Publications of the group


CV. Frost, N. Schwierz, M. Zacharias
Efficient and accurate binding free energy calculation of Aβ9-40 protofilament propagation
Proteins 2024

M. Kienlein, M. Zacharias, MM. Reif
Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations
J Chem Theory Comput. 2024

PK. Quoika, M. Zacharias
Liquid-Vapor Coexistence and Spontaneous Evaporation at Atmospheric Pressure of Common Rigid Three-Point Water Models in Molecular Simulations
J Phys Chem B. 2024; 128(10):2457-2468

AM. Fischer, A. Tichy, J. Kokot, VJ. Hoerschinger, RF. Wild, JR. Riccabona, JR. Loeffler, F. Waibl, PK. Quoika, P. Gschwandtner, S. Forli, AB.Ward, KR. Liedl, M. Zacharias, ML. Fernández-Quintero
The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics
J Chem Theory Comput. 2024;20(5):2321-2333

M. Shein, M. Hitzenberger, TC. Cheng, SR. Rout, KD. Leitl, Y. Sato, M. Zacharias, E. Sakata, AK. Schütz
Characterizing ATP processing by the AAA+ protein p97 at the atomic level
Nat Chem. 2024,16(3):363-372

SA. Abdel-Rahman, BL. Santini, L. Calvo-Barreiro, M. Zacharias, M. Gabr
Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction
Bioorg Med Chem Lett. 2024, 1;99:129599

M. Marcisz, S. Anila, M. Gaardløs, M. Zacharias, SA. Samsonov
Studying specificity in protein-glycosaminoglycan recognition with umbrella sampling
Beilstein J Org Chem. 2023, 19:1933-1946


SY. Chen, M. Koch, L. Chávez-Gutiérrez, M. Zacharias
How Modulator Binding at the Amyloidβ-γ-Secretase Interface Enhances Substrate Binding and Attenuates Membrane Distortion
J Med Chem. 2023, 28; 66(24):16772-16782

M. Koch, T. Enzlein, SY. Chen, D. Petit, S. Lismont, M. Zacharias, C. Hopf, L. Chávez-Gutiérrez
APP substrate ectodomain defines amyloid-β peptide length by restraining γ-secretase processivity and facilitating product release
EMBO J. 2023 Dec 1; 42(23):e114372

I. Aschenbrenner, T. Siebenmorgen, A. Lopez, M. Parr, P. Ruckgaber, A. Kerle, F. Rührnößl, D. Catici, M. Haslbeck, D. Frishman, M. Sattler, M. Zacharias, MJ. Feige
Assembly-dependent Structure Formation Shapes Human Interleukin-23 versus Interleukin-12 Secretion
J Mol Biol. 2023, 1; 435(23):168300

M. Kienlein, M. Zacharias, MM. Reif
Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations
Structure. 2023, 2;31(11):1473-1484.e6

J. Qiu, A. Gasperotti, N. Sisattana, M. Zacharias, K. Jung
The LytS-type histidine kinase BtsS is a 7-transmembrane receptor that binds pyruvate
mBio 2023, 31;14(5):e0108923

SY. Chen, LP. Feilen, L. Chávez-Gutiérrez, H. Steiner, M. Zacharias
Enzyme-substrate hybrid β-sheet controls geometry and water access to the γ-secretase active site
Commun Biol. 2023, 24;6(1):670

T. Pradhan, R. Sarkar, KM. Meighen-Berger, MJ. Feige, M. Zacharias, B. Reif
Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain variable domain protein FOR005
Nat Commun. 2023, 23;14(1):3755

A. Nayis, K. Liebl, M. Zacharias
Coupling of conformation and CPD damage in nucleosomal DNA
Biophys Chem. 2023, 5;300:107050

U. Günsel, K. Klöpfer, E. Häusler, M. Hitzenberger, B. Bölter, LE. Sperl, M. Zacharias, J. Soll, F. Hagn
Structural basis of metabolite transport by the chloroplast outer envelope channel OEP21
Nat Struct Mol Biol. 2023, 30(6):761-769

JN. Dienemann, SY. Chen, M. Hitzenberger, ML. Sievert, SM. Hacker, ST. Prigge, M. Zacharias, M. Groll, SA. Sieber
A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites
Angew Chem Int Ed Engl. 2023, 30:e202304533

RL. Zschau, M. Zacharias
Mechanism of β-hairpin formation in AzoChignolin and Chignolin
J Comput Chem. 2023, 5;44(9):988-1001

SY. Chen, M. Zacharias
What Makes a Good Protein-Protein Interaction Stabilizer: Analysis and Application of the Dual-Binding Mechanism
ACS Cent Sci. 2023, 14;9(5):969-979

O. Melse, I. Antes, VRI. Kaila, M. Zacharias
Benchmarking biomolecular force field-based Zn2+ for mono- and bimetallic ligand binding sites
J Comput Chem. 2023, 30;44(8):912-926

K. Liebl, M. Zacharias
Toward Force Fields with Improved Base Stacking Descriptions
J Chem Theory Comput. 2023, 14;19(5):1529-1536

GJ. Rottenaicher, RM. Absmeier, L. Meier, M. Zacharias, J. Buchner
A constant domain mutation in a patient-derived antibody light chain reveals principles of AL amyloidosis
Commun Biol. 2023, 23;6(1):209


K. Liebl, M. Zacharias
The development of nucleic acids force fields: From an unchallenged past to a competitive future
Biophys J. 2022, 20:S0006-3495(22)03932-7

A. Zanotti, JPL. Coelho, D. Kaylani, G. Singh, M. Tauber, M. Hitzenberger, D. Avci, M. Zacharias, RB. Russell, MK. Lemberg, MJ. Feige
The human signal peptidase complex acts as a quality control enzyme for membrane proteins
Science. 2022, 2;378(6623):996-1000

N. Bloemeke, K. Meighen-Berger, M. Hitzenberger, NC. Bach, M. Parr, JP. Coelho, D. Frishman, M. Zacharias, SA. Sieber, MJ. Feige
Intramembrane client recognition potentiates the chaperone functions of calnexin
EMBO J. 2022, 15;41(24):e110959

S. Banerjee, J. Baur, C. Daniel, PB. Pfeiffer, M. Hitzenberger, L. Kuhn, S. Wiese, J. Bijzet, C. Haupt, KU. Amann, M. Zacharias, BPC. Hazenberg, GT. Westermark, M. Schmidt, M. Fändrich
Amyloid fibril structure from the vascular variant of systemic AA amyloidosis. Nat Commun
Nat Commun. 2022, 25;13(1):7261

D. Petit, M. Hitzenberger, M. Koch, S. Lismont, KM. Zoltowska, T. Enzlein , C. Hopf , M. Zacharias,
L. Chávez-Gutiérrez
Enzyme-substrate interface targeting by imidazole-based γ-secretase modulators activates γ-secretase and stabilizes its interaction with APP
EMBO J. 2022, 19, e111084

M. Ravichandran, D. Rafalski, CI. Davies, O. Ortega-Recalde, X. Nan, CR. Glanfield, A. Kotter, K. Misztal, AH. Wang, M. Wojciechowski, M. Rażew, IM. Mayyas, O. Kardailsky, U. Schwartz, K. Zembrzycki, IM. Morison, M. Helm, D. Weichenhan, RZ. Jurkowska, F. Krueger, C. Plass, M. Zacharias, M. Bochtler, TA. Hore, TP. Jurkowski
Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function
Sci Adv. 2022, 9, 8(36), eabm2427

A. Hadeler, A. Saikia, M. Zacharias, S. Springer
Rapid peptide exchange on MHC class I by small molecules elucidates dynamics of bound peptide
Curr Res Immunol. 2022,18, 3, 167-174

J. Hartmann, M. Zacharias
Analysis of amyloidogenic transthyretin mutations using continuum solvent free energy calculations
Proteins. 2022, 16

M. Meixner, M. Zachmann, S. Metzler, J. Scheerer, M. Zacharias, I. Antes
Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock
J Chem Inf Model. 2022, 25, 62(14), 3426-3441

