Publications

2024

  1. Ly, T.T.B., May T.-T. T., Raffaele, A., Urlacher, V.B., Nguyen, T.T., Hutter, M.C., Vu, H.-N. T., Le, D.T.T., Quach, T.N., Phi, Q.-T. (2024) Archives of Biochemistry and Biophysics, 762, 11019n, doi:10.1016/j.abb.2024.110192. New CYP154C4 from Streptomyces cavourensis YBQ59 performs regio- and stereo-selective 3β-hydroxlation of nootkatone.
  2. Baek, I-H, Helms, V., Kim, Y. (2024) Journal of Functional Biomaterials, 15, 314, doi:10.3390/jfb15110314. Genetically engineered filamentous bacteriophages displaying TGF-β1 promote angiogenesis in 3D Microenvironments.
  3. Sorout, N., Helms, V. (2024) Journal of Molecular Recognition, e3108, doi:10.1002/jmr.3108. Towards understanding the mechanism of client-selective small molecule inhibitors of the Sec61 translocon.
  4. Fischer, A.A.M., Robertson, H.B., Kong, D., Grimm, M.M., Grether, J., Groth, J., Baltes, C., Fliegauf, M., Lautenschläger, F., Grimbacher, B., Ye, H., Helms, V., Weber, W. (2024) Small, 2311834, doi:0.1002/smll.202311834. Engineering material properties of transcription factor condensates to control gene expression in mammalian cells and mice.
  5. Johannsen, S., Gierse, R.M., Krüger, A., Edwards, R.L., Nanna, V., Fontana, A., Zhu, D., Masini, T., Pessanha de Carvalho, L., Poizat, M., Kieftenbelt, B., Hodge, D.M., Alvarez, S., Bunt, D., Lacour, A., Shams, A., Meissner, K.A., de Souza, E.E., Dröge, M., van Vliet, B., den Hartog, J., Hutter, M.C., Held, J., Odom John, A.R., Wrenger, C., Hirsch, A.K.H. (2024) ACS Infect. Dis, 10, 1000-1022, doi:10.1021/acsinfecdis.3c00670. High target homology does not guarantee inhibition: aminothiazoles emerge as inhibitors of Plasmodium falciparum.

2023

  1. Do, T.H.T., Shanak, S., Barghash, A., Helms, V. (2023) Scientific Reports, 13, 12256, doi:10.1038/s41598-023-38879-z. Differential exon usage of developmental genes is associated with deregulated epigenetic marks.
  2. Zöphel, S., Schäfer, G., Nazarieh, M., Konetzki, V., Hoxha, C., Meese, E., Hoth, M., Helms, V., Hamed, M., Schwarz, E.C. (2023) Molecular Immunology, 157, 202-213, doi:10.1016/j.molimm.2023.04.002. Molecular Immunology. Identification of molecular candidates which regulate calcium-dependent CD8+ T-cell cytotoxicity.
  3. Röder, A., Hüsken, S., Hutter, M.C., Rettie, A.E., Hanenberg, H., Wiek, C., Girhard, M. (2023) International Journal of Molecular Sciences, 24, 2038, doi:10.3390/ijms24032038. Spotlight on CYP4B1.
  4. Barbieri, G., Simon, J., Lupusella, C., Pereira, F., Elia, F., Meyer, H., Schuldiner, M., Hanes, S.D., Nguyen, D., Helms, V., Römisch, K. (2023) Journal of Biological Chemistry, 102895, doi:10.1016/j.jbc.2023.102895. Sec61 channel subunit Sbh1/Sec61beta promotes ER translocation of proteins with suboptimal targeting sequences and is fine-tuned by phosphorylation.
  5. Santiago-Tirado, F., Hurtaux, T., Geddes-McAlister, J., Nguyen, D., Helms, V., Doering, T., Römisch, K. (2023) mBio, 14, doi:10.1128/mbio.03384-22. The ER protein translocation channel subunit Sbh1 controls virulence of Cryptococcus neoformans.

2022

  1. Helms, V. (2022) Transcription factor – DNA complexes, in: Protein Interactions: The Molecular Basis of Interactomics, chapter 10, 195-211, doi:10.1002/9783527830503.ch10.
  2. Künzel, N., Helms, V. (2022) Kinatics and thermodynamics of protein-protein encounter, in: Protein Interactions: The Molecular Basis of Interactomics, chapter 8, 143-162, doi:10.1002/9783527830503.ch8.
  3. Thangamurugan, S., Hollander, M., Helms, V. (2022) Identification of putative protein complexes in protein–protein interaction networks, in: Protein Interactions: The Molecular Basis of Interactomics, chapter 5, 77-99, doi:10.1002/9783527830503.ch5.
  4. Helms, V. (2022) Protein structures and conformational dynamics, in: Protein Interactions: The Molecular Basis of Interactomics, chapter 1, 1-13, doi:10.1002/9783527830503.ch1.
  5. Carius, Y., Hutter, M., Kiss, F., Bernhardt, R., Lancaster, C.R.D. (2022) FEBS Letters, doi: 10.1002/1873-3468.14502. Structural comparison of the cytochrome P450 enzymes CYP106A1 and CYP106A2 provides insight into their differences in steroid conversion.
  6. Denger, A., Helms, V. (2022) Journal of Chemical Information and Modeling, 62(23), 6242–6257, doi: 10.1021/acs.jcim.2c00850. Optimized data set and feature construction for substrate prediction of membrane transporters.
  7. Tirincsi, A., O`Keefe, S., Nguyen, D., Sicking, M., Dudek, J., Förster, F.G., Jung, M., Hadzibeganovic, D., Helms, V., High, S., Zimmermann, R., Lang, S. (2022), Cells 2022, 11(18), 2925, doi:10.3390/cells11182925. Proteomics identifies substrates and a novel component in hSnd-dependent ER protein targeting.
  8. Bhadra, P., Römisch, K., Helms, V. (2022), BBA – Biomembranes, vol. 1864, 184050, doi:10.1016/j.bbamem.2022.184050. Effect of Sec62 on the conformation of the Sec61 channel in yeast.
  9. O’Keefe, S., Bhadra,P., Duah,K.B., Zong, G., Tenay, L., Andrews, L, Schneider, H., Anderson, A., Hu, Aljewari, H.S., Hall, B.S., Simmonds, R.E., Helms, V., High, S., Shi, W.Q. (2022), Molecules, 27, 4419, doi:10.3390/molecules27144419. Synthesis, biological evaluation and docking studies of ring-openedanalogues of Ipomoeassin F.
  10. Hutter, M.C. (2022) Journal of Chemical Information and Modeling. doi:10.1021/acs.jcim.2c00242. Differential multimolecule fingerprint for similarity search-making use of active and inactive compound sets in virtual screening.
  11. Lang, S., Nguyen, D., Bhadra, P., Jung, M., Helms, V., Zimmermann, R. (2022) Frontiers in Physiology, 13:833540. doi: 10.3389/fphys.2022.833540. Signal peptide features determining the substrate specificities of targeting and translocation components in human ER protein import.
  12. Künzel, N., Helms, V. (2022) Journal of Chemical Theory and Computation, doi:10.1021/acs.jctc.1c01140. How peptides bind to PSD-95/Discs-Large/ZO-1 domains.
  13. Lyschik, S., Lauer, A.A., Roth, T., Janitschke, D., Hollander, M., Will, T., Hartmann, T., Kopito, R.R., Helms, V., Grimm, M.O.W., Schrul; B. (2022) Frontiers in Cell and Developmental Biology, section Membrane Traffic, 10:859052. doi: 10.3389/fcell.2022.859052. PEX19 coordinates neutral lipid storage in cells in a peroxisome-independent fashion.
  14. Trautmann, S., Künzel, N., Fecher-Trost, C., Barghash, A., Dudek, J., Flockerzi, V., Helms, V., Hannig, M. (2022) Proteomics Clinical Applications, doi:10.1002/prca.202100109. Is the proteomic composition of the salivary pellicle dependent on the substrate material?
  15. Yang, W., Denger, A., Diener, C., Küppers, F., Soriano-Baguet, L., Schäfer, G., Yanamandra, A.K., Zhao, R., Knörck, A., Schwarz E.C., Hart, M., Lammert, F., Prates Roma, L., Brenner, D., Christidis, G., Helms, V., Meese, E., Hoth, M., Qu, B. (2022) Frontiers in Immunology, 13:831680. doi: 10.3389/fimmu.2022.831680. Unspecific CTL killing is enhanced by high glucose via TNF-related apoptosis-inducing ligand.
  16. Sicking, M., Živná, M., Bhadra, P., Barešová, V., Tirincsi, A., Hadzibeganovic, D., Hodaňová, K., Vyleťal, P., Sovová, J., Jedličkova, I., Jung, M., Bell, T., Helms, V., Kmoch, S., Cavalié, A., Lang, S. (2022) Life Science Alliance, vol. 5, e202101150, doi: 10.26508/lsa.202101150. Phenylbutyrate rescues the transport defect of the Sec61α mutations V67G and T185A for renin.

2021

  1. Knapp, M., Alansary, D., Poth, V., Förderer, K., Sommer, F., Zimmer, D., Schwarz, Y., Künzel, N., Kless, A., Machaca, K., Helms, V., Mühlhaus, T., Schroda, M., Lis, A., Niemeyer, B. (2021, accepted) EMBO reports. A longer isoform of Stim1 is a negative SOCE regulator but increases cAMP modulated NFAT signaling.
  2. Zimmermann, R., Lang, S., Lerner, M., Förster, F., Nguyen, D., Helms, V., Schrul B. (2021, accepted) International Journal of Molecular Sciences. Quantitative proteomics and differential protein abundance analysis after depletion of PEX3 from human cells identifies additional aspects of protein targeting to the ER.
  3. Bhadra, P., Dos Santos, S., Gamayun, I., Pick, T., Neumann, C., Ogbechi, J., Hall, B.S., Zimmermann, R., Helms, V., Simmonds, R.E., Cavalié, A. (2021) Biochemical Journal, vol 478, p. 4005-4024, doi:10.1042/BCJ20210345. Mycolactone enhances the Ca2+ leak from endoplasmic reticulum by trapping Sec61 translocons in a Ca2+ permeable state.
  4. Bhadra, P., Helms, V. (2021) International Journal of Molecular Sciences, vol. 22, 10705, doi:10.3390/ijms221910705. Molecular modeling of signal peptide recognition by eukaryotic Sec complexes.
  5. Worst, E.G., Finkler, M., Schenkelberger, M., Kurt, Ö., Helms, V., Noireaux, V., Ott, A. (2021) ACS Synthetic Biology, doi:10.1021/acssynbio.1c00326. A methylation-directed synthetic pap switch based on self-complementary regulatory DNA reconstituted in an all E.coli cell-free expression system.
  6. Capello, S., Sung, H.-M., Ickes, C., Gibhardt, C.S., Vultur, A., Bhat, H., Hu, Z., Brafford, P., Denger, A., Stejerean-Todoran, I., Köhn, R.-M., Lorenz, V., Künzel, N., Salinas, G., Stanisz, H., Legler, T., Rehling, P., Schön, M.P., Lang, K.S., Helms, V., Herlyn, M., Hoth, M., Kummerow, C., Bogeski, I. (2021) Cancer Research, doi:10.1158/0008-5472.CAN-21-0164. Protein signatures of NK cell-mediated melanoma killing predict response to immunotherapies.
  7. Hoppstädter, J., Dembek, A., Höring, M., Schymik, H.S., Dahlem, C., Sultan, A., Wirth, N., Al-Fityan, S., Diesel, B., Gasparoni, G., Walter, J., Helms, V., Huwer, H., Simon, M., Liebisch, G., Schulz, M.H., Kiemer, A.K. (2021) EBioMedicine, vol. 72, 103578. Dysregulation of cholesterol homeostasis in human lung cancer tissue and tumour-associated macrophages.
  8. Hollander, M., Do, T.H.T., Will, T., Helms, V. (2021) Frontiers in Bioinformatics – Network Bioinformatics, 1:724297, doi:10.3389/fbinf.2021.724297/full. Detecting rewiring events in protein-protein interaction networks based on transcriptomic data.
  9. Künzel, N., Helms, V. (2021) Proteins: Stucture, Function, and Bioinformatics, doi:full/10.1002/prot.26224. How peptide phosphorylation affects its interaction with 14-3-3η domains.
  10. Hoffmann, S.L., Kohlstedt, M., Jungmann, L., Hutter, M., Poblete-Castro, I., Becker, J., Wittmann, C. (2021) Metabolic Engineering, vol. 67, p. 293-307, doi:10.1016/j.ymben.2021.07.010. Cascaded valorization of brown seaweed to produce L-lysine and value-added products using Corynebacterium glutamicum streamlined by systems metabolic engineering.
  11. Nazarieh, M., Hoeppner, M., Helms, V. (2021) Frontiers in Bioinformatics, section Network Bioinformatics, 1:653054, doi:10.3389/fbinf.2021.653054. Identification of biomarkers controlling cell fate in blood cell evelopment.
  12. Hartz, P., Strohmaier, S.J., El-Gayar, B.M., Abdulmughni, A., Hutter, M.C., Hannemann, F., Gillam, E.M.J., Bernhardt, R. (2021) FEBS Journal, doi:10.1111/febs.16054. Resurrection and characterization of ancestral CYP11A1 enzymes.
  13. Putkaradze, N., Hartz, P., Hutter, M.C., Zapp, J., Thevis, M., Bernhardt, R. (2021) Journal of Steroid Biochemistry and Molecular Biology, v. 212, 105927, doi:10.1016/j.jsbmb.2021.105927. Metabolism of oral turinabol by the human brain cholesterol 24-hydroxylase CYP46A1.
  14. Bhadra, B., Lerner, M., Schorr, S., Nguyen, D., Dudek, J., Förster, F., Helms, V., Lang, S., Zimmermann, R. (2021) Molecules, v. 26, 3591, doi:10.3390/molecules26123591. Quantitative proteomics and differential protein abundance analysis after depletion of putative mRNA receptors in the ER membrane of human cells identifies novel aspects of mRNA targeting to the ER.
  15. Bokel, A., Hutter, M.C., Urlacher, V.B. (2021) Chemical Communications, v. 57, p. 520-523, doi: 10.1039/d0cc06729f. Molecular evolution of a cytochrome P450 for the synthesis of potential antidepressant (2R,6R)-hydroxynorketamine.
  16. Hollander, M., Rasp, D., Aziz, M., Helms, V. (2021) Journal of Chemical Information and Modeling, doi:10.1021/acs.jcim.1c00154. ProPores2: web service and stand-alone tool for identifying, manipulating, and visualizing pores in protein structures.
  17. Bhadra, P., Yadhanapudi, L., Römisch, K., Helms, V. (2021) PLOS Computational Biology, vol. 17, e1008855, doi: 10.1371/journal.pcbi.1008855. How does Sec63 affect the conformation of Sec61 in yeast?

2020

  1. Bokel, A., Rühlmann, A., Hutter, M.C., Urlacher, V.B. (2020) ACS Catalysis, v. 10, p. 4151-4159, doi:10.1021/acscatal.9b05384. Enzyme-mediated two-step regio- and stereoselective synthesis of potential rapid-acting antidepressant (2S,6S)-hydroxynorketamine.
  2. Lenhof, J., Hutter, M.C., Huch, V., Jauch, J. (2020) European Journal of Organic Chemistry, v. 2020, p. 5833-5840, doi:10.1002/ejoc.202000586. Towards the total synthesis of jerangolids ‐ synthesis of an advanced intermediate for the pharmacophore substructure.
  3. Zhou, Y., Zhao, R., Schwarz, E.C., Akbar, R., Kaba, M., Pattu, V., Helms, V., Rieger, H., Nunes-Hasler, P., Qu, B. (2020) Journal of Immunology, v. 205, p. 2988-3000, doi:10.4049/jimmunol.2000195 . Inter-organelle tethering to endocytic organelles determines directional cytokine transport in CD4+ T cells.
  4. Shanak, S., Helms, V. (2020) Developmental Biology, v. 464, p. 145-160, doi:10.1016/j.ydbio.2020.06.001. DNA methylation and the core pluripotency network.
  5. Trautmann, S., Künzel, N., Fecher-Trost, C., Barghash, A., Schalkowsky, B., Dudek, J., Delius, J., Helms, V., Hannig, M. (2020) Proteomics Clinical Applications, v. 14, 1900090, doi:10.1002/prca.201900090. Deep proteomic insights into the individual short-term pellicle formation on enamel – an in situ pilot study.
  6. König, L., Brixius-Anderko, S., Milhim, M., Tavouli-Abbas, D., Hutter, M.C., Hannemann, B., Bernhardt, R. (2020) Biotechnology and Bioengineering, v. 117, p. 901-911, doi:10.1002/bit.27246. Identification and circumvention of bottlenecks in CYP21A2-mediated premedrol production using Escherichia coli.
  7. Aprà, E., et al. (2020) The Journal of Chemical Physics, v. 152, 184102, doi:10.1063/5.0004997. NWChem: Past, present, and future.
  8. Schorr, S., Nguyen, D., Haßdenteufel, S., Nagaraj, N., Cavalié, A., Greiner, M., Weissgerber, P., Loi, M., Paton, A,W, Paton, J.C., Molinari, M.,  Förster, F., Dudek, J., Lang, S., Helms, V. and Zimmermann, R. (2020) FEBS Journal, doi:10.1111/febs.15274. Identification of signal peptide features for substrate specificity in human Sec62/Sec63-dependent ER protein import.
  9. Putkaradze, N., König, L., Hutter, M.C., Bernhardt, R. (2020, accepted) Biochemical and Biophysical Research Communications, doi:10.1016/j.bbrc.2020.01.091. Highly regio- and stereoselective hydroxylation of vitamin D2 by CYP109E1.
  10. Klein, M.C., Lerner, M., Nguyen, D., Pfeffer, M., Dudek, J., Förster, F., Helms, V., Lang, S., Zimmermann, R. (2020) Channels, doi:10.1080/19336950.2020.1724759. TRAM1 protein may support ER protein import by modulating the phospholipid bilayer near the lateral gate of the Sec61-channel.
  11. Gaidar, D., Jordan, A., Akulenko, R., Ruffing, U., Herrmann, M., Helms, V., von Müller, L. (2020) International Journal of Medical Microbiology, v. 310, no. 151411, doi:10.1016/j.ijmm.2020.151411. Analysis of the dynamics of Staphylococcus aureus binding to white blood cells using whole blood assey and geno-to-pheno mapping.

2019

  1. Tesseling, F.A., Hutter, M., Wiek, C., Kowalski, J.P., Rettie, A.E., Girhard, M. (2019) Archives of Biochemistry and Biophysics, vol. 679, 108216, doi:10.1016/j.abb.2019.108216. Novel insights into oxidation of fatty acids and fatty alcohols by cytochrome P450 monooxygenase CYP4B1.
  2. König, L., Brixius-Anderko, S., Milhim, M., Hutter, M., Hannemann, F., Bernhardt, R. (2019) Biotechnology and Bioengineering, doi: 10.1002/bit.27246. Identification and circumvention of bottlenecks in CYP21A2‐mediated premedrol production using recombinant Escherichia coli.
  3. Nazarieh, M., Helms, V. (2019) Scientific Reports, vol. 9, no. 19472, doi:10.1038/s41598-019-55945-6. TopControl: a tool to prioritize candidate disease-associated genes based on topological network features.
  4. Nazarieh, M., Hamed, M., Spaniol, C., Will, T., Helms, V. (2019) Bioinformatics, btz 871, doi:10.1093/bioinformatics/btz871. TFmiR2: Constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks.
  5. Kröhler, T., Kessler, S.M., Hosseini, K., List, M., Barghash, A., Patial, S., Laggai, S., Gemperlein, K., Haybaeck, J., Müller, R., Helms, V., Schulz M.H., Hoppstädter, J., Blackshear, P.J., Kiemer, A.K. (2019) Cancers, vol. 11, 1754, doi:10.3390/cancers11111754. The mRNA-binding protein TTP/ZFP36 in hepatocarcinogenesis and hepatocellular carcinoma.
  6. Nazarieh, M., Rajula, H.S.R., Helms, V. (2019) BMC Bioinformatics, no. 550, doi:10.1186/s12859-019-3107-8. Topology consistency of disease specific differential co-regulatory networks.
  7. Czepukojc, B., Abuhaliema, A., Barghash, A., Tierling, S., Naß, N.,  Simon, Y., Körbel, C., Cadenas, C., van Hul, N., Sachinidis, A., Hengstler, J.G.G., Helms, V., Laschke, M.W., Walter, J., Haybaeck, J., Leclercq, I., Kiemer, A.K., Kessler, S.M. (2019) Frontiers in Medicine, section Pathology, doi:10.3389/fmed.2019.00179/full. IGF2 mRNA binding protein 2 transgenic mice are more prone to develop a ductular reaction and to progress towards cirrhosis.
  8. Haßdenteufel, S., Nguyen, D., Zimmermann, R., Helms, V., Lang, S. (2019) FEBS Letters, vol. 593, p. 2506-2524. ER-import of small human presecretory proteins: components and mechanisms.
  9. Zhang, X., Gibhardt, C.S., Will, T., Stanisz, H., Körbel, C., Cappello, S., Dudek, J., Mitkovski, M., Laschke, M.W., Simmen, T., Schön, M.P., Helms, V., Niemeyer, B.A., Rehling, P., Vultur, A., Bogeski, I. (2019) EMBO Journal. Redox signals at the ER-mitochondria interface control melanoma progression.
  10. Will, T., Helms, V. (2019) BMC Bioinformatics, 20:300, doi:10.1186/s12859-019-2852-z. Differential analysis of combinatorial protein complexes with CompleXChange.
  11. Gamayun, I., O’Keefe, S., Klein, M.-C., Pick, T., Nguyen, D., McKibbin, C., Piacenti, M.,  Williams, H.M., Flitsch, S.L., Whitehead, R.C., Swanton, E., Helms, V., High, S., Zimmermann, R., Cavalié, A. (2019) Cell Chemical Biology, vol. 26, p. 578-583, doi:10.1016/j.chembiol.2019.01.010. Eeyarestatin compounds selectively enhance Sec61-mediated Ca2+ leakage from the endoplasmic reticulum.
  12. Neininger, K., Marschall, T., Helms, V. (2019) PLOS ONE, doi:10.1371/journal.pone.0214816. SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome.
  13. Fehlmann, T., Hutter, M.C. (2019) Journal of Chemical Information and Modeling, vol. 59, p. 1314-1323, doi:10.1021/acs.jcim.8b00757. Conservation and relevance of pharmacophore point types.
  14. Ahmad, M., Helms, V., Kalinina, O., Lengauer, T. (2019) Journal of Chemical Theory and Computation, vol. 15, p. 2166-2178. Relative principal components analysis: application to analyzing biomolecular conformational changes.
  15. Putkaradze, N., Litzenburger, M., Hutter, M.C., Bernhardt, R. (2019) ChemBioChem, doi:10.1002/cbic.201800595. CYP109E1 from Bacillus megaterium acts as 24- and 25-hydroxylase for cholesterol.
  16. Sagadin, T., Riehm, J., Putkaradze, N., Hutter, M.C., Bernhardt, R. (2019) FEBS Journal, doi:10.1111/febs.14722. Novel approach to improve progesterone hydroxylation selectivity by CYP106A2 via rational design of adrenodoxin binding.
  17. Trautmann, S., Barghash, A., Fecher-Trost, C., Schalkowsky, P., Hannig, C., Kirsch, J., Rupf, S., Helms, V., Hannig, M. (2019) Proteomics Clinical Applications, doi:10.1002/prca.201800143. Proteomic analysis of the initial oral pellicle in caries-active and caries-free individuals.

2018

  1. Humaidan, D., Breinig, F., Helms, V. (2018) PLOS ONE, no. 0208515, doi: 10.1371/journal.pone.0208515. Adding phosphorylation events to the core oscillator driving the cell cycle of fission yeast.
  2. Kim, J., Fischer, M., Helms, V. (2018) Chemical Research in Toxicology, vol. 31, p. 1138-1150, doi:10.1021/acs.chemrestox.8b00164. Prediction of synergistic toxicity of binary mixtures to Vibrio fischeri based on biomolecular interaction networks.
  3. Nguyen, D., Stutz, R., Schorr, S., Lang, S., Pfeffer, S., Freeze, H.H., Förster, F., Helms, V., Dudek, J., Zimmermann, R. (2018) Nature Communications, vol. 9, no. 3765, doi:10.1038/s41467-018-06188-z. Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import.
  4. Baek, I.-h., Han, H.-S., Baik, S., Helms, V., Kim, Y (2018) Polymers, vol. 10, no. 974, doi:10.3390/polym10090974. Detection of acidic pharmaceutical compounds using virus-based molecularly imprinted polymers.
  5. Sagadin, T., Riehm, J.L., Milhim, M., Hutter, M.C., Bernhardt, R. (2018) Communications Biology, vol. 1, no. 99, doi: 10.1038/s42003-018-0104-9. Binding modes of CYP106A2 redox partners determine differences in progesterone hydroxylation product patterns.
  6. Hutter, M.C. (2018) Future Medicinal Chemistry, vol. 10, p. 1623-1635, doi: 10.4155/fmc-2017-0303. The current limits in virtual screening and property prediction.
  7. Klein, M.-C., Zimmermann, K., Schorr, S., Landini, M., Klemens, P.A.W., Altensell, J., Jung, M., Krause, E., Nguyen, D., Helms, V., Rettig, J., Fecher-Trost, C., Cavalié, A., Hoth, M., Bogeski, I., Neuhaus, H.E., Zimmermann, R., Lang, S., Haferkamp, I. (2018) Nature Communications, vol. 9, no. 3489, doi: 10.1038/s41467-018-06003-9. AXER is an ATP/ADP exchanger in the membrane of the endoplasmic reticulum.
  8. Tran, V.H., Kiemer, A., Helms, V., (2018) Cancer Genomics & Proteomics, vol. 15, p. 365-378, doi: 10.21873/cgp.20095 . Copy number alterations in tumor genomes deleting antineoplastic drug targets partially compensated by complementary amplifications.
  9. Irhimeh, M., Hamed, M., Barthelmes, D., Gladbach, Y., Helms, V., Shen, W., Gillies, M. (2018) PLOS ONE, vol. 13, no. e0200194, doi: 10.1371/journal.pone.0200194. Identification of novel diabetes impaired miRNA-transcription factor co-regulatory networks in bone marrow-derived Lin–/VEGF-R2+ endothelial progenitor cells.
  10. Khatri, Y., Jóźwik, I.K., Ringle, M., Ionescu,I. A., Litzenburger, M., Hutter, M.C., Thunnissen, A.W.H, Bernhardt, R. (2018) ACS Chemical Biology, vol. 13, p. 1021-1028, doi: 10.1021/acschembio.8b00026. Structure-based engineering of steroidogenic CYP260A1 for stereo- and regioselective hydroxylation of progesterone.
  11. Akbar, R., Helms, V. (2018) Chemical Biology & Drug Design, vol. 91, p. 845-853, doi: 10.1111/cbdd.13161. ALLO: A tool to discriminate and prioritize allosteric pockets.
  12. Tran, V.H., Barghash, A., Helms, V. (2018) Journal of Proteomics & Bioinformatics, vol. 11, p. 868-874, doi: 10.4172/jpb.1000468. Annotating the function of protein-coding genes based on Gene Ontology terms of neighboring co-expressed genes.
  13. Hollander, M., Hamed, M., Helms, V., Neininger, K. (2018) Bioinformatics, vol. 34, p. 864-866. doi: 10.1093/bioinformatics/btx687. MutaNET: a tool for automated analysis of genomic mutations in gene regulatory Networks.

2017

  1. Schultheiss, C.S., Laggai, S., Czepukojc, B., Hussein, U.K., List, M., Barghash, A., Tierling, S., Hosseini, K., Golob-Schwarzl, N., Pokorny, J., Hachenthal, N., Schulz, M., Helms, V., Walter, J.,  Zimmer, V., Lammert, F., Bohle, R.,M., Dandolo, L., Haybaeck, J., Kiemer, A.K., Kessler, S.M. (2017) Cell Stress, vol. 1, p. 37-54, doi: 10.15698/cst2017.10.105. The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma.
  2. Lang, S., Pfeffer, S., Lee, P.H., Cavalié, A., Helms, V., Förster, F., Zimmermann, R. (2017) Frontiers in Physiology, vol. 8, no. 887, doi: 10.3389/2Ffphys.2017.00887.  An update on Sec61 channel functions, mechanisms, and related diseases.
  3. Bakkes, P.J., Riehm, J.L., Sagadin, T., Rühlmann, A., Schubert, P., Biemann, S., Girhard, M., Hutter, M.C., Bernhardt, R., Urlacher, V.B. (2017) Scientific Reports, vol. 7, no. 9570, doi: 10.1038/s41598-017-10075-w. Engineering of versatile redox partner fusions that support monooxygenase activity of functionally diverse cytochrome P450s.
  4. Schoppmeyer, R., Zhao, R., Cheng, H., Hamed, M., Liu, C., Zhou, X., Schwarz, E.C., Zhou, Y., Knörck, A., Schwär, G., Ji, S., Liu, L., Long, J., Helms, V., Hoth, M., Yu, X., Qu, B. (2017). European Journal of Immunology, vol. 47, p. 1562-1572, doi: 10.1002/eji.201747124. Human profilin 1 is a negative regulator of CTL mediated cell-killing and migration.
  5. Sadegh, S., Nazarieh, M., Spaniol, C., Helms, V. (2017) Journal of Integrative Bioinformatics, vol. 14, no. 20170017, doi: 10.1515/jib-2017-0017. Randomization strategies affect motif significance analysis in TF-miRNA-gene regulatory networks.
  6. Shanak, S., Ulucan, Ö., Helms, V. (2017) Journal of Molecular Modeling, vol. 23, no. 152, doi: 10.1007/s00894-017-3318-8, Methylation-targeted specificity of the DNA binding proteins R.DpnI and MeCP2 studied by molecular dynamics simulations.
  7. Ruffing, U., Alabi, A., Kazimoto, T., Vubil, D.C., Akulenko, R., Abdulla, S., Alonso, P., Bischoff, P., Germann, A., Grobusch, M.P., Helms, V., Hoffmann, J., Kern, W.V., Kremsner, P.G., Mandomando, I., Mellmann, A., Peters, G., Schaumburg, F., Schubert, S., Strauß, L., Tanner, M., von Briesen, H., Wende, L., von Müller, L., Herrmann, M. (2017) Scientific Reports, vol. 7, no. 154, doi: 10.1038/s41598-017-00214-8. Community-associated Staphylococcus aureus from Sub-Saharan Africa and Germany: A cross-sectional geographic correlation study.
  8. Zhou, X., Zhao, R., Schwarz, K., Mangeat, M., Schwarz, E., Hamed, M., Bogeski, I., Helms, V., Rieger, H., Qu,. B. (2017) Scientific Reports, vol. 7, no. 44357, doi: 10.1038/srep44357. Bystander cells enhance NK cytotoxic efficiency by reducing search time.
  9. Schenkelberger, M., Shanak, S., Finkler, M., Worst, E., Noireaux, V., Helms, V., Ott, A. (2017) Physical Biology, vol. 14, p. 026002, doi: 10.1088/1478-3975/aa5d37. Expression regulation by a methyl-CpG binding domain in an E. coli based, cell-free TX-TL system.
  10. Will, T., Helms, V. (2017) BMC Systems Biology, vol. 11, no. 44, doi: 10.1186/s12918-017-0400-x. Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.
  11. Putkaradze, N., Kiss, F.M., Schmitz, D., Zapp, J., Hutter, M.C., Bernhardt, R. (2017) Journal of Biotechnology, vol. 242, p. 101-110, doi: 10.1016/j.jbiotec.2016.12.011. Biotransformation of prednisone and dexamethasone by cytochrome P450 based systems – identification of new potential drug candidates.
  12. Yang, X., Hutter, M., Goh, W.W.B., Bureik, M. (2017) Current Pharmaceutical Design, vol. 23, p. 2060-2064, doi: 10.2174/1381612823666170207150156. CYP4Z1 – A human cytochrome P450 enzyme that might provide the key to treat breast cancer.
  13. Ahmad, M., Helms, V., Kalinina, O.V., Lengauer, T. (2017) Journal of Chemical Physics, vol. 146, no. 014105, doi: 10.1063/1.4973349. Elucidating the energetic contributions to the binding free energy..
  14. Hamed, M., Trumm, J., Spaniol, C., Sethi, R., Irhimeh, M.R., Fuellen, G., Paulsen, M., Helms, V. (2017) PLOS ONE, vol. 12, no. e0166852, doi: 10.1371/journal.pone.0166852. Linking hematopoietic differentiation to co-expressed sets of pluripotency-associated and imprinted genes and to regulatory microRNA-transcription factor motifs.
  15. Akbar, R., Jusoh, S.A., Amaro, R., Helms, V. (2017) Chemical Biology & Drug Design, vol. 89, p. 762-771, doi: 10.1111/cbdd.12900. ENRI: A tool for selecting structure-based virtual screening target conformations.

2016

  1. Reuter, K., Biehl, A., Koch, L., Helms, V. (2016) PLOS Computational Biology, vol. 12, no. e1005170, doi: 10.1371/journal.pcbi.1005170. PreTIS: a tool to predict non-canonical 5′ UTR translational initiation sites in human and mouse.
  2. Akulenko, R., Merl, M., Helms, V. (2016) PLOS ONE, vol. 11, no. e0159921. doi: 10.1371/journal.pone.0159921. BEclear: Batch effect detection and adjustment in DNA methylation data.
  3. Nazarieh, M., Wiese, A., Will, T., Hamed, M., Helms, V. (2016) BMC Systems Biology, vol. 10, no. 88, doi: 10.1186/s12918-016-0329-5. Identification of key player genes in gene regulatory networks.
  4. Barghash, A., Golob-Schwarzl, N., Helms, V., Haybaeck, J., Kessler, S.M. (2016) Oncotarget, vol. 7, p. 49743-49750, doi: 10.18632/oncotarget.10439. Elevated expression of the IGF2 mRNA binding protein 2 (IGF2BP2/IMP2) is linked to short survival and metastasis in esophageal adenocarcinoma.
  5. Janocha, