, L., Zacharias, M. & Gabr, M., 1 Feb 2024, In: Bioorganic and Medicinal Chemistry Letters. 99, 129599.Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
Efficient and accurate binding free energy calculation of Aβ9–40 protofilament propagation
Frost, C. V., Schwierz, N. & Zacharias, M., 2024, (Accepted/In press) In: Proteins: Structure, Function and Bioinformatics.Research output: Contribution to journal › Article › peer-review
Open Access -
Helical reorganization in the context of membrane protein folding: Insights from simulations with bacteriorhodopsin (BR) fragments
Chatterjee, H., Mahapatra, A. J., Zacharias, M. & Sengupta, N., Jun 2024, In: Biochimica et Biophysica Acta - Biomembranes. 1866, 5, 184333.Research output: Contribution to journal › Article › peer-review
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How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations
Kienlein, M. & Zacharias, M., Jul 2024, In: Protein Science. 33, 7, e5077.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Liquid-Vapor Coexistence and Spontaneous Evaporation at Atmospheric Pressure of Common Rigid Three-Point Water Models in Molecular Simulations
Quoika, P. K. & Zacharias, M., 14 Mar 2024, In: Journal of Physical Chemistry B. 128, 10, p. 2457-2468 12 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Peptide vaccines get an OS update
Zacharias, M. & Springer, S., May 2024, In: Nature Chemical Biology. 20, 5, p. 549-550 2 p.Research output: Contribution to journal › Comment/debate
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Rational design of glycosaminoglycan binding cyclic peptides using cPEPmatch
Santini, B. L., Gaardløs, M., Wyrzykowski, D., Rothemund, S., Penk, A., Zacharias, M. & Samsonov, S. A., Dec 2024, In: Computational and Structural Biotechnology Journal. 23, p. 2985-2994 10 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Refinement of Docked Protein-Protein Complexes Using Repulsive Scaling Replica Exchange Simulations
Siebenmorgen, T., Saremi Nanji, Y. & Zacharias, M., 2024, In: Methods in molecular biology (Clifton, N.J.). 2780, p. 289-302 14 p.Research output: Contribution to journal › Article › peer-review
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RNA dynamics from experimental and computational approaches
Bussi, G., Bonomi, M., Gkeka, P., Sattler, M., Al-Hashimi, H. M., Auffinger, P., Duca, M., Foricher, Y., Incarnato, D., Jones, A. N., Kirmizialtin, S., Krepl, M., Orozco, M., Palermo, G., Pasquali, S., Salmon, L., Schwalbe, H., Westhof, E. & Zacharias, M., 5 Sep 2024, In: Structure.Research output: Contribution to journal › Article › peer-review
Open Access -
Screening Privileged Alkyl Guanidinium Motifs under Host-Mimicking Conditions Reveals a Novel Antibiotic with an Unconventional Mode of Action
Schum, D., Elsen, F. A. V., Ruddell, S., Schorpp, K., Junca, H., Müsken, M., Chen, S. Y., Fiedler, M. K., Pickl, T., Pieper, D. H., Hadian, K., Zacharias, M. & Sieber, S. A., 2024, (Accepted/In press) In: JACS Au.Research output: Contribution to journal › Article › peer-review
Open Access -
Structural Insights into Seeding Mechanisms of hIAPP Fibril Formation
Suladze, S., Sustay Martinez, C., Rodriguez Camargo, D. C., Engler, J., Rodina, N., Sarkar, R., Zacharias, M. & Reif, B., 22 May 2024, In: Journal of the American Chemical Society. 146, 20, p. 13783-13796 14 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations
Walter, L. J., Quoika, P. K. & Zacharias, M., 22 Apr 2024, In: Journal of Chemical Information and Modeling. 64, 8, p. 3465-3476 12 p.Research output: Contribution to journal › Article › peer-review
Open Access -
The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics
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., 12 Mar 2024, In: Journal of Chemical Theory and Computation. 20, 5, p. 2321-2333 13 p.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Unraveling the mechanism of small molecule induced activation of Staphylococcus aureus signal peptidase IB
Chen, S. Y., Fiedler, M. K., Gronauer, T. F., Omelko, O., von Wrisberg, M. K., Wang, T., Schneider, S., Sieber, S. A. & Zacharias, M., Dec 2024, In: Communications Biology. 7, 1, 895.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
2023
A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites
Dienemann, J. N., Chen, S. Y., Hitzenberger, M., Sievert, M. L., Hacker, S. M., Prigge, S. T., Zacharias, M., Groll, M. & Sieber, S. A., 1 Aug 2023, In: Angewandte Chemie International Edition in English. 62, 31, e202304533.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