MM. Reif, M. Zacharias
Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications
J Chem Theory Comput. 2022, 14,18(6), 3873-3893

J. Saatz, DB. Mangarova, M. Zacharias, WE. Kempf, T. Schwaar, M. Ponader, LC. Adams, J. Möckel, RM. Botnar, M. Taupitz, L. Mägdefessel, H. Traub, B. Hamm, MG. Weller, MR. Makowski
ADAMTS4-specific MR probe to assess aortic aneurysms in vivo using synthetic peptide libraries
Nat Commun. 2022, 23, 13(1), 2867

SY. Chen, M. Zacharias
An internal docking site stabilizes substrate binding to γ-secretase: Analysis by molecular dynamics simulations
Biophys J. 2022, 21, 121(12), 2330-2344

LP. Feilen, SY. Chen, A. Fukumori, R. Feederle, M. Zacharias, H. Steiner
Active site geometry stabilization of a presenilin homolog by the lipid bilayer promotes intramembrane proteolysis
Elife. 2022, 17, 11, e76090

M. Rieger, M. Zacharias
Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations
J Phys Chem B. 2022, 26, 126(20), 3640-3647

C. Dirscherl, S. Löchte, Z. Hein, JD. Kopicki, AR. Harders, N. Linden, A. Karner, J. Preiner, J. Weghuber, M. Garcia-Alai, C. Uetrecht, M. Zacharias, J. Piehler, P. Lanzerstorfer, S. Springer
Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers
J Cell Sci. 2022, 1, 135(9), jcs259489

BL. Santini, M. Zacharias
Rapid Rational Design of Cyclic Peptides Mimicking Protein-Protein Interfaces
Methods Mol Biol. 2022, 2405, 231-244

T. Heerde, M. Rennegarbe, A. Biedermann, D. Savran, PB. Pfeiffer, M. Hitzenberger, J. Baur, I. Puscalau-Girtu, M. Zacharias, N. Schwierz, C. Haupt, M. Schmidt, M. Fändrich
Cryo-EM demonstrates the in vitro proliferation of an ex vivo amyloid fibril morphology by seeding
Nat Commun. 2022, 10, 13(1), 85

MM. Reif, M. Zacharias
Computational Tools for Accurate Binding Free-Energy Prediction
Methods Mol Biol. 2022, 2385, 255-292

M. Zacharias
Match_Motif: A rapid computational tool to assist in protein-protein interaction design
Protein Sci. 2022, 31(1), 147-157


P. Cacciotto, A. Basciu, F. Oliva, G. Malloci, M. Zacharias, P. Ruggerone, AV Vargiu
Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA
Comput Struct Biotechnol J. 2021, 20, 252-260

U. Grupa, K. Liebl, M. Zacharias
Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations
J Phys Chem B. 2021, 30, 125(51), 13850-13857

G. Gouridis, YA. Muthahari, M. de Boer, DA. Griffith, A. Tsirigotaki, K. Tassis, N. Zijlstra, R. Xu, N. Eleftheriadis, Y. Sugijo, M. Zacharias, A. Dömling, S. Karamanou, C. Pozidis, A. Economou, T. Cordes
Structural dynamics in the evolution of a bilobed protein scaffold
Proc Natl Acad Sci U S A. 2021, 7, 118(49), e2026165118

HL. Svilenov, J. Sacherl, U. Protzer, M. Zacharias, J. Buchner
Mechanistic principles of an ultra-long bovine CDR reveal strategies for antibody design
Nat Commun. 2021, 18, 12(1), 6737

K. Liebl, M. Zacharias
Tumuc1: A New Accurate DNA Force Field Consistent with High-Level Quantum Chemistry
J Chem Theory Comput. 2021, 9, 17(11), 7096-7105

M. Marcisz, M. Zacharias, SA. Samsonov
Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter?
J Chem Inf Model. 2021, 27, 61(9), 4475-4485

C. Gebhardt, M. Lehmann, MM. Reif, M. Zacharias, G. Gemmecker, T. Cordes
Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series
Chemphyschem. 2021, 4, 22(15), 1546

MF. de Souza Degenhardt, PAM. Vitale, LA. Abiko, M. Zacharias, M. Sattler, CLP. Oliveira, RK. Salinas
Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS
Biophys J. 2021, 7, 120(17), 3664-3675

D. Pourjafar-Dehkordi, M. Zacharias
Binding induced functional domain motions in the argonaute characterized by adaptive advanced sampling
PLoS Comput Biol., 2021, 29, 17(11)

J. Hartmann, M. Zacharias
Mechanism of collagen folding propagation studied by Molecular Dynamics simulations
PLoS Comput Biol., 2021, 8, 17

D. Pourjafar-Dehkordi, M. Zacharias
Influence of a Ser111‐phosphorylation on Rab1b GTPase conformational dynamics studied by advanced sampling simulations
Proteins. 2021, 31

J. Fauser, B. Gulen, V. Pogenberg, C. Pett, D. Pourjafar-Dehkordi, C. Krisp, D. Höpfner, G. König, H. Schlüter, MJ. Feige, M. Zacharias, C. Hedberg, A. Itzen
Specificity of AMPylation of the human chaperone BiP is mediated by TPR motifs of FICD
Nat Commun. 2021, 23, 12(1), 2426

K. Liebl, M. Zacharias
Accurate modeling of DNA conformational flexibility by a multivariate Ising model
Proc Natl Acad Sci U S A, 2021, 13, 118(15)

M. Maszota-Zieleniak, M. Marcisz, MM. Kogut, T. Siebenmorgen, M. Zacharias, SA. Samsonov
Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans
J Comput Chem., 2021, 5, 42(15), 1040-1053

GJ. Rottenaicher, B. Weber, F. Rührnößl, P. Kazman, RM. Absmeier, M. Hitzenberger, M. Zacharias, J. Buchner
Molecular mechanism of amyloidogenic mutations in hypervariable regions of antibody light chains
J Biol Chem. 2021, 296, 100334


M. Silber, M. Hitzenberger, M. Zacharias, C. Muhle-Goll
Altered Hinge Conformations in APP Transmembrane Helix Mutants May Affect Enzyme-Substrate Interactions of γ-Secretase
ACS Chem Neurosci, 2020, 16;11(24):4426-4433

S. Savitskiy, R. Wachtel, D. Pourjafar-Dehkordi, H.S. Kang, V. Trauschke, D.C. Lamb, M. Sattler, M. Zacharias, A. Itzen
Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation
iScience 24 (1), 2020

A. Nayis, K. Liebl, C.V. Frost, M. Zacharias
Targeting Telomeres: Molecular dynamics and free energy simulation of gold-carbene binding to DNA
Biophysical Journal 120 (1), 2020, 101-108

M. Kienlein, M. Zacharias
Ligand binding and global adaptation of the GlnPQ substrate binding domain 2 revealed by molecular dynamics simulations
Protein Science 29 (12), 2020, 2482-2494

C.V. Frost, M Zacharias
From monomer to fibril: Abeta‐amyloid binding to Aducanumab antibody studied by molecular dynamics simulation
Proteins: Structure, Function, and Bioinformatics 88 (12), 2020, 1592-1606

M. Silber, M. Hitzenberger, M. Zacharias, C. Muhle-Goll
Altered Hinge Conformations in APP Transmembrane Helix Mutants May Affect Enzyme–Substrate Interactions of γ-Secretase
ACS Chemical Neuroscience 11 (24), 2020, 4426-4433

M. Zacharias
Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation
The Journal of Physical Chemistry B 124 (46), 2020, 10345-10352

T. Siebenmorgen, M. Zacharias
Efficient Refinement and Free Energy Scoring of Predicted Protein–Protein Complexes Using Replica Exchange with Repulsive Scaling
Journal of Chemical Information and Modeling 60 (11), 2020, 5552-5562

S.-Y. Chen, M. Zacharias
How Mutations perturb γ-Secretase active site studied by Free Energy Simulations
ACS Chemical Neuroscience 11 (20), 2020, 3321-3332

G. Glashagen, S. de Vries, U. Uciechowska‐Kaczmarzyk, S.A. Samsonov, S. Murail, P. Tuffery, M. Zacharias
Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach
Proteins: Structure, Function, and Bioinformatics 88 (8), 2020, 1018-1028

