Other publications of group members

2010 & 2009

2008 & 2007

Bauer RA, Bourne PE, Formella A, Frömmel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Pöschel T, Wittig B, Ziegler V, Preissner R. (2008)
Superimpose: a 3D structural superposition server. Nucleic Acids Res., 36(Web Server issue):W47-54. [PubMed]

Flajolet M, Wang Z, Futter M, Shen W, Nuangchamnong N, Bendor J, Wallach I, Nairn AC, Surmeier DJ, Greengard P. (2008) FGF acts as a co-transmitter through adenosine A(2A) receptor to regulate synaptic plasticity. Nat Neurosci., 11(12):1402-9. [PubMed]

Hildebrand PW, Günther S, Goede A, Forrest L, Frömmel C, Preissner R. (2008)
Hydrogen-bonding and packing features of membrane proteins: functional implications. Biophys J., 94(6):1945-53. [PubMed]

Günther S, May P, Hoppe A, Frömmel C, Preissner R. (2007)
Docking without docking: ISEARCH--prediction of interactions using known interfaces. Proteins., 69(4):839-44. [PubMed]

Schlicker A, Huthmacher C, Ramírez F, Lengauer T, Albrecht M. (2007)
Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics., 23(7):859-65. [PubMed]

2006

Binder B, Ebenhöh O, Hashimoto K, Heinrich R. (2006)
Expansion of signal transduction networks. Syst Biol (Stevenage), 153(5):364-8. [PubMed]

Booms P, Ney A, Barthel F, Moroy G, Counsell D, Gille C, Guo G, Pregla R, Mundlos S, Alix AJ, Robinson PN. (2006)
A fibrillin-1-fragment containing the elastin-binding-protein GxxPG consensus sequence upregulates matrix metalloproteinase-1: biochemical and computational analysis. J Mol Cell Cardiol., 40(2):234-46. [PubMed]

Gille C. (2006)
Structural interpretation of mutations and SNPs using STRAP-NT. Protein Science., 15, 208-210. [PubMed]

Gille C, Robinson PN. (2006)
HotSwap for bioinformatics: a STRAP tutorial. BMC Bioinformatics., 7:64. [PubMed, http://www.charite.de/bioinf/strap/]

Goede A, Michalsky E, Schmidt U, Preissner R. (2006)
SuperMimic--fitting peptide mimetics into protein structures. BMC Bioinformatics., 7:11. [PubMed]

Günther S, Senger C, Michalsky E, Goede A, Preissner R. (2006)
Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinformatics., 7:293. [PubMed]

Hildebrand PW, Lorenzen S, Goede A, Preissner R. (2006)
Analysis and prediction of helix-helix interactions in membrane channels and transporters. Proteins., 64(1):253-62. [PubMed]

Hoppe A, Frömmel C. (2006)
Total surface comparison - Glimpse into the morphogenesis of Proteins. In: QSAR and Molecular Modelling in Rational Design of Bioactive Molecules. Editors: Esin Aki Sener and Ismail Yalcin. Computer-aided drug design & development society in Turkey. ISBN 975-00782-0-9.

Mordmüller B, Fendel R, Kreidenweiss A, Gille C, Hurwitz R, Metzger WG, Kun JF, Lamkemeyer T, Nordheim A, Kremsner PG. (2006)
Plasmodia express two threonine-peptidase complexes during asexual development. Mol Biochem Parasitol., 148(1):79-85. [PubMed]

Rother, K., Dunkel, M., Michalsky, E., Trissl, S., Goede, A., Leser, U., Preissner, R. (2006)
A structural keystone for drug design. Journal of Integrative Bioinformatics

Tolmachov O, Palaszewski I, Bigger B, Coutelle C. (2006)
RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia coli strain for Cre mediated production of minicircle DNA. BMC Biotechnol., 10;6:17. [PubMed]

2005

Albrecht M, Huthmacher C, Tosatto SC, Lengauer T. (2005)
Decomposing protein networks into domain-domain interactions. Bioinformatics., 21 Suppl 2:ii220-1. [PubMed]

Binder B, Heinrich R. (2005)
Structural and dynamical analyses of the kinase network derived from the transpath database. Genome Inform., 16(1):164-73. [PubMed]

Bölling C, Fiehn O. (2005)
Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation. Plant Physiol., 139(4):1995-2005. [PubMed]

Goede A, Dunkel M, Mester N, Frommel C, Preissner R. (2005)
SuperDrug: a conformational drug database. Bioinformatics., 21(9):1751-3. [PubMed]