A constant domain mutation in a patient-derived antibody light chain reveals principles of AL amyloidosis
Rottenaicher, G. J., Absmeier, R. M., Meier, L., Zacharias, M. & Buchner, J., Dec 2023, In: Communications Biology. 6, 1, 209.Research output: Contribution to journal › Article › peer-review
Open Access12 Scopus citations -
APP substrate ectodomain defines amyloid-β peptide length by restraining γ-secretase processivity and facilitating product release
Koch, M., Enzlein, T., Chen, S. Y., Petit, D., Lismont, S., Zacharias, M., Hopf, C. & Chávez-Gutiérrez, L., 1 Dec 2023, In: EMBO Journal. 42, 23, e114372.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Assembly-dependent Structure Formation Shapes Human Interleukin-23 versus Interleukin-12 Secretion
Aschenbrenner, I., Siebenmorgen, T., Lopez, A., Parr, M., Ruckgaber, P., Kerle, A., Rührnößl, F., Catici, D., Haslbeck, M., Frishman, D., Sattler, M., Zacharias, M. & Feige, M. J., 1 Dec 2023, In: Journal of Molecular Biology. 435, 23, 168300.Research output: Contribution to journal › Article › peer-review
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Benchmarking biomolecular force field-based Zn2+ for mono- and bimetallic ligand binding sites
Melse, O., Antes, I., Kaila, V. R. I. & Zacharias, M., 30 Mar 2023, In: Journal of Computational Chemistry. 44, 8, p. 912-926 15 p.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
Coupling of conformation and CPD damage in nucleosomal DNA
Nayis, A., Liebl, K. & Zacharias, M., Sep 2023, In: Biophysical Chemistry. 300, 107050.Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations
Kienlein, M., Zacharias, M. & Reif, M. M., 2 Nov 2023, In: Structure. 31, 11, p. 1473-1484.e6Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site
Chen, S. Y., Feilen, L. P., Chávez-Gutiérrez, L., Steiner, H. & Zacharias, M., Dec 2023, In: Communications Biology. 6, 1, 670.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Mechanism of β-hairpin formation in AzoChignolin and Chignolin
Zschau, R. L. & Zacharias, M., 5 Apr 2023, In: Journal of Computational Chemistry. 44, 9, p. 988-1001 14 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain variable domain protein FOR005
Pradhan, T., Sarkar, R., Meighen-Berger, K. M., Feige, M. J., Zacharias, M. & Reif, B., Dec 2023, In: Nature Communications. 14, 1, 3755.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21
Günsel, U., Klöpfer, K., Häusler, E., Hitzenberger, M., Bölter, B., Sperl, L. E., Zacharias, M., Soll, J. & Hagn, F., Jun 2023, In: Nature Structural and Molecular Biology. 30, 6, p. 761-769 9 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Studying specificity in protein-glycosaminoglycan recognition with umbrella sampling
Marcisz, M., Anila, S., Gaardløs, M., Zacharias, M. & Samsonov, S. A., 2023, In: Beilstein Journal of Organic Chemistry. 19, p. 1933-1946 14 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
The development of nucleic acids force fields: From an unchallenged past to a competitive future
Liebl, K. & Zacharias, M., 25 Jul 2023, In: Biophysical Journal. 122, 14, p. 2841-2851 11 p.Research output: Contribution to journal › Review article › peer-review
27 Scopus citations -
The LytS-type histidine kinase BtsS is a 7-transmembrane receptor that binds pyruvate
Qiu, J., Gasperotti, A., Sisattana, N., Zacharias, M. & Jung, K., Oct 2023, In: mBio. 14, 5Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Toward Force Fields with Improved Base Stacking Descriptions
Liebl, K. & Zacharias, M., 14 Mar 2023, In: Journal of Chemical Theory and Computation. 19, 5, p. 1529-1536 8 p.Research output: Contribution to journal › Article › peer-review
6 Scopus citations -
Water model determines thermosensitive and physicochemical properties of poly(N-isopropylacrylamide) in molecular simulations
Quoika, P. K., Kamenik, A. S., Fernández-Quintero, M. L., Zacharias, M. & Liedl, K. R., 19 Jan 2023, In: Frontiers in Materials. 10, 1005781.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
What Makes a Good Protein-Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism
Chen, S. Y. & Zacharias, M., 24 May 2023, In: ACS Central Science. 9, 5, p. 969-979 11 p.Research output: Contribution to journal › Article › peer-review
Open Access18 Scopus citations -
2022
Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis
Feilen, L. P., Chen, S. Y., Fukumori, A., Feederle, R., Zacharias, M. & Steiner, H., May 2022, In: eLife. 11, e76090.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
ADAMTS4-specific MR probe to assess aortic aneurysms in vivo using synthetic peptide libraries
Kaufmann, J. O., Brangsch, J., Kader, A., Saatz, J., Mangarova, D. B., Zacharias, M., Kempf, W. E., Schwaar, T., Ponader, M., Adams, L. C., Möckel, J., Botnar, R. M., Taupitz, M., Mägdefessel, L., Traub, H., Hamm, B., Weller, M. G. & Makowski, M. R., Dec 2022, In: Nature Communications. 13, 1, 2867.Research output: Contribution to journal › Article › peer-review
Open Access7 Scopus citations -
Amyloid fibril structure from the vascular variant of systemic AA amyloidosis
Banerjee, S., Baur, J., Daniel, C., Pfeiffer, P. B., Hitzenberger, M., Kuhn, L., Wiese, S., Bijzet, J., Haupt, C., Amann, K. U., Zacharias, M., Hazenberg, B. P. C., Westermark, G. T., Schmidt, M. & Fändrich, M., Dec 2022, In: Nature Communications. 13, 1, 7261.Research output: Contribution to journal › Article › peer-review
Open Access16 Scopus citations -
Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations
Hartmann, J. & Zacharias, M., Dec 2022, In: Proteins: Structure, Function and Bioinformatics. 90, 12, p. 2080-2090 11 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
An internal docking site stabilizes substrate binding to γ-secretase: Analysis by molecular dynamics simulations
Chen, S. Y. & Zacharias, M., 21 Jun 2022, In: Biophysical Journal. 121, 12, p. 2330-2344 15 p.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Case Report: DPM1-CDG: Novel Variant with Severe Phenotype and Literature Review
Lausmann, H., Zacharias, M., Neuhann, T. M., Locher, M. K. & Schettler, K. F., 13 Jul 2022, In: Frontiers in Genetics. 13, 889829.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Computational Protein–Protein Docking
Zacharias, M., 1 Jan 2022, Protein Interactions: The Molecular Basis of Interactomics. wiley, p. 53-76 24 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
1 Scopus citations -
Computational Tools for Accurate Binding Free-Energy Prediction
Reif, M. M. & Zacharias, M., 2022, Methods in Molecular Biology. Humana Press Inc., p. 255-292 38 p. (Methods in Molecular Biology; vol. 2385).Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
3 Scopus citations -
Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding
Heerde, T., Rennegarbe, M., Biedermann, A., Savran, D., Pfeiffer, P. B., Hitzenberger, M., Baur, J., Puscalau-Girtu, I., Zacharias, M., Schwierz, N., Haupt, C., Schmidt, M. & Fändrich, M., Dec 2022, In: Nature Communications. 13, 1, 85.Research output: Contribution to journal › Article › peer-review
Open Access20 Scopus citations -
Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers
Dirscherl, C., Löchte, S., Hein, Z., Kopicki, J. D., Harders, A. R., Linden, N., Karner, A., Preiner, J., Weghuber, J., Garcia-Alai, M., Uetrecht, C., Zacharias, M., Piehler, J., Lanzerstorfer, P. & Springer, S., May 2022, In: Journal of Cell Science. 135, 9, jcs259498.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock
Meixner, M., Zachmann, M., Metzler, S., Scheerer, J., Zacharias, M. & Antes, I., 25 Jul 2022, In: Journal of Chemical Information and Modeling. 62, 14, p. 3426-3441 16 p.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
Enzyme–substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
Petit, D., Hitzenberger, M., Koch, M., Lismont, S., Zoltowska, K. M., Enzlein, T., Hopf, C., Zacharias, M. & Chávez-Gutiérrez, L., 2 Nov 2022, In: EMBO Journal. 41, 21, e111084.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes
Marcisz, M., Gaardløs, M., Bojarski, K. K., Siebenmorgen, T., Zacharias, M. & Samsonov, S. A., 15 Sep 2022, In: Journal of Computational Chemistry. 43, 24, p. 1633-1640 8 p.Research output: Contribution to journal › Article › peer-review
8 Scopus citations -
Fast peptide exchange on major histocompatibility complex class I molecules by acidic stabilization of a peptide-empty intermediate
Saikia, A., Hadeler, A., Prasad, P., Zacharias, M. & Springer, S., Dec 2022, In: Protein Science. 31, 12, e4478.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications
Reif, M. M. & Zacharias, M., 14 Jun 2022, In: Journal of Chemical Theory and Computation. 18, 6, p. 3873-3893 21 p.Research output: Contribution to journal › Article › peer-review
6 Scopus citations