J. Lee, M. Hitzenberger, M. Rieger, N.R. Kern, M. Zacharias, W. Im
CHARMM-GUI supports the Amber force fields
The Journal of Chemical Physics 153 (3), 2020, 035103

T. Siebenmorgen, M. Engelhard, M. Zacharias
Prediction of protein–protein complexes using replica exchange with repulsive scaling
Journal of Computational Chemistry 41 (15), 2020, 1436-1447

S.M. Hofmann, C.V. Frost, T. Podewin, M. Gailer, E. Weber, M. Zacharias, A. Hoffmann-Röder, W. Zinth
Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs Within 100 ns
The Journal of Physical Chemistry B 124 (25), 2020, 5113–5121

M. Hitzenberger, A. Götz, S. Menig, B. Brunschweiger, M. Zacharias, C. Scharnagl
The dynamics of γ-secretase and its substrates
Seminars in Cell & Developmental Biology 105, 2020, 86-101

K. Liebl, M. Zacharias
How global DNA unwinding causes non-uniform stress distribution and melting of DNA
PloS one 15 (5), 2020, e0232976

E. Apra, E.J. Bylaska, W.A. De Jong, N. Govind, K. Kowalski, T.P. Straatsma.(2020)
NWChem: Past, present, and future
The Journal of chemical physics 152 (18), 2020, 184102

T. Siebenmorgen, M. Zacharias
Computational prediction of protein–protein binding affinities
Wiley Interdisciplinary Reviews: Computational Molecular Science 10 (3), 2020, e1448

H. Dohnalová, T. Dršata, J. Sponer, M. Zacharias, J. Lipfert, F. Lankaš
Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation
Journal of Chemical Theory and Computation 16 (4), 2020, 2857-2863

R. Anjanappa, M. Garcia-Alai, J. D. Kopicki, J. Lockhauserbäumer, M. Aboelmagd, J. Hinrichs, & R. Meijers
Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection
Nature Communications, 11 (1), 2020, 1-11

P. Kazman, M.T. Vielberg, M.D.P. Cendales, L. Hunziger, B. Weber, M. Zacharias, J. Buchner
Fatal amyloid formation in a patient’s antibody light chain is caused by a single point mutation
Elife 9, 2020, e52300

D. Pourjafar-Dehkordi, M. Zacharias
Prediction of protein–protein complex structures by docking
Protein Interactions Chapter 3, 2020, 59-85

B.L. Santini, M. Zacharias
Rapid in silico design of potential cyclic peptide binders targeting protein-protein interfaces
Frontiers in chemistry 8, 2020, 933

S. De, G. Sabu, M. Zacharias
Molecular mechanism of Be2+-ion binding to HLA-DP2: tetrahedral coordination, conformational changes and multi-ion binding
Phys Chem Chem Phys. 22 (2), 2020, 799-810


C.J.O. Kaiser, C. Peters, P.W.N. Schmid, M. Stavropoulou, J. Zou, V. Dahiya, E.V. Mymrikov, B. Rockel, S. Asami, M. Haslbeck, J. Rappsilber, B. Reif, M Zacharias, J. Buchner, S. Weinkauf
The structure and oxidation of the eye lens chaperone αA-crystallin
Nature Structural & Molecular Biology 26 (12), 2019, 1141-1150

M. Schmidt, S. Wiese, V. Adak, J. Engler, S. Agarwal, G. Fritz, P. Westermark, M. Zacharias, M. Fändrich
Cryo-EM structure of a transthyretin-derived amyloid fibril from a patient with hereditary ATTR amyloidosis
Nature communications 10 (1), 2019, 1-9

F. Kandzia, K. Ostermeir, M. Zacharias
Global dynamics of yeast Hsp90 middle and C-terminal dimer studied by advanced sampling simulations
Frontiers in molecular biosciences 6, 2019, 93

D. Dedden, S. Schumacher, C.F. Kelley, M. Zacharias, C. Biertümpfel
The architecture of Talin1 Reveals an Autoinhibition Mechanism
Cell 179 (1), 2019, 120-131. e13

D. Pourjafar-Dehkordi, S. Vieweg, A. Itzen, M. Zacharias
Phosphorylation of Ser111 in Rab8a modulates Rabin8-dependent activation by perturbation of side chain interaction networks
Biochemistry 58 (33), 2019, 3546-3554

S.K. Saini, T. Tamhane, R. Anjanappa, A. Saikia, S. Ramskov, M. Donia, M. Zacharias, S. Springer
Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells
Science immunology 4 (37), 2019

D. Petit, M. Hitzenberger, S. Lismont, Zoltowska, M. Katarzyna, S. Ryan Natalie, M. Mercken, F. Bischoff, M. Zacharias, Marting, Chávez-Gutiérrez, Lucía
Extracellular interface between APP and Nicastrin regulates Ab length and response to c-secretase modulators
The EMBO journal, 38, 2019, e101494

M. Hitzenberger, M. Zacharias
Uncovering the Binding Mode of γ -Secretase Inhibitors, ACS Chem
Neurosci 10 (8), 2019, 3398-3403

M. Hitzenberger, M. Zacharias,
Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing
ACS Chem. Neurosci, 10 (3), 2019, 1826-1840

M. Zacharias
Atomic resolution insight on Sac7d protein binding to DNA and associated global changes by Molecular Dynamics Simulations
Angewandte Chemie 58 (18) 2019, 5967-5972

S.I. Müller, I. Aschenbrenner, M. Zacharias, M.J. Feige
An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27
Journal of molecular biology, S0022-2836(19), 2019, 30239-6

F. Kandzia, M. Zacharias
Dynamics of the full-length yeast Hsp90 dimer
The European Physical Journal Special Topics 227.14, 2019, 1693-1704

S.A. Samsonov, M. Zacharias, I. Chauvot de Beauchene
Modeling large protein–glycosaminoglycan complexes using a fragment‐based approach
Journal of computational chemistry, 40 (14), 2019, 1429-1439

M. Hitzenberger, M. Zacharias
Structural Modeling of γ-Secretase Aβ n Complex Formation and Substrate Processing
ACS chemical neuroscience 10 (3), 2019, 1826-1840

T. Siebenmorgen, M. Zacharias
Evaluation of predicted protein-protein complexes by binding free energy simulations
Journal of chemical theory and computation) 15 (3), 2019, 2071-2086

M. Reif, M. Zacharias
Computer Modelling and Molecular Dynamics Simulation of Biomolecules Biomolecular and Bioanalytical Techniques
Theory, Methodology and Applications, 2019, 501-535

M. Reif, M. Fischer, K. Fredriksson, F. Hagn, M. Zacharias
The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding
Journal of Molecular Biology, 431, 2019, 223-243

S. I. Müller, A. Friedl, I. Aschenbrenner, J. Esser-von Bieren, M. Zacharias, O. Devergne, M. J. Feige
Proceedings of the National Academy of Sciences (2019), 116(5):1585-1590
PNAS, 116, (5), 2019, 1585-1590

C. E. M. Schindler, E. Hollenbach, T. Mietzner, K.‐J. Schleifer, M. Zacharias
Free energy calculations elucidate substrate binding, gating mechanism, and tolerance‐promoting mutations in herbicide target 4‐hydroxyphenylpyruvate dioxygenase
Protein Science, 28 (6) 2, 2019, 1048-1058


M. Schickinger, M. Zacharias, H. Dietz
Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices
Proceedings of the National Academy of Sciences 115.32, 2018, 2018, E7512-E7521

M. Hitzenberger, M. Zacharias
γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding
Frontiers in Chemistry 6, 2018, 640

B. Weber, M. J. Brandl, M. D. Pulido Cendales, C. Berner, T. Pradhan, G.M. Feind, M. Zacharias, B. Reif, J. Buchner
A single residue switch reveals principles of antibody domain integrity
Journal of Biological Chemistry, 293, 2018, 17107-17118

A. Spanopoulou, L. Heidrich, H.-R. Chen, C. Frost, D. Hrle, E. Malideli, K. Hille, A. Grammatikopoulos, J. Bernhagen, M. Zacharias, G. Rammes, A. Kapurniotu
Designed Macrocyclic Peptides as Nanomolar Amyloid Inhibitors Based on Minimal Recognition Elements
Angew. Chem. Int. Ed., 57, 2018, 14503-14508

N. Harrer, C. E. M. Schindler, E.M. and L. K. Bruetzel, I. Forné, J. Ludwigsen, A. Imhof, M. Zacharias, J. Lipfert, F. Mueller-Planitz
Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling
Structure, 26, 2018, 282-294

K. Liebl, M. Zacharias,
How methyl-sugar interactions determine DNA structure and flexibility
Nucleic Acids Research, 2018, gky1237

F. Kriegel, C. Matek, T. Dršata, K. Kulenkampff, S. Tschirpke, M. Zacharias, F. Lankaš, J. Lipfert
The temperature dependence of the helical twist of DANN
Nucleic acids research, 46, 2018, 7998-8009


Z. Zhang, U. Ehmann, M. Zacharias
Monte Carlo replica-exchange based ensemble docking of protein conformations
Proteins: Structure, Function and Bioinformatics, 85, 2017, 924-937

F. Zeller, M. Zacharias
Thermodynamics Kinetics of Nucleobase Stacking Oligomerization revealed by Molecular Dynamics Simulations
Journal of Chemical Theory and Computation, 13, 6, 2017, 3005–3011

M. Zacharias
Predicting allosteric changes from conformational ensembles
Structure, 25, 2017, 393-568

S. J. de Vries, J. Rey, C. E. M. Schindler, M. Zacharias, P. Tuffery
The pepATTRACT web server for blind, large-scale peptide-protein docking
Nucleic Acids Research, 45, W1, 2017, W361–W364

S. J. de Vries, M. Zacharias
Fast and accurate grid representations for atom-based docking with partner flexibility
Journal of Computational Chemistry, 38, 2017, 1538-1546

T. Siebenmorgen, M. Zacharias
Origin of Ion Specificity of Telomeric DNA G-Quadruplexes Investigated by Free-Energy Simulations
Biophysical Journal, 112, 2017, 2280-2290

N. Schwierz, C. V. Frost, P. L. Geissler, M. Zacharias
From Aß Filament to Fibril: Molecular Mechanism of Surface-Activated Secondary Nucleation from All-Atom MD Simulations
J. Phys. Chem. B, 121, 2017, 671-682

C. E. M. Schindler, M. Zacharias
Application of the ATTRACT Coarse-Grained Docking and Atomistic Refinement for Predicting Peptide-Protein Interactions
Modeling Peptide-Protein Interactions: Methods and Protocols, 2017, 49-68

K. Ostermeir, M. Zacharias
Accelerated flexible protein-ligand docking using Hamiltonian replica exchange with a repulsive biasing potential
PloS one, 12, 2017, e0172072

M. P. Luitz, Barth, E. Crevenna, H. Alvaro R. Bomblies, D. C. Lamb, M. Zacharias
Covalent dye attachment influences the dynamics and conformational properties of flexible peptides
PloS one, 12, 2017, e0177139

J. Ludwigsen, S. Pfennig, A. K. Singh, C. E. M. Schindler, N. Harrer, I. Forné, M. Zacharias, F. Mueller-Planitz
Concerted regulation of ISWI by an autoinhibitory domain and the H4 N-terminal tail
eLife, 6, 2017, e21477

A. Knips, M. Zacharias
Both DNA global deformation and repair enzyme contacts mediate flipping of thymine dimer damage
Scientific Reports, 7, 2017, 41324

B. Hellenkamp, P. Wortmann, F. Kandzia, M. Zacharias, T. Hugel
Multidomain structure and correlated dynamics determined by self-consistent FRET networks
Nature methods, 14, 2017, 174-180

J.-B. Chéron, M. Zacharias, S. Antonczak, S. Fiorucci
Update of the ATTRACT force field for the prediction of protein-protein binding affinity
Journal of Computational Chemistry, 2017

R. Bomblies, M. P. Luitz, S. Scanu, T. Madl, M. Zacharias
Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations
PloS one, 12, 2017, e0174337


G. La Rosa, M. Zacharias
Global deformation facilitates flipping of damaged 8-oxo-guanine and guanine in DANN
Nucleic Acids Res, 2016

F. Kilchherr, C. Wachauf, B. Pelz, M. Rief, M. Zacharias, H. Dietz
Single-molecule dissection of stacking forces in DANN
Science, 353, 2016

F. Häse, M. Zacharias
Free energy analysis and mechanism of base pair stacking in nicked DANN
Nucleic Acids Res, 44, 2016, 7100-7108

C. E. M. Schindler, I. Chauvot de Beauchêne, S. de Vries, M. Zacharias
Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins: Structure, Function, and Bioinformatics
Wiley Online Library, 2016

K. Szameit, K. Berg, S. Kruspe, E. Valentini, E. Magbanua, M. Kwiatkowski, I. Chauvot de Beauchêne, B. Krichel, K. Schamoni, C. Uetrecht, D. I. Svergun, H.Schlüter, M. Zacharias, U. Hahn
Structure and target interaction of a G-quadruplex RNA-aptamer
RNA Biol, 13, 2016, 973-987

C. N. Nokwe, M. Hora, M. Zacharias, H. Yagi, J. Peschek, B. Reif, Y. Goto, J. Buchner
A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions
J Mol Biol, 428, 2016, 1315-1332

M. P. Luitz, R. Bomblies, E. Ramcke, A. Itzen, M. Zacharias
Adenylylation of Tyr77 stabilizes Rab1b GTPase in an active state: A molecular dynamics simulation analysis
Sci Rep, 6, 2016, 19896

M. M. Reif, M. Zacharias
Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules
J Comput Chem, 37, 2016, 1711-1724

N. Schwierz, C. V. Frost, P. L. Geissler, M. Zacharias
Dynamics of Seeded Aβ40-Fibril Growth from Atomistic Molecular Dynamics Simulations: Kinetic Trapping and Reduced Water Mobility in the Locking Step
J Am Chem Soc, 138, 2016, 527-539

N. Schwierz, S. Krysiak, T. Hugel, M. Zacharias
Mechanism of Reversible Peptide-Bilayer Attachment: Combined Simulation and Experimental Single-Molecule Study
Langmuir, 32, 2016, 810-821

C. N. Nokwe, M. Hora, M. Zacharias, H. Yagi, J. Peschek, B. Reif, Y. Goto, J. Buchner
A Stable Mutant Predisposes Antibody Domains to Amyloid Formation through Specific Non-Native Interactions
J Mol Biol, 2016

I. Chauvot de Beauchene, S. J. de Vries, M. Zacharias
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach
PLoS Comput Biol, 12, 2016, e1004697

S. J. de Vries, I. Chauvot de Beauchêne, C. E. M. Schindler, M. Zacharias
Cryo-EM Data Is Superior to Contact and Interface Information in Integrative Modeling
Biophys J, 2016

B. Pelz, G. Žoldák, F. Zeller, M. Zacharias, M. Rief
Subnanometre enzyme mechanics probed by single-molecule force spectroscopy
Nat Commun, 16, 7, 2016, 10848

R. Bomblies, M. P. Luitz, M. Zacharias
Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation
The Journal of Physical Chemistry B, 2016

C. E. M. Schindler, S. J. de Vries, A. Sasse, M. Zacharias
SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes
Structure, 24, 2016, 387-1397

R. Bomblies, M. P. Luitz, M. Zacharias
Mechanism of pKID/KIX Association Studied by Molecular Dynamics Free Energy Simulations
J. Phys. Chem. B, 120, 2016, 8186-8192

P. Schöppner, G. Csaba, T. Braun, M. Daake, B. Richter, O. F.  Lange, M. Zacharias, R. Zimmer, M. Haslbeck
Regulatory Implications of Non-Trivial Splicing: Isoform 3 of Rab1A Shows Enhanced Basal Activity and Is Not Controlled by Accessory Proteins
J Mol Biol, 428, 2016, 1544-1557

