124.) Leis S., Zacharias M. (2011) Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. J Comput Chem. 32(16), 3433-3439
123.) Setny P., Zacharias M. (2011) A coarse-grained force field for Protein-RNA docking .Nucleic Acids Res. [Epub ahead of print]
122.) Garstka M.A., Fritzsche S., Lenart I., Hein Z., Jankevicius G., Boyle LH., Elliott T., Trowsdale J., Antoniou A.N., Zacharias M.,Springer S. (2011) Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility. FASEB J.[Epub ahead of print]
121.) Kannan S. , Zacharias M. (2011) Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations.Nucleic Acids Res. [Epub ahead of print]
120.) Vargiu AV., Collu F., Schulz R., Pos KM., Zacharias M., Kleinekathoefer U, Ruggerone P. (2011) Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations.J Am Chem Soc.133(28):
10704-10707.
119.) Droescher M., Begitt A., Marg A., Zacharias M., Vinkemeier U. (2011) 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).J Biol Chem.286(21):
18731-46.
118.) Koch N., Zacharias M., König A., Temme S., Neumann J., Springer S. (2011) Stoichiometry of HLA class II-invariant chain oligomers.PLoS One6(2):
e17257.
117.) Fiorucci S., Zacharias M. (2010) Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.Proteins78(15):
3131-9.
116.) Liang S., Zheng D., Standley DM., Yao B., Zacharias M., Zhang C. (2010) EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results.BMC Bioinformatics11:
381.
115.) Kannan S., Zacharias M. (2010) Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent. Proteins 78(13):
2809-19.
114.) Beier C., Zacharias M. (2010) Tackling the challenges posed by target flexibility in drug design. Expert Opinion on Drug Discovery, 5(4):
347-359.
113.) Soriani M., Petit P., Grifantini R., Petracca R., Gancitano G., Frigimelica E., Nardelli F., Garcia C., Spinelli S., Scarabelli G., Fiorucci S., Affentranger R., Ferrer-Navarro M., Zacharias M., Colombo G., Vuillard L., Daura X., Grandi G. (2010) 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. J Biol Chem.285(39):
30126-38.
112.) Zoda MS., Zacharias M., Reissmann S. (2010) 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. J Pept Sci. 16(8):
403-13.
111.) Setny P., Zacharias M. (2010) Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies. J Phys Chem B.114(26):
8667-75.
109.) Zacharias,
M. (2010) Accounting for conformational changes during protein-protein docking. Curr. Opin. Struct. Biol.20:180-186.
108.) Leis, S.,
Schneider, S. and M. Zacharias
(2010) In silico prediction of binding sites on proteins. Curr. Med. Chem.17, 1550-1562. ->pdf
107.)
El-Barghouti, M. I., Saleh, A. I. , Ghandour, A., Ghanem, R. and M. Zacharias (2010) Examining the
potency of suggested inhibitors for the phosphatase activity of the
human soluble epoxide hydrolase by molecular dynamics simulations. J. Mol. Struct.: Theochem. 944, 97-104.
106.)S. Fiorucci and M.
Zacharias (2010)
Prediction of
protein-protein interaction sites using electrostatic desolvation
profiles Biophys. J.98, 1921-1930.
105.) W. Lee, L.
Vojcic, D.
Despotovic, R. Prodanovic, K.-He. Maurer, U. Schwaneberg and M. Zacharias (2010) Rationalizing perhydrolase
activity of aryl-esterase and subtilisin
carlsberg mutants by molecular dynamics simulations of the second
tetrahedral
intermediate state.Theoretical Chem. Acc. 125, 375-386.
104.)R. Yaneva, C. Schneeweiss, M. Zacharias and S. Springer
(2010) Peptide binding to MHC class I and II proteins: new avenues from
new
methods. Mol. Immunol. 47, 449-455.
103.)B. Müller, M.