Goede A, Jaeger IS, Preissner R. (2005)
SUPERFICIAL--surface mapping of proteins via structure-based peptide library design. BMC Bioinformatics., 6:223. [PubMed]

Hildebrand PW, Rother K, Goede A, Preissner R, Frömmel C. (2005)
Molecular packing and packing defects in helical membrane proteins. Biophys J., 88(3):1970-7. [PubMed]

Hornberg JJ, Binder B, Bruggeman FJ, Schoeberl B, Heinrich R, Westerhoff HV. (2005)
Control of MAPK signalling: from complexity to what really matters. Oncogene., 24(36):5533-42. [PubMed]

Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, de Vaate AJ, Lankelma J, Heinrich R, Westerhoff HV. (2005)
Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. FEBS J., 272(1):244-58. [PubMed]

Lorenzen S, Peters B, Goede A, Preissner R, Frömmel C. (2005)
Conservation of cis prolyl bonds in proteins during evolution. Proteins., 58(3):589-95. [PubMed]

Michalsky E, Dunkel M, Goede A, Preissner R. (2005)
SuperLigands - a database of ligand structures derived from the Protein Data Bank. BMC Bioinformatics., 6:122. [PubMed]

2004

Binder B, Heinrich R. (2004)
Interrelations between dynamical properties and structural characteristics of signal transduction networks. Genome Inform., 15(1):13-23. [PubMed]

Michalsky E, Goede A, Preißner R, May P and Steinke T. (2004)
A distributed pipeline for structure prediction. In: CASP6 Methods Abstracts. 6. Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. Gaeta, Italy 2004, pp. 112-114 (Konferenzbeitrag)

Thimm M, Goede A, Hougardy S, Preissner R. (2004)
Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database. J Chem Inf Comput Sci., 44(5):1816-22. [PubMed]

2003

Hoppe A.,Frömmel C. (2003)
The molecular mimicry hypothesis: Foundation and limits of rational drug design. In: Designing Drugs and Crop Protectants: processes, problems and solutions. Editors: Martyn Ford, David Livingston, John Dearden, Han Van de Waaterbeemd. Blackwell Publishings 2003. ISBN 1-4051-2516-0.

Hoppe A.,Frömmel C. (2003)
NeedleHaystack: A program for the rapid recognition of local structures in large sets of atomic coordinates. J. Appl. Cryst., 36, 1090-1097. [html]

Dandekar T, Moldenhauer F, Bulik S, Bertram H, Schuster S. (2003)
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Biosystems., 70(3):255-70. [PubMed]

Frömmel C, Gille C, Goede A, Gröpl C, Hougardy S, Nierhoff T, Preissner R, Thimm M. (2003)
Accelerating screening of 3D protein data with a graph theoretical approach. Bioinformatics., 19(18):2442-7. [PubMed]

Gille C, Goede A, Schlöetelburg C, Preissner R, Kloetzel PM, Göbel UB, Frömmel C. (2003)
A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome. J Mol Biol., 326(5):1437-48. [PubMed]

Gille C, Lorenzen S, Michalsky E, Frömmel C. (2003)
KISS for STRAP: user extensions for a protein alignment editor. Bioinformatics., 19(18):2489-91. [PubMed]

Lorenzen S, Gille C, Preissner R, Frömmel C. (2003)
Inverse sequence similarity of proteins does not imply structural similarity. FEBS Lett., 545(2-3):105-9. [PubMed]

Michalsky E, Goede A, Preissner R. (2003)
Loops In Proteins (LIP)--a comprehensive loop database for homology modelling. Protein Eng., 16(12):979-85. [PubMed]

Pöschel T, Frömmel C, Gille C. (2003)
Online tool for the discrimination of equi-distributions. BMC Bioinformatics., 4:58. [PubMed]

Rother K, Preissner R, Goede A, Frömmel C. (2003)
Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics., 19(16):2112-21. [PubMed]

2002

Binder B, Heinrich R. (2002)
Dynamic stability of signal transduction networks depending on downstream and upstream specificity of protein kinases. Molecular biology reports, 29, 51-55. [Abstract]

Daehmlow S, Erdmann J, Knueppel T, Gille C, Froemmel C, Hummel M, Hetzer R, Regitz-Zagrosek V. (2002)
Novel mutations in sarcomeric protein genes in dilated cardiomyopathy. Biochem Biophys Res Commun.,298(1):116-20. [PubMed]

Gille C, Gille A. (2002)
TGGE-STAR: primer design for melting analysis using PCR gradient gel electrophoresis. Biotechniques., 32(2):264, 266, 268. [PubMed]

Herbik A, Bölling C, Buckhout TJ. (2002)
The involvement of a multicopper oxidase in iron uptake by the green algae Chlamydomonas reinhardtii. Plant Physiol., 130(4):2039-48. [PubMed]

Mrowka R, Schuchhardt J, Gille C. (2002)
Oligodb--interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics., 18(12):1686-7. [PubMed]

2001 & before

Bigger BW, Tolmachov O, Collombet JM, Fragkos M, Palaszewski I, Coutelle C. (2001) An araC-controlled bacterial cre expression system to produce DNA minicircle vectors for nuclear and mitochondrial gene therapy. J Biol Chem., 276(25):23018-27. [PubMed]

Gille C, Frömmel C. (2001)
STRAP: editor for structural alignments of proteins. Bioinformatics, 17(4):377-8. [PubMed]

Preissner R, Goede A, Rother K, Osterkamp F, Koert U, Froemmel C. (2001)
Matching organic libraries with protein-substructures. J Comput Aided Mol Des., 15(9):811-7. [PubMed]

Gille C, Goede A, Preissner R, Rother K, Frömmel C. (2000)
Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits. J Mol Biol., 299(4):1147-54. [PubMed]

Preissner R, Goede A, Frömmel C. (1999)
Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP). Bioinformatics., 15(10):832-6. [PubMed]

Preissner R, Goede A, Frömmel C. (1999)
Spare parts for helix-helix interaction. Protein Eng., 12(10):825-32. [PubMed]

Preissner R, Goede A, Frömmel C. (1998)
Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches. J. Mol. Biol. 280(3):535-50. [PubMed]

Goede A, Preißner R and Frömmel C. (1997)
Voronoi cell - a new method for the allocation of space among atoms: avoidance of errors in calculation of atomic volume and density. J. Comput. Chem., 18: 1113-1123.

Preissner R, Goede A, Michalski E, Frömmel C. (1997)
Inverse sequence similarity in proteins and its relation to the three-dimensional fold. FEBS Lett., 414(2):425-9. [PubMed]

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Home Research VirtualLiver People Publications Software Positions Events Contact		Other publications of group members 2010 & 2009 2008 & 2007 Bauer RA, Bourne PE, Formella A, Frömmel C, Gille C, Goede A, Guerler A, Hoppe A, Knapp EW, Pöschel T, Wittig B, Ziegler V, Preissner R. (2008) Superimpose: a 3D structural superposition server. Nucleic Acids Res., 36(Web Server issue):W47-54. [PubMed] Flajolet M, Wang Z, Futter M, Shen W, Nuangchamnong N, Bendor J, Wallach I, Nairn AC, Surmeier DJ, Greengard P. (2008) FGF acts as a co-transmitter through adenosine A(2A) receptor to regulate synaptic plasticity. Nat Neurosci., 11(12):1402-9. [PubMed] Hildebrand PW, Günther S, Goede A, Forrest L, Frömmel C, Preissner R. (2008) Hydrogen-bonding and packing features of membrane proteins: functional implications. Biophys J., 94(6):1945-53. [PubMed] Günther S, May P, Hoppe A, Frömmel C, Preissner R. (2007) Docking without docking: ISEARCH--prediction of interactions using known interfaces. Proteins., 69(4):839-44. [PubMed] Schlicker A, Huthmacher C, Ramírez F, Lengauer T, Albrecht M. (2007) Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics., 23(7):859-65. [PubMed] 2006 Binder B, Ebenhöh O, Hashimoto K, Heinrich R. (2006) Expansion of signal transduction networks. Syst Biol (Stevenage), 153(5):364-8. [PubMed] Booms P, Ney A, Barthel F, Moroy G, Counsell D, Gille C, Guo G, Pregla R, Mundlos S, Alix AJ, Robinson PN. (2006) A fibrillin-1-fragment containing the elastin-binding-protein GxxPG consensus sequence upregulates matrix metalloproteinase-1: biochemical and computational analysis. J Mol Cell Cardiol., 40(2):234-46. [PubMed] Gille C. (2006) Structural interpretation of mutations and SNPs using STRAP-NT. Protein Science., 15, 208-210. [PubMed] Gille C, Robinson PN. (2006) HotSwap for bioinformatics: a STRAP tutorial. BMC Bioinformatics., 7:64. [PubMed, http://www.charite.de/bioinf/strap/] Goede A, Michalsky E, Schmidt U, Preissner R. (2006) SuperMimic--fitting peptide mimetics into protein structures. BMC Bioinformatics., 7:11. [PubMed] Günther S, Senger C, Michalsky E, Goede A, Preissner R. (2006) Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinformatics., 7:293. [PubMed] Hildebrand PW, Lorenzen S, Goede A, Preissner R. (2006) Analysis and prediction of helix-helix interactions in membrane channels and transporters. Proteins., 64(1):253-62. [PubMed] Hoppe A, Frömmel C. (2006) Total surface comparison - Glimpse into the morphogenesis of Proteins. In: QSAR and Molecular Modelling in Rational Design of Bioactive Molecules. Editors: Esin Aki Sener and Ismail Yalcin. Computer-aided drug design & development society in Turkey. ISBN 975-00782-0-9. Mordmüller B, Fendel R, Kreidenweiss A, Gille C, Hurwitz R, Metzger WG, Kun JF, Lamkemeyer T, Nordheim A, Kremsner PG. (2006) Plasmodia express two threonine-peptidase complexes during asexual development. Mol Biochem Parasitol., 148(1):79-85. [PubMed] Rother, K., Dunkel, M., Michalsky, E., Trissl, S., Goede, A., Leser, U., Preissner, R. (2006) A structural keystone for drug design. Journal of Integrative Bioinformatics Tolmachov O, Palaszewski I, Bigger B, Coutelle C. (2006) RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia coli strain for Cre mediated production of minicircle DNA. BMC Biotechnol., 10;6:17. [PubMed] 2005 Albrecht M, Huthmacher C, Tosatto SC, Lengauer T. (2005) Decomposing protein networks into domain-domain interactions. Bioinformatics., 21 Suppl 2:ii220-1. [PubMed] Binder B, Heinrich R. (2005) Structural and dynamical analyses of the kinase network derived from the transpath database. Genome Inform., 16(1):164-73. [PubMed] Bölling C, Fiehn O. (2005) Metabolite profiling of Chlamydomonas reinhardtii under nutrient deprivation. Plant Physiol., 139(4):1995-2005. [PubMed] Goede A, Dunkel M, Mester N, Frommel C, Preissner R. (2005) SuperDrug: a conformational drug database. Bioinformatics., 21(9):1751-3. [PubMed] Goede A, Jaeger IS, Preissner R. (2005) SUPERFICIAL--surface mapping of proteins via structure-based peptide library design. BMC Bioinformatics., 6:223. [PubMed] Hildebrand PW, Rother K, Goede A, Preissner R, Frömmel C. (2005) Molecular packing and packing defects in helical membrane proteins. Biophys J., 88(3):1970-7. [PubMed] Hornberg JJ, Binder B, Bruggeman FJ, Schoeberl B, Heinrich R, Westerhoff HV. (2005) Control of MAPK signalling: from complexity to what really matters. Oncogene., 24(36):5533-42. [PubMed] Hornberg JJ, Bruggeman FJ, Binder B, Geest CR, de Vaate AJ, Lankelma J, Heinrich R, Westerhoff HV. (2005) Principles behind the multifarious control of signal transduction. ERK phosphorylation and kinase/phosphatase control. FEBS J., 272(1):244-58. [PubMed] Lorenzen S, Peters B, Goede A, Preissner R, Frömmel C. (2005) Conservation of cis prolyl bonds in proteins during evolution. Proteins., 58(3):589-95. [PubMed] Michalsky E, Dunkel M, Goede A, Preissner R. (2005) SuperLigands - a database of ligand structures derived from the Protein Data Bank. BMC Bioinformatics., 6:122. [PubMed] 2004 Binder B, Heinrich R. (2004) Interrelations between dynamical properties and structural characteristics of signal transduction networks. Genome Inform., 15(1):13-23. [PubMed] Michalsky E, Goede A, Preißner R, May P and Steinke T. (2004) A distributed pipeline for structure prediction. In: CASP6 Methods Abstracts. 6. Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. Gaeta, Italy 2004, pp. 112-114 (Konferenzbeitrag) Thimm M, Goede A, Hougardy S, Preissner R. (2004) Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database. J Chem Inf Comput Sci., 44(5):1816-22. [PubMed] 2003 Hoppe A.,Frömmel C. (2003) The molecular mimicry hypothesis: Foundation and limits of rational drug design. In: Designing Drugs and Crop Protectants: processes, problems and solutions. Editors: Martyn Ford, David Livingston, John Dearden, Han Van de Waaterbeemd. Blackwell Publishings 2003. ISBN 1-4051-2516-0. Hoppe A.,Frömmel C. (2003) NeedleHaystack: A program for the rapid recognition of local structures in large sets of atomic coordinates. J. Appl. Cryst., 36, 1090-1097. [html] Dandekar T, Moldenhauer F, Bulik S, Bertram H, Schuster S. (2003) A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Biosystems., 70(3):255-70. [PubMed] Frömmel C, Gille C, Goede A, Gröpl C, Hougardy S, Nierhoff T, Preissner R, Thimm M. (2003) Accelerating screening of 3D protein data with a graph theoretical approach. Bioinformatics., 19(18):2442-7. [PubMed] Gille C, Goede A, Schlöetelburg C, Preissner R, Kloetzel PM, Göbel UB, Frömmel C. (2003) A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome. J Mol Biol., 326(5):1437-48. [PubMed] Gille C, Lorenzen S, Michalsky E, Frömmel C. (2003) KISS for STRAP: user extensions for a protein alignment editor. Bioinformatics., 19(18):2489-91. [PubMed] Lorenzen S, Gille C, Preissner R, Frömmel C. (2003) Inverse sequence similarity of proteins does not imply structural similarity. FEBS Lett., 545(2-3):105-9. [PubMed] Michalsky E, Goede A, Preissner R. (2003) Loops In Proteins (LIP)--a comprehensive loop database for homology modelling. Protein Eng., 16(12):979-85. [PubMed] Pöschel T, Frömmel C, Gille C. (2003) Online tool for the discrimination of equi-distributions. BMC Bioinformatics., 4:58. [PubMed] Rother K, Preissner R, Goede A, Frömmel C. (2003) Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. Bioinformatics., 19(16):2112-21. [PubMed] 2002 Binder B, Heinrich R. (2002) Dynamic stability of signal transduction networks depending on downstream and upstream specificity of protein kinases. Molecular biology reports, 29, 51-55. [Abstract] Daehmlow S, Erdmann J, Knueppel T, Gille C, Froemmel C, Hummel M, Hetzer R, Regitz-Zagrosek V. (2002) Novel mutations in sarcomeric protein genes in dilated cardiomyopathy. Biochem Biophys Res Commun.,298(1):116-20. [PubMed] Gille C, Gille A. (2002) TGGE-STAR: primer design for melting analysis using PCR gradient gel electrophoresis. Biotechniques., 32(2):264, 266, 268. [PubMed] Herbik A, Bölling C, Buckhout TJ. (2002) The involvement of a multicopper oxidase in iron uptake by the green algae Chlamydomonas reinhardtii. Plant Physiol., 130(4):2039-48. [PubMed] Mrowka R, Schuchhardt J, Gille C. (2002) Oligodb--interactive design of oligo DNA for transcription profiling of human genes. Bioinformatics., 18(12):1686-7. [PubMed] 2001 & before Bigger BW, Tolmachov O, Collombet JM, Fragkos M, Palaszewski I, Coutelle C. (2001) An araC-controlled bacterial cre expression system to produce DNA minicircle vectors for nuclear and mitochondrial gene therapy. J Biol Chem., 276(25):23018-27. [PubMed] Gille C, Frömmel C. (2001) STRAP: editor for structural alignments of proteins. Bioinformatics, 17(4):377-8. [PubMed] Preissner R, Goede A, Rother K, Osterkamp F, Koert U, Froemmel C. (2001) Matching organic libraries with protein-substructures. J Comput Aided Mol Des., 15(9):811-7. [PubMed] Gille C, Goede A, Preissner R, Rother K, Frömmel C. (2000) Conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal subunits. J Mol Biol., 299(4):1147-54. [PubMed] Preissner R, Goede A, Frömmel C. (1999) Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP). Bioinformatics., 15(10):832-6. [PubMed] Preissner R, Goede A, Frömmel C. (1999) Spare parts for helix-helix interaction. Protein Eng., 12(10):825-32. [PubMed] Preissner R, Goede A, Frömmel C. (1998) Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches. J. Mol. Biol. 280(3):535-50. [PubMed] Goede A, Preißner R and Frömmel C. (1997) Voronoi cell - a new method for the allocation of space among atoms: avoidance of errors in calculation of atomic volume and density. J. Comput. Chem., 18: 1113-1123. Preissner R, Goede A, Michalski E, Frömmel C. (1997) Inverse sequence similarity in proteins and its relation to the three-dimensional fold. FEBS Lett., 414(2):425-9. [PubMed] Top