I. Chauvot de Beauchene, S. J. de Vries, M. Zacharias
Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins
Nucleic Acids Research, 44, 2016, 4565-4580


Z. Zhang, C. E. M. Schindler, O. F. Lange, M. Zacharias, Martin
Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta
PLoS One, 2015, e0125941

F. Zeller, M. Zacharias
Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase
Biophysical Journal, 109, 2015, 1978-1985

C. N. Nokwe, M. Hora, M. Zacharias, H. Yagi, C. John, B. Reif, Y. Goto, J. Buchner
The Antibody Light-Chain Linker Is Important for Domain Stability and Amyloid Formation
J Mol Biol, 427, 2015, 3572-3586

F. Mittelberger, C. Meyer, G. H. Waetzig, M. Zacharias, E. Valentini, D. I. Svergun, K. Berg, I. Lorenzen, J. Grötzinger, S. Rose-John, U. Hahn
RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity
RNA Biol, 12, 2015, 1043-1053

M. P. Luitz, R. Bomblies, K. Ostermeir, M. Zacharias
Exploring biomolecular dynamics and interactions using advanced sampling methods
Journal of Physics: Condensed Matter, 27, 2015, 323101

S. J. de Vries, C E. M. Schindler, I. Chauvot de Beauchêne, M. Zacharias
A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT
Biophys J, 108, 2015, 462-465

H. G. Hocking, F. Häse, T. Madl, M. Zacharias, M. Rief, G. Žoldák
A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain
Biophys J, 108, 2015, 678-686

K. Liebl, T. Drsata, F. Lankas, J. Lipfert, M. Zacharias
Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis
Nucleic Acids Res, 43, 2015, 10143-10156

C. N. Cavasotto, R. Bomblies, M. P. Luitz, M. Zacharias
Free Energy Calculations of Ligand-Protein Binding
CRC Press, 2015

B. Boyer, J. Ezelin, P. Poulain, A. Saladin, M. Zacharias, C. H. Robert, C. Prévost
An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA
PLoS One, 2015, e0116414

C. E. M. Schindler, S. J. de Vries, M. Zacharias
Fully Blind Peptide-Protein Docking with pepATTRACT
Structure, 23, 2015, 1507-1515

E. T. Abualrous, S. K. Saini, V. R. Ramnarayan, F. T. Ilca, M. Zacharias, S. Springer
The Carboxy Terminus of the Ligand Peptide Determines the Stability of the MHC Class I Molecule H-2Kb: A Combined Molecular Dynamics and Experimental Study
PLoS One, 2015, e0135421


F. Zeller, M. Zacharias
Efficient calculation of relative binding free energies by umbrella sampling perturbation
Journal of Computational Chemistry, Wiley-Blackwell, 2014, 2256-2262

K. Ostermeir, M. Zacharias
Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations
Proteins: Structure, Function, and Bioinformatics, 82, 2014, 3410-3419

M. Kara, T. Drsata, F. Lankas, M. Zacharias
Effect O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations
Biopolymers, 103, 2014, 23-32

C. E. M. Schindler, S. J. de Vries, M. Zacharias
iATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement
Proteins: Structure, Function, and Bioinformatics, 83, 2014, 248-258

A. Knips, M. Zacharias
Influence of a cis, syn-cyclobutane pyrimidine dimer damage on DNA conformation studied by molecular dynamics simulations
Biopolymers, 103, 2014, 215-222

A. Saladin, J. Rey, P. Thévenet, M. Zacharias, G. Moroy, P. Tufféry
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces
Nucleic Acids Res, 42, 2014

M. P. Luitz, M. Zacharias
Protein-ligand docking using Hamiltonian replica exchange simulations with soft core potentials
J Chem Inf Model, 54, 6, 2014, 1669-1675

S. Kannan, M. Zacharias
Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations
PLoS One, 9, 2014, e88383

F. Zeller, M. Zacharias
Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations
The Journal of Physical Chemistry B, 118, 27, 2014, 7467-7474

S. Temme, M. Zacharias, J. Neumann, S. Wohlfromm, A. König, N. Temme, S. Springer, J. Trowsdale, N. Koch
A novel family of human leukocyte antigen class II receptors may have its origin in archaic human species
J Biol Chem, 289, 2014, 639-653

K. Ostermeir, M. Zacharias
Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles
J Comput Chem, 35, 2014, 150-158

S. K. Mishra, M. Kara, M. Zacharias, J. Koca
Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation
Glycobiology, 24, 2014, 70-84

S. Fiorucci, M. Zacharias
Computational Antigenic Epitope Prediction by Calculating Electrostatic Desolvation Penalties of Protein Surfaces Immunoinformatics
Springer Science, Business Media, 2014, 365-374

F. Zeller, M. Zacharias
Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations
Journal of Chemical Theory and Computation, 10, 2014, 703-710

K. Ostermeir, S. Springer, M. Zacharias
Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations
Molecular Immunology, 63, 2, 2014

K. Ostermeir, M. Zacharias
Rapid Alchemical Free Energy Calculation Employing a Generalized Born Implicit Solvent Model
The Journal of Physical Chemistry B, 119, 3, 2014, 968-975

C. N. Nokwe, M. Zacharias, H. Yagi, M. Hora, B. Reif, Y.Goto, J. Buchner
A Residue-specific Shift in Stability and Amyloidogenicity of Antibody Variable Domains
Journal of Biological Chemistry, 289, 2014, 26829-26846

M. F. Lensink, I. H. Moal, P. A. Bates, P. L. Kastritis, A. S. J. Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A. M. J. J. Bonvin, M. Eisenstein, B. Jiménez-García, S. Grosdidier, A. Solernou, L. Pérez-Cano, C. Pallara, J. Fernández-Recio, J. Xu, P. Muthu, K. Praneeth Kilambi, J. J. Gray, S. Grudinin, G. Derevyanko, J. C. Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, D. M. Standley, M. Shirota, K. Kinoshita, H. Nakamura, M. Chavent, D. W. Ritchie, H. Park, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, P. J. Kundrotas, I. A. Vakser, B. G. Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, H. J. Wolfson, M. Zacharias, S. Qin, H-X. Zhou, S.-Y.Huang, X. Zou, J. A. Wojdyla, C. Kleanthous, S. J. Wodak
Blind prediction of interfacial water positions in CAPRI
Proteins, 2014, 82, 620-632


S. K. Saini, K. Ostermeir, V. R. Ramnarayan, H. Schuster, M. Zacharias, S. Springer
Dipeptides promote folding and peptide binding of MHC class I molecules
Proceedings of the National Academy of Sciences, 110, 2013

T. Dršata, M. Kara, M. Zacharias, F. Lankaš
Effect of 8-Oxoguanine on DNA Structure and Deformability
J Phys Chem B, 117, 39, 2013, 11617-11622

D. Despotovic, L. Vojcic, M. Blanusa, K.-H.Maurer, M. Zacharias, M. Bocola, R. Martinez, U. Schwaneberg
Redirecting catalysis from proteolysis to perhydrolysis in subtilisin Carlsberg
Journal of Biotechnology, 167, 2013, 279-286

K. Ostermeir, M. Zacharias
Advanced replica-exchange sampling to study the flexibility and plasticity of peptides and proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
Elsevier, 1834, 2013, 847-853

A. Schütt, M. Zacharias, N. Schneider, S. Horn, J. Grötzinger, S. Rose-John, D. Schmidt-Arras
gp130 activation is regulated by D2-D3 interdomain connectivity
Biochemical Journal, 450, 2013, 487-496

M. P. Luitz, M. Zacharias
Role of tyrosine hot-spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study
Wiley Blackwell (John Wiley & Sons) 81, 2013, 461-468

M. Kara, M. Zacharias
Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations
Biophysical Journal, 104, 2013, 1089-1097

G. Jankevicius, M. Hassler, B. Golia, V. Rybin, M. Zacharias, G. Timinszky, A. G. Ladurner
A family of macrodomain proteins reverses cellular mono-{ADP}-ribosylation
Nature Structural \& Molecular Biology, 20, 2013, 508-514

M. Klähn, M. Zacharias
Transformations in plasma membranes of cancerous cells and resulting consequences for cation insertion studied with molecular dynamics
Physical Chemistry Chemical Physics, 15, 2013, 14427

M. Kara, M. Zacharias
Stabilization of duplex DNA and RNA by dangling ends studied by free energy simulations
Biopolymers, 101, 4, 2013, 307-439

A. Nuccitelli, C. D. Rinaudo, B. Brogioni, R. Cozzi, M. Ferrer-Navarro, D. Yero, J. L. Telford, G. Grandi, X. Daura, M. Zacharias, D. Maione
Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus
PLoS Computational Biology, 9, 2013, e1003115

B. Steuten, P. Setny, M. Zacharias, R. Wagner
Mapping the Spatial Neighborhood of the Regulatory 6S RNA Bound to Escherichia coli RNA Polymerase Holoenzyme
Journal of Molecular Biology, 425, 19, 2013, 3649-3661

M. Kara, M. Zacharias
Theoretical studies of nucleic acids folding
Wiley Interdisciplinary Reviews: Computational Molecular Science, 4, 2, 2013, 116-126

M. Zacharias
Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling
Wiley Blackwell (John Wiley & Sons), 81,1, 2013, 81-92

S. J. de Vries, M. Zacharias
Flexible docking and refinement with a coarse-grained protein model using
Wiley Blackwell (John Wiley & Sons), 81, 12, 2013, 2167-2174

H. Uchtenhagen, E. T. Abualrous, E. Stahl, E. B. Allerbring, M. Sluijter, M. Zacharias, T. Sandalova, T. van Hall, S. Springer, P.-A.Nygren, A. Achour
Proline substitution independently enhances H-{2D} b complex stabilization and TCR recognition of melanoma-associated peptides
European Journal of Immunology, 43, 11, 2013, 3051-3060

A. Bracher, C. Kozany, A. Hähle, P. Wild, M. Zacharias, F. Felix
Crystal Structures of the Free and Ligand-Bound FK1-FK2 Domain Segment of FKBP52 Reveal a Flexible Inter-Domain Hinge
Journal of Molecular Biology,425, 22, 2013, 4134-4144


P. Setny, R. Bahadur, M. Zacharias
Protein-{DNA} docking with a coarse-grained force field
BMC Bioinformatics, 228, 13, 2012

S. Schneider, A. Saladin, S. Fiorucci, C. Prevost, M. Zacharias
ATTRACT and PTOOLS: Open Source Programs for Protein-Protein Docking
Methods in Molecular Biology, 819, 2012, 221-232

S. Leis, M. Zacharias
ReFlexIn: A Flexible Receptor Protein-Ligand Docking Scheme Evaluated on HIV-1 Protease
PLoS ONE, 7 ,2012, e48008

S. Schneider, M. Zacharias
Atomic resolution model of the antibody Fc interaction with the complement C1q component
Molecular Immunology, 51, 2012, 66-72

R. F. Albu, M. Zacharias, T. P. Jurkowski, A. Jeltsch
DNA Interaction of the CcrM DNA Methyltransferase: A Mutational and Modeling Study
ChemBioChem, 13, 2012, 1304-1311

S. Schneider, M. Zacharias
Scoring optimisation of unbound protein-protein docking including protein binding site predictions
Journal of Molecular Recognition, 25, 2012, 15-23

S. J. de Vries, Sjoerd, M. Zacharias
ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps
PLoS ONE, 7, 2012, e49733

S. Schneider, M. Zacharias
Combining geometric pocket detection and desolvation properties to detect putative ligand binding sites on proteins
Journal of Structural Biology, 180, 2012, 546-550


S. Kannan, M. Zacharias
M. Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations
Nucleic Acids Research, 39, 2011, 8271-8280

P. Setny, M. Zacharias
A coarse-grained force field for Protein-RNA docking. Nucleic Acids Research, Nov, 2011, 39, 9118-9129
Oxford University Press 39, 21, 2011, 9118-9129

M. A. Garstka, S. Fritzsche, I. Lenart, Z. Hein, G. Jankevicius, L. H. Boyle, T. Elliott, J. Trowsdale, A. N. Antoniou, M. Zacharias, et al
Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility
The FASEB Journal, 25, 2011, 3989-3998

M. Droescher, A. Begitt, A. Marg, M. Zacharias, U. Vinkemeier
Cytokine-induced Paracrystals Prolong the Activity of Signal Transducers and Activators of Transcription (STAT) and Provide a Model for the Regulation of Protein Solubility by Small Ubiquitin-like Modifier (SUMO)
Journal of Biological Chemistry, 286, 2011, 18731-18746

S. Leis, M. Zacharias
Efficient inclusion of receptor flexibility in grid-based protein-ligand docking
Journal of Computational Chemistry, 32, 2011, 3433-3439

A. V. Vargiu, F. Collu, R. Schulz, K. M. Pos, M. Zacharias, U. Kleinekathöfer, P. Ruggerone
Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations
Journal of the American Chemical Society, 133, 28, 2011, 10704-10707

N. Braun, M. Zacharias, J. Peschek, A. Kastenmuller, J. Zou, M. Hanzlik, M. Haslbeck, J. Rappsilber, J. Buchner, S. Weinkauf
Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach
Proceedings of the National Academy of Sciences, 108, 2011, 20491-20496


A. Saladin, C. Amourda, P. Poulain, N. Ferey, M. Baaden, M. Zacharias
Delalande, O. and Prevost, C. Modeling the early stage of {DNA} sequence recognition within RecA nucleoprotein filaments
Nucleic Acids Research, 38, 2010, 6313-6323

S. Kannan, M. Zacharias
Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent
Proteins: Structure, Function, and Bioinformatics, 78, 2010, 2809-2819

S. Leis, S. Schneider, M. Zacharias
In Silico Prediction of Binding Sites on Proteins
Current Medicinal Chemistry, 17, 15, 2010, 1550-1562

S. Fiorucci, M. Zacharias
Prediction of protein-protein interaction sites using electrostatic desolvation profiles
Biophys J, 98, 2010, 1921-1930

W. Lee, L. Vojcic, D. Despotovic, R. Prodanovic, K.-H. Maurer, U. Schwaneberg, M. Zacharias
Rationalizing perhydrolase activity of aryl-esterase and subtilisin Carlsberg mutants by molecular dynamics simulations of the second tetrahedral intermediate state
Theoretical Chemistry Accounts, 125, 2010, 375-386

M. I. El-Barghouthi, A. I. Saleh, A. Ghandour, R. Ghanem, M. Zacharias
Examining the potency of suggested inhibitors for the phosphatase activity of the human soluble epoxide hydrolase by molecular dynamics simulations
Journal of Molecular Structure: 944, 2010, 97-104

S. Liang, D. Zheng, D. M. Standley, B. Yao, M: Zacharias, C. Zhang
EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results
BMC Bioinformatics, 11, 381, 2010, 1471-2105

M. S. Zoda, M. Zacharias, S. Reissmann
Syntheses and activities of backbone-side chain cyclic octapeptide ligands with N-functionalized phosphotyrosine for the N-terminal SH2-domain of the protein tyrosine phosphatase SHP-1
Journal of Peptide Science, 16, 8, 2010, 403-413

K. Teichmann, T. Niksch, K. Wieligmann, M. Zacharias, D. Imhof
Synthetic Strategies to a Backbone-Side Chain Cyclic SHP-1 N-SH2 Ligand Containing N-Functionalized Alkyl Phosphotyrosine
Protein \& Peptide Letters, 17, 2010, 809-816

P. Setny, M. Zacharias
Hydration in Discrete Water. A Mean Field, Cellular Automata Based Approach to Calculating Hydration Free Energies
The Journal of Physical Chemistry B, 114, 2010, 8667-8675

R. Yaneva, C. Schneeweiss, M. Zacharias, S. Springer
Peptide binding to MHC class I and II proteins: New avenues from new methodsolecular Immunology
Elsevier, 47, 2010, 649-657

K. Keichmann, T. Kühl, I. Könnig, K. Wieligmann, M. Zacharias, D. Imhof
Modulation of SHP-1 phosphatase activity by monovalent and bivalent SH2 phosphopeptide ligands
Biopolymers, 93, 2010, 102-112

S. Fiorucci, M. Zacharias
Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT
Proteins: Structure, Function, and Bioinformatics, 78, 2010, 3131—3139

B. Mueller, M. Zacharias, K. Rezwan, Kurosch
Bovine Serum Albumin and Lysozyme Adsorption on Calcium Phosphate Particles
Advanced Engineering Materials, 12, 2010, B53-B61

M. Zacharias
Accounting for conformational changes during protein-protein docking
Current Opinion in Structural Biology, 20, 2010, 180-186

C. Beier, M. Zacharias
Tackling the challenges posed by target flexibility in drug design
Expert Opinion on Drug Discovery, 5, 2010, 347-359


A. Saladin, S. Fiorucci, P. Poulain, C. Prevost, M: Zacharias
PTools: an opensource molecular docking library
BMC Structural Biology, 9, 2009, 27

J. Curuksu, J. Sponer, M. Zacharias
Elbow Flexibility of the kt38 RNA Kink-Turn Motif Investigated by Free-Energy Molecular Dynamics Simulations
Biophysical Journal, 97, 2009, 2004-2013

S. Kannan, M. Zacharias
Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica-Exchange Molecular Dynamics Simulations
International Journal of Molecular Sciences, 10, 2009, 1121-1137

S. Liang, D. Zheng, C. Zhang, M: Zacharias
Prediction of antigenic epitopes on protein surfaces by consensus scoring
BMC Bioinformatics, 10, 2009, 302

S. Kannan, M. Zacharias
Simulation of {DNA} double-strand dissociation and formation during replica-exchange molecular dynamics simulations
Physical Chemistry Chemical Physics, 11, 2009, 10589

F. Sieker, A. May, M. Zacharias
Predicting Affinity and Specificity of Antigenic Peptide Binding to Major Histocompatibility Class I Molecules
Current Protein \& Peptide Science, 10, 2009, 286-296

S. Kannan, M. Zacharias
Simulated annealing coupled replica exchange molecular dynamics: An efficient conformational sampling method
Journal of Structural Biology, 166, 2009, 288-294

J Curuksu, M. Zacharias, R. Lavery, K. Zakrzewska
Local and global effects of strong {DNA} bending induced during molecular dynamics simulations
Nucleic Acids Research, 37, 2009, 3766-3773

R. Yaneva, S. Springer, M. Zacharias
Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study
Biopolymers, 91, 2009, 14-27

S. Frickenhaus, S. Kannan, M. Zacharias
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping
Journal of Computational Chemistry, 30, 2009, 479-492

R. P. Bahadur, S. Kannan, M. Zacharias
Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations
Biophysical Journal, 97, 2009, 3139-3149

J. Curuksu, M: Zacharias
Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach
The Journal of Chemical Physics, 130, 2009, 104110

S. Kannan, M. Zacharias
Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations
Proteins: Structure, Function, and Bioinformatics, 76, 2009, 448-460


M. Zacharias
Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
Journal of Chemical Theory and Computation, 4, 2008, 477-487

A. Hölzle, S. Fischer, R. Heyer, S. Schutz, M. Zacharias, P. Walther, T. Allers, A. Marchfelder
Maturation of the 5S rRNA 5' end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii
RNA, 14, 2008, 928-937

M. Niemann, M. Brecht, E. Schluter, K. Weitzel, M. Zacharias, H. U. Goringer, H. U.
TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanism
Nucleic Acids Research, 36, 2008, 4465-4473

A. May, M. Zacharias
Protein-Ligand Docking Accounting for Receptor Side Chain and Global Flexibility in Normal Modes: Evaluation on Kinase Inhibitor Cross Docking
Journal of Medicinal Chemistry, 51, 2008, 3499-3506

A. May, F. Sieker, M. Zacharias
How to Efficiently Include Receptor Flexibility During Computational Docking
Current Computer Aided-Drug Design, 4, 2008, 143-153

A. May, M. Zacharias
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
Proteins: Structure, Function, and Bioinformatics, 70, 2008, 794-809

J. Curuksu, K. Zakrzewska, M. Zacharias
Magnitude and direction of {DNA} bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites
Nucleic Acids Research, 36, 2008, 2268-2283

R. P. Bahadur, M. Zacharias, J. Janin
Dissecting protein-RNA recognition sites
Nucleic Acids Research, 36, 2008, 2705-2716

F. Sieker, T. P. Straatsma, S. Springer, M. Zacharias
Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study
Molecular Immunology, 45, 2008, 3714-3722

R. P. Bahadur, M. Zacharias
The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
Cellular and Molecular Life Sciences, 65, 2008, 1059-1072


S. Kannan, M. Zacharias
Folding of a {DNA} Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations
Biophysical Journal, 93, 2007, 3218-3228

D. Roccatano, H. Sahoo, M. Zacharias, W. M. Nau
Temperature Dependence of Looping Rates in a Short Peptide
The Journal of Physical Chemistry B, 111, 2007, 2639-2646

S. Kannan, M. Zacharias
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
Proteins: Structure, Function, and Bioinformatics, 66, 2007, 697-706

A. May, M. Zacharias
Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
Proteins: Structure, Function, and Bioinformatics, 69, 2007, 774-780

D. Roccatano, A. Barthel, M. Zacharias
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
Biopolymers, 85, 2007, 407-421


S. Kannan, K. Kohlhoff, M. Zacharias
B-{DNA} Under Stress: Over- and Untwisting of {DNA} during Molecular Dynamics Simulations
Biophysical Journal, 91, 2006, 2956-2965

F. Razga, M. Zacharias, K. Reblova, J. Koca, J. Sponer
RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics
Structure, 14, 2006, 825-835

K. Bastard, C. Prevost, M. Zacharias
Accounting for loop flexibility during protein-protein docking
Proteins: Structure, Function, and Bioinformatics, 62, 2006, 956-969

H. Sahoo, D. Roccatano, M. Zacharias, W. M. Nau
Distance Distributions of Short Polypeptides Recovered by Fluorescence Resonance Energy Transfer in the 10 Å Domain
Journal of the American Chemical Society, 128, 2006, 8118-8119

T. S. Wong, D. Roccatano, M. Zacharias, U. Schwaneberg
A Statistical Analysis of Random Mutagenesis Methods Used for Directed Protein Evolution
Journal of Molecular Biology, 355, 2006, 858-871

H. U. Göringer, M. Homann, M. Zacharias, A. Adler
RNA Aptamers as Potential Pharmaceuticals Against Infections with African Trypanosomes
Springer-Verlag, 2006, 375-393

F. Sieker, S. Springer, M. Zacharias
Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles
Protein Science, 16, 2006, 299-308

D. Roccatano, T. S. Wong, U. Schwaneberg, M. Zacharias
Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: A molecular dynamics simulation study
Biopolymers, 83, 2006, 467-476

T. Heck, M. Limbach, B. Geueke, M. Zacharias, J. Gardiner, H.-P. Kohler, D. Seebach
Enzymatic Degradation of beta- and Mixed alpha, beta-Oligopeptides
Chemistry & Biodiversity, 3, 2006, 1325-1348

Zacharias, Martin
Minor Groove Deformability of {DNA}: A Molecular Dynamics Free Energy Simulation Study
Biophysical Journal, 91, 2006, 882-891

U.H. Goringer, M. Zacharias, M. Engstler, M. Homann, M. Lorger
Serum-Stable RNA Aptamers to an Invariant Surface Domain of Live African Trypanosomes
Combinatorial Chemistry & High Throughput Screening, 9, 2006, 491-499

K. Hampel, I. Kaufhold, M. Zacharias, F. D. Böhmer, D. Imhof
Phosphopeptide Ligands of the SHP-1 N-SH2 Domain: Effects on Binding and Stimulation of Phosphatase Activity
ChemMedChem, 1, 2006, 869-877

A. Barthel, M. Zacharias
Conformational Transitions in RNA Single Uridine and Adenosine Bulge Structures: A Molecular Dynamics Free Energy Simulation Study
Biophysical Journal, 90, 2006, 2450-2462


M. Zacharias
Vorhersage von Protein-Protein Wechselwirkungen durch Docking-Simulationen
Bioforum, 2, 2005, 38-39

A. Szymoszek, M. Zacharias
Structure Prediction of Segments with Low Target–Template Similarity in Comparative Protein Modeling Using a Reduced Protein Model
Internet Electron. J. Mol. 4, 2005, 659–670

D. Roccatano, M. Fioroni, M. Zacharias, G. Colombo
Effect of hexafluoroisopropanol alcohol on the structure of melittin: A molecular dynamics simulation study
Protein Science, 14, 2005, 2582-2589

D. Imhof, K. Wieligmann, K. Hampel, D. Nothmann, M. S. Zoda, D. Schmidt-Arras, M. Zacharias, F. D. Böhmer, S. Reissmann
Design and Biological Evaluation of Linear and Cyclic Phosphopeptide Ligands of the N-Terminal SH2 Domain of Protein Tyrosine Phosphatase SHP-1
Journal of Medicinal Chemistry, 48, 2005, 1528-1539

Y. Ihle, O. Ohlenschläger, S. Häfner, E. Duchardt, M. Zacharias, S. Seitz, R. Zell, R. Ramachandran, M. Görlach
A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA
Nucleic Acids Research, 33, 2005, 2003-2011

A. May, M. Zacharias
Accounting for global protein deformability during protein-protein and protein-ligand docking
Biochimica et Biophysica Acta (BBA), Proteins and Proteomics, 1754, 2005, 225-231

M. Zacharias
ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
Proteins: Structure, Function, and Bioinformatics, 60, 2005, 252-256

D. Roccatano, T. S. Wong, U. Schwaneberg, M. Zacharias
Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture
Biopolymers, 78, 2005, 259-267

R. N. Riemann, M. Zacharias
Refinement of protein cores and protein-peptide interfaces using a potential scaling approach
Protein Engineering Design and Selection, 18, 2005, 465-476

B. Stix, M. Leber, P. Bingemer, C. Gross, J. Rüschoff, M. Fändrich, D. F. Schorderet, C. K. Vorwerk, M. Zacharias, A. Roessner, C. Röcken
Hereditary Lattice Corneal Dystrophy Is Associated with Corneal Amyloid Deposits Enclosing C-Terminal Fragments of Keratoepithelin
Investigative Ophthalmology & Visual Science, 46, 2005, 1133-1139


M. Zacharias, J. W. Engels
Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulations
Nucleic Acids Research, 32, 2004, 6304-6311

T. P. Monie, J. S. Greatorex, M. Zacharias, A. Lever
The Human T-Cell Lymphotropic Virus Type-I Dimerization Initiation Site Forms a Hairpin Loop, Unlike Previously Characterized Retroviral Dimerization Motifs
Biochemistry, 2004, 43, 6085-6090

G. Gessner, M. Zacharias, S. Bechstedt, R. Schönherr, Heinemann, S.H.
Molecular Determinants for High-Affinity Block of Human EAG Potassium Channels by Antiarrhythmic Agents
Molecular Pharmacology, 2004, 1120-1129

M. Zacharias
Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP
Proteins: Structure, Function, and Bioinformatics, 542004, 759-767

C. A. Wright, P. Kozik, M. Zacharias, S. Springer
Tapasin and other chaperones: models of the MHC class I loading complex
Biological Chemistry, 2004, 385

C. Frank, C. Burkhardt, D. Imhof, J. Ringel, O. Zschörnig, K. Wieligmann, M. Zacharias, F. D. Böhmer
Effective Dephosphorylation of Src Substrates by SHP-1
Journal of Biological Chemistry, 279, 2004, 11375-11383

G. Villescas-Diaz, M. Zacharias
Efficient Search on Energy Minima for Structure Prediction of Nucleic Acid Motifs
Journal of Biomolecular Structure and Dynamics, 22, 2004, 355-364

D. Roccatano, W. M. Nau, M. Zacharias
Structural and Dynamic Properties of the CAGQW Peptide in Water: A Molecular Dynamics Simulation Study Using Different Force Fields
The Journal of Physical Chemistry B, 108, 2004, 18734-18742

R. N. Riemann, M. Zacharias
Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides
Journal of Peptide Research, 63, 2004, 354-364


M. Zacharias
Perspectives of Drug Design that Targets RNA
Current Medicinal Chemistry-Anti-Infective Agents, 2, 2003, 161-172

M. Zacharias
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
Protein Science, 12, 2003, 1271-1282

G. Villescas-Diaz, M: Zacharias
Sequence Context Dependence of Tandem Guanine:Adenine Mismatch Conformations in RNA: A Continuum Solvent Analysis
Biophysical Journal, 85, 2003, 416-425

M. Zacharias
Continuum Solvent Modeling of Nonpolar Solvation: Improvement by Separating Surface Area Dependent Cavity and Dispersion Contributions
The Journal of Physical Chemistry A, 107, 2003, 3000-3004


K. Wieligmann, L. F. P. De Castro, M. Zacharias
Molecular Dynamics Simulations on the Free and Complexed N-Terminal SH2 Domain of SHP-2
In Silico Biology, 2, 2002, 305-311

L. F. P. De Castro, M. Zacharias
DAPI binding to the {DNA} minor groove: a continuum solvent analysis
Journal of Molecular Recognition, 15, 2002, 209-220


M. Zacharias, H. Sklenar
Conformational Deformability of RNA: A Harmonic Mode Analysis
Biophysical Journal, 78, 2000, 2528-2542

M. Zacharias
Simulation of the structure and dynamics of nonhelical RNA motifs
Current Opinion in Structural Biology, 10, 2000, 311-317

M. Zacharias
Comparison of molecular dynamics and harmonic mode calculations on RNA
Biopolymers, 54, 2000, 547-560


M. Zacharias, P. J. Hagerman
The Influence of Symmetric Internal Loops on the Flexibility of RNA
Journal of Molecular Biology, 257, 1996, 276-289


M. Zacharias, P. J. Hagerman
Bulge-Induced Bends in RNA: Quantification by Transient Electric Birefringence
Journal of Molecular Biology, 247, 1995, 486-500

M: Zacharias, T. P. Straatsma
Path Dependence of Free Energy Components in Thermodynamic Integration
Molecular Simulation, 14, 1995, 417-423


M: Zacharias, T. P. Straatsma, J. A. McCammon
Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration
The Journal of Chemical Physics, 1994, 100, 9025

M. Zacharias, B. A. Luty, M. E. Davis, J. A. McCammon
Combined Conformational Search and Finite-Difference Poisson-Boltzmann Approach for Flexible Docking
Journal of Molecular Biology, 238, 1994, 455-465


R. Wagner, G. Theißen, M: Zacharias
Regulation of Ribosomal RNA Synthesis and Control of Ribosome Formation in E. Coli
1993, 119-130

T. P. Straatsma, M: Zacharias, J. A. McCammon
Free energy difference calculations in biomolecular systems
Computer Simulation of Biomolecular Systems, 2, 1993, 349-367

M. Zacharias, T. P. Straatsma, J. A. McCammon, F. A. Quiocho
Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins
Biochemistry, 32, 1993, 7428-7434


T. P. Straatsma, M. Zacharias, J. A. McCammon
Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations
Chemical Physics Letters, 196, 1992, 297-302


M. Zacharias, G. Theissen, C. Bradaczek, R. Wagner
Analysis of sequence elements important for the synthesis and control of ribosomal RNA in E coli
Biochimie, 73, 1991, 699-712


M. Zacharias, R. Wagner, H. U. Göringer
Polyacrylamide gradient gel electrophoresis for the detection of bended {DNA} fragments
Nucleic Acids Research, 18, 1990, 2827-2827

M. Zacharias, H. U. Goeringer, R. Wagner
The signal for growth rate control and stringent sensitivity in E. coli is not restricted to a particular sequence motif within the promoter region
Nucleic Acids Research, 18, 1990, 6271-6275

G. Theißen, J. Eberie, M. Zacharias, L. Tobias, R. Wagner
The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions
Nucleic Acids Research, 18, 1990, 3893-3901