Zacharias and
K. Rezwan (2009) Bovine
serum albumin and lysozyme adsorption on calcium phosphate particles. Adv. Eng.
Mat. 12, B53-B61
102.)R. Bahadur, S. Kannan and M. Zacharias (2009) Binding of the
bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular
dynamics
simulations. Biophys. J.97, 3139-3149..
101.)S. Kannan and M.Zacharias (2009) Simulation of DNA double-strand
dissociation and formation during
replica-exchange molecular dynamics simulations.Phys. Chem.
Chem. Phys.
11, 10589-10595.
100.)Curuksu J, Sponer J, Zacharias
M.
(2009) Elbow flexibility of the kt38 RNA kink-turn motif investigated
by
free-energy molecular dynamics simulations. Biophys J.97, 2004-2013.
99.) Liang S, Zheng D, Zhang C, Zacharias
M.
(2009) Prediction of antigenic epitopes on protein surfaces by
consensus
scoring. BMC Bioinformatics 10, 302.
98.) Teichmann K, Kühl T, Könnig I,
Wieligmann K, Zacharias
M,
Imhof D. (2009) Modulation of SHP-1 phosphatase activity by mono- and
bivalent
SH2 phosphopeptide ligands. BiopolymersSep 18. [Epub
ahead of print]
97.) Curuksu J, Zacharias M, Lavery R,
Zakrzewska K. (2009) Local and global effects of strong DNA bending
induced
during molecular dynamics simulations. Nucleic Acids Res.37, 3766-3773.
96.) Teichmann K, Niksch T, Wieligmann K, Zacharias
M,
Imhof D. (2009) Synthetic Strategies to a Backbone-side Chain Cyclic
SHP-1 N-SH2
Ligand Containing N-Functionalized Alkyl Phosphotyrosine. Protein
Pept. Lett.2009
Sep
13.
[Epub ahead of
print]
95.) Saladin A, Fiorucci S, Poulain P,
Prévost C, Zacharias
M. (2009)
PTools: an opensource molecular docking library. BMC
Struct. Biol.
9:27-38.
94.) Kannan S, Zacharias M. (2009) Folding
of Trp-cage Mini Protein Using Temperature and Biasing Potential
Replica-Exchange Molecular Dynamics Simulations. Int. J. Mol. Sci.10, 1121-1137.
93.) S. Kannan and M.Zacharias (2009) Simulated
Annealing coupled Replica Exchange Molecular Dynamics - an Efficient
Conformational Sampling Method. J.Struct.
Biol.166,
288-294.
92.) J. Curuksu and M.Zacharias (2009) Enhanced
conformational sampling of nucleic acids by a new Hamiltonian replica
exchange molecular
dynamics approach. J. Chem. Phys. 130, 104110.
91.) S. Kannan and
M.Zacharias (2009) Folding simulations
of Trp-cage mini protein in explicit solvent using biasing potential
replica-exchange molecular dynamics simulations. Proteins76, 448-460.
90.) R. Yaneva, S. Springer, and M.
Zacharias (2009)
Flexibility of the MHC class II peptide binding cleft in the
bound, partially filled and empty states: A molecular dynamics
simulation
study. Biopolymers 91, 14-27.
89.)S. Frickenhaus, S. Kannan and M.
Zacharias (2009)
Efficient evaluation of sampling quality of molecular dynamics
simulations by clustering of dihedral torsion angles and Sammon
mapping. J.
Comput. Chem.30,
479-492.
88.)F. Sieker, A. May and M. Zacharias (2008) Predicting affinity and
specificity of antigenic peptide binding
to major histocompatibility class I molecules. Curr.
Pept. Sci.10,
286-296.
87.)M.
Niemann, M. Brecht, E. Schlüter,
K. Weitzel, M.
Zacharias and H. Göringer (2008) TbMP42 is a
structure-sensitive
ribonuclease that likely follows a metal-ion catalysis mechanism. Nucleic
Acids
Res. 36,
4465-4473.
86.)R. P.
Bahadur, M. Zacharias, and J. Janin (2008) Dissecting
Protein-RNA
recognition sites. Nucleic Acids Res 36, 2705-2716.
85.)A. May and M. Zacharias
(2008)
Protein ligand docking accounting for receptor side chain and global
flexibility in normal modes: Evaluation on kinase inhibitor cross
docking. J.
Med. Chem. 51, 3499-3506
84.)F.
Sieker,
T.
P.
Straatsma, S. Springer, M. Zacharias (2008) Differential
tapasin
dependence of MHC class I molecules correlates with conformational
changes upon
peptide dissociation: A molecular dynamics simulation study. Mol.
Immunol. 45, 3714-3722.
83.)M.
Zacharias (2008) Combining elastic network analysis and molecular
dynamics
simulations by Hamiltonian replica exchange. J. Chem Theory
Comput.
4, 477-487.
82.)A. Hölzle,
S. Fischer, R. Heyer, S. Schütz, M. Zacharias, P. Walther,
T. Allers,
and A. Marchfelder (2008) Maturation of the 5S rRNA 5' end is catalyzed
in
vitro by the endonuclease tRNase Z in the archaeon H. volcanii. RNA,
14,
928-937.
81.)A. May and M. Zacharias (2008)
Energy minimization in
low-frequency normal modes to
efficiently allow for global flexibility during systematic
protein-protein
docking. Proteins, 70, 794-809.
80.)R. P.
Bahadur and M. Zacharias (2008) The Interface of
Protein-Protein
Complexes: Analysis of Contacts and Prediction of Interactions. Cellul.
Mol.
Life
Sci., 65, 1059-1072.
79.)A. May and M. Zacharias (2008)
Protein-protein docking in CAPRI
using ATTRACT to account for global and local flexibility. Proteins,
69,
774-780.
78.)
J.
Curuksu, K. Zakrzewska and M. Zacharias (2008) A new approach
to study
magnitude and direction of DNA bending: Influence of sequence,
mismatches and
abasic sites. Nucleic Acids Res., 36,
2268-2283.
77.)
A. May, F.
Sieker and M. Zacharias (2008) How
to efficiently include receptor flexibility during computational
docking. Curr.
Comput. Aided Drug Des., 4, 143-153.
76.)S. Kannan, and M.
Zacharias (2007) Folding of a DNA hairpin loop
structure in explicit solvent using replica-exchange molecular dynamics
simulations. Biophys. J.,93,
3218-3228.
75.)D.
Roccatano, A. Barthel and M. Zacharias (2007)
Structural flexibility of the nucleosome core particle at atomic
resolution
studied by molecular dynamics simulation. Biopolymers,
85, 407-421.
74.)D.
Roccatano, S. Sahoo, M.
Zacharias and Werner Nau(2007)
Temperature Dependence of Looping Rates in a Short Peptide. J.
Phys. Chem B, 111, 2639-2646.
73.)F. Sieker,
S. Springer, and M. Zacharias (2007)
Comparative molecular dynamics analysis of tapasin-depnendent and
independent
MHC class I alleles. Protein Science,
16, 299-308.
72.)T. Heck,
M. Limbach, B. Geueke, M. Zacharias,
J. Gardiner, H.P. Kohler, and D. Seebach (2006) Enzymatic degradation
of beta-
and mixed alpha,beta-oligopeptides.Chem Biodivers. 3,
1325-1348.
71.)S. Kannan,
and M. Zacharias (2007) Enhanced
sampling of peptide and protein conformations using replica exchange
simulations with a peptide backbone biasing-potential. Proteins. 66, 697-706.
70.)M. Homann, M. Lorger, M.
Engstler, M. Zacharias, H.U. Göringer (2006)
Serum-stable RNA aptamers to an invariant surface domain of live
African
trypanosomes. Comb Chem High Throughput Screen.
9,
491-499.
69.)D.
Roccatano, T.S. Wong, U. Schwaneberg, M. Zacharias (2006) Toward
understanding
the inactivation mechanism of monooxygenase P450 BM-3 by organic
cosolvents: A
molecular dynamics simulation study. Biopolymers.
83,
467-476.
68.)
H. Sahoo,
D. Roccatano, M. Zacharias, and W.
M. Nau (2006) Distance Distributions of Short Polypeptides Recovered by
Fluorescence Resonance Energy Transfer in the 10 Å Domain. J. Am. Chem. Soc. 128,
8118-8119.
67.)
S. Kannan,
K. Kohlhoff, and M. Zacharias (2006)
B-DNA Under Stress: Over and Un-Twisting of DNA during Molecular
Dynamics
Simulations. Biophys. J. 91, 2956-2965.
66.)
K. Hampel, I. Kaufhold, M.
Zacharias, F. D. Böhmer, and
D. Imhof (2006) Phosphotyrosyl Peptide Ligands of the SHP-1 N-SH2
Domain:
Effects on Binding and Stimulation of Phosphatase Activity. Chem.
Med. Chem. 1, 869-877.
65.)
D. Imhof,
A. S. Wavreille, A. May, M. Zacharias,
S. Tridandapani, and D. Pei (2006) Sequence specificity of SHP-1 and
SHP-2 SH2
domains: Critical roles of residues beyond the pY+3 position. J.
Biol. Chem., 28, 20271-82.
64.)M. Zacharias (2006) Minor
groove
deformability of DNA: A Molecular dynamics free energy simulation study. Biophys
J. 91, 882-91.
63.)
F. Razga,
M. Zacharias, K. Reblova, J. Koca, and J. Sponer (2006) RNA kink-turns
as
molecular elbows: hydration, cation binding, and large-scale dynamics. Structure
14, 825-835.
62.)
S. Wong,
D. Roccatano, M. Zacharias, and U.
Schwaneberg (2006) A Statistical Analysis of Random Mutagenesis Methods
Used
for Directed Protein Evolution. J. Mol. Biol.355, 858-871.
61.) A. Barthel, and M. Zacharias
(2006) Conformational Transitions in RNA Single Uridine and Adenosine
Bulge
Structures: A Molecular Dynamics Free Energy Simulation Study. Biophys.
J. 90, 2450-2462.
60.) K. Bastard, Prevost, C., and M.
Zacharias (2006) Accounting for loop flexibility during
protein-protein
docking. Proteins, 62, 956-969.
59.) H. U. Göringer, M. Homann, M.
Zacharias,
andA. Adler (2005)
RNA aptamers as potential pharmaceuticals against infections with
African
trypanosomes.H. of Experimental Pharmacology,
173,
375-393.
58.) A. May, and M. Zacharias
(2005) Accounting for global protein deformability during
protein-protein and
protein-ligand docking. Biochem. Biophys. Acta,
1754,
225-231.
57.)A.
Szymoszek, and M. Zacharias (2005)
Structure prediction of segments with low target-template similarity in
comparative protein modelling using a reduced protein model. IE J.
of Mol. Design 4, 659-670.
56.)
N. Riemann and M. Zacharias
(2005) Refinement of protein cores and protein-peptide interfaces using
a
potential scaling approach. Prot. Engineering,
18,
465-476.
55.)
D.
Roccatano, M. Fioroni, M. Zacharias,
and G. Colombo (2005) Effect of hexafluoroisopropanol alcohol on the
structure
of Melittin: a molecular dynamics simulation study. Prot. Sci. 14, 2582-2589.
54.)
M. Zacharias
(2005)
ATTRACT: Protein-Protein Docking in CAPRI
Using a Reduced Protein Model. Proteins
60, 252-256.
53.)
D. Roccatano, T.S.
Wong, U. Schwaneberg, and M. Zacharias (2005)
Structural and dynamic properties of cythocrome
P450 BM3 in pure water and in DMSO/water mixture. Biopolymers, 78, 259-267.
52.) M.
Zacharias (2005) Vorhersage von Protein-Protein Wechselwirkungen
durch
Docking-Simulationen. Bioforum 2/2005,
38-39.
51.) Y. Ihle, O.
Ohlenschlager, S. Hafner, E.
Duchardt, M. Zacharias, S. Seitz, R.
Zell, R. Ramachandran, and M. Gorlach (2005) A novel cGUUAg tetraloop
structure
with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of
bovine
enterovirus 1 RNA. Nucleic Acids Res.
33, 2003-2011.
50.) D. Imhof, Wieligmann K,
Hampel K,
Nothmann D, Zoda MS, Schmidt-Arras D, Zacharias
M, Bohmer FD, Reissmann S. (2005) Design and biological evaluation
of
linear and cyclic phosphopeptide ligands of the N-terminal SH2 domain
of
protein tyrosine phosphatase SHP-1. J. Med.
Chem. 48, 1528-1539.
49.) Stix B, Leber M,
Bingemer P, Gross C,
Ruschoff J, Fandrich M, Schorderet DF, Vorwerk CK, Zacharias
M, Roessner A, Rocken C. (2005) Hereditary lattice
corneal dystrophy is associated with corneal amyloid deposits enclosing
C-terminal fragments of keratoepithelin. Invest
Ophthalmol
Vis
Sci. 46,
1133-1139.
48.) Wong, T. S., N. Wu, D.
Roccatano, M.
Zacharias, U. Schwaneberg (2005) Sensitive assay for laboratory
evolution
of hydroxylases toward aromatic and heterocyclic compounds. J. Biomol. Screen.
10, 246-252.
47.) M. Zacharias, and J. W.
Engels (2004) Influence of a fluorobenzene nucleobase analogue on the
conformational flexibility of RNA studied by molecular dynamics
simulations. Nucleic
Acids Res. 32, 6304-6311.
46.) D. Roccatano, W. Nau, and M.
Zacharias (2004) Structural and dynamical properties of CAGQW
peptide in
water: A molecular dynamics simulation study using different force
fields. J.
Phys. Chem. B 108,
18734-18742.
45.) T. P. Monie, J. S. Greatorex, M.
Zacharias, and A. M. L. Lever. (2004) The human T-cell lymphotopic
virus
type-1 dimerisation initiation site forms a hairpin loop unlike
previously
characterized retroviral dimerisation motifs. Biochemistry
43,
6085-6090.
44.) M. Zacharias, and S. Springer
(2004) Conformational flexibility of the MHC class I α1-α2 domain in
peptide
bound and free states:
A
molecular
dynamics
simulation study. Biophys. J.,
87,
2203-2214.
43.) C. A. Wright, P. Kozik, M.
Zacharias, and S. Springer (2004) Tapasin and other chaperones:
Models of
the MHC class I loading complex. Biol. Chem.385, 763-778.
42.) N. Riemann and M. Zacharias
(2004) Reversible scaling of dihedral angle barriers during molecular
dynamics
to improve structure prediction of cyclic peptides and protein loops”. J.
Peptide Res. 63, 354-364.
41.) M. Zacharias (2004) Rapid
Protein-ligand docking including soft degrees of freedom from molecular
dynamics simulations to account for protein flexibility: FK506 binding
to FKBP
binding protein as an example. Proteins
54, 759-767.
40.) G. Villescas and M.
Zacharias (2004) Efficient search approaches on energy minima for
structure
prediction of nucleic acid motifs. J. Biomol.
Struct. Dyn. 22, 355-364.
39.) C. Frank, C. Burkhardt, D. Imhof, J. Ringel,
O. Zschörnig, K.
Wieligmann, M. Zacharias, F.D.
Böhmer (2004) Effective dephosphorylation of Src substrates by
SHP-1. J.
Biol. Chem. 279, 11375-11383.
38.) G. Gessner, M. Zacharias, S. Bechstedt, , R.
Schönherr, S.H. Heinemann. (2004)
Molecular determinants for high-affinity block of human EAG potassium
channels
by antiarrythmic agents. Mol. Pharmacology,
65,
1120-1129.
37.) M. Zacharias (2003) Perspectives of Drug
design that targets RNA. Curr.
Med. Chem.-Anti-Infective Agents2,
161-172.
36.) G. Villescas, and M.
Zacharias (2003) Sequence context dependence of tandem guanine:
adenine
mismatch conformations in RNA: A continuum solvent analysis. Biophys.
J. 85, 1311-1321.
35.) M. Zacharias (2003)
Continuum solvent modelling of non-polar solvation: Improvement by
separating
surface area dependent cavity and dispersion contributions.
J. Phys. Chem. A,
107,
3000-3004.
34.) M. Zacharias (2003)
Protein-protein docking with a reduced protein model accounting for
side-chain
flexibility. Protein Sci. 12,
1271-1282.
33.) K. Wieligmann, F. Pineda, and M.
Zacharias (2002) Conformational preferences of SH2 domains in
ligand-bound
and free states studied by molecular dynamics simulations.In Silico Biol.
2, 305-311.
32.) F. Pineda, and M. Zacharias
(2002) DAPI binding to the DNA minor groove: A continuum solvent
analysis. J. Mol. Recog.15, 209-220.
31.) M. Zacharias (2001)
Conformational analysis of DNA-trinucleotide-hairpin-loop structures
using a
continuum solvent model. Biophys. J.
80, 2350-2363.
30.) M. Feig, M. Zacharias,
and M. E. Pettitt (2001) Conformation of an adenine bulge in a DNA
octamer and
its influence on DNA structure from molecular dynamics simulations. Biophys.
J. 81, 352-370.
29.) C. Burkhardt, and M.
Zacharias (2001) Modeling ion binding to AA-platform motifs in RNA:
A
continuum solvent study including conformational adaptation.
Nucleic Acids Res. 29,
3910-3918.
28.) M. Zacharias, and H.
Sklenar (2000) Conformational deformability of RNA: A harmonic mode
analysis. Biophys.
J. 78, 2528-2542.
27.) M. Zacharias (2000)
Simulation of the structure and dynamics of non-helical RNA motifs. Curr.
Opin. Struct. Biol. 10, 311-317.
26.) M. Zacharias (2000) Comparison of
molecular dynamics and harmonic mode calculations on RNA. Biopolymers, 54, 547-560.
25.)M. Zacharias, and H.
Sklenar (1999) Harmonic modes as variables to approximately account for
receptor flexibility in ligand-receptor docking simulations:
Application to a
DNA minor groove ligand complex. J. Comput.
Chem. 20, 287-300.
24.)M. Zacharias, and H.
Sklenar (1999) Conformational analysis of single base bulges in A-form
DNA and
RNA using a hierarchical approach and energetic evaluation with a
continuum
solventmodel. J.
Mol. Biol. 289,
261-27.
23.)M. Zacharias, and P. J.
Hagerman (1997) Influence of static and dynamic bends on the
birefringence
decay profile of RNA helices: Brownian dynamics simulations. Biophys.
J. 73, 318-327.
22.)M. Zacharias, and H.
Sklenar (1997) Analysis of the stability of looped out and stacked in
conformations of an adenine bulge in DNA using a continuum model for
solvent
and ions. Biophys. J. 73, 2990-3003.
21.) M. Zacharias, and P. J.
Hagerman (1996) The influence of symmetric internal loops on the
flexibility of
RNA.
J. Mol. Biol. 257, 276-289.
20.) B.
L.
Luty,
Z. R. Wasserman, P. F. W. Stouten, C. N. Hodge, M.
Zacharias, and J. A. McCammon (1995)
A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor
Interactions. J. Comp. Chem. 16,
454-464.
19.)M. Zacharias, and P. J. Hagerman (1995)
The bend in RNA created by the trans- activation response element bulge
of
human immunodeficiency virus is straightened by arginine and by
Tat-derived
peptide. Proc. Natl. Acad. Sci. USA
92, 6052-6056.
18.)M. Zacharias, and T. P.
Straatsma (1995) Path Dependence of Free Energy Components in
Thermodynamic
Integration. Molecular Simulations 14,
417-423.
17.)M. Zacharias, and P. J.
Hagerman (1995) Bulge-Induced Bends in RNA: Quantification by Transient
Electric Birefringence. J. Mol. Biol.
247, 486-500.
16.)M. Zacharias, B. A. Luty,
M. E. Davis, and J. A. McCammon (1994) Combined Conformational Search
and
Finite-Difference Poisson-Boltzmann Approach for Flexible Docking:
Application
to an Operator Mutation in the lambda Repressor-Operator Complex. J.
Mol. Biol., 238, 455-465.
15.)M. Zacharias, T. P.
Straatsma, and J. A. McCammon (1994) Separation-shifted scaling, a new
scaling
method for Lennard-Jones interactions in thermodynamic integration. J.
Chem. Phys.100, 9025-9031.
14.) T.
P.
Straatsma,
M.
Zacharias, and J. A. McCammon (1993) Free energy difference
calculations in
biomolecular systems. pp 349-367, in: Computer
Simulation of Biomolecular Systems,
Vol. 2 (ed. van Gunsteren, W.F., Weiner, P.K., and Wilkinson, A.J.),
Escom
Science Publishers, Leiden.
13.)M.
Zacharias, T. P. Straatsma, and J. A. McCammon (1993) Inversion of
Receptor
Binding Preferences by Mutagenesis: Free Energy Thermodynamic
Integration
Studies on Sugar Binding to L-Arabinose Binding Proteins. Biochemistry32, 7428-7434.
12.)M. Zacharias, H. U.
Göringer, and R. Wagner (1992) Analysis of the Fis-dependent
and
Fis-Independent
Transcription Activation Mechanisms of the Escherichia
coli Ribosomal RNA P1 Promoter. Biochemistry31,
2621-2628.
11.) T.
P.
Straatsma,
M.
Zacharias, and J. A. McCammon (1992) Holonomic Constraint
Contribution in
Thermodynamic Integration Free Energy Calculations. Chem. Phys. Lett. 196,
297-301.
10.)M. Zacharias, B. A. Luty,
M. E. Davis, and J. A. McCammon (1992) Poisson-Boltzmann analysis of
the
lambda-repressor-operator interaction. Biophys.
J. 63, 1280-1285.
9.) R. Wagner, G. Theißen, and M.
Zacharias (1992) in: Regulation of ribosomal RNA synthesis and
control of
ribosome formation in E. coli. USA,
Plenum Press Publishing Corp.
8.)M. Zacharias, G. Theißen,
C. Bradaczek, and R. Wagner (1991) Analysis of sequence elements
important for
the synthesis of ribosomal RNA in E.
coli. Biochimie73, 699-712.
7.)M. Zacharias, H. U.
Göringer, and R. Wagner (1990) Polyacrylamide gradient
electrophoresis for the
detection of bent DNA fragments. Nucleic Acids
Res. 18, 2827.
6.) G. Theißen, J. Eberle, M.
Zacharias, L. Tobias, and R.Wagner (1990) The tL-structure
within
the
leader
region of Escherichia
coli ribosomal RNA operons has post-transcriptional functions. Nucleic
Acids Res. 18, 3893-3901.
5.)M. Zacharias, H. U.
Göringer, and R. Wagner (1990) 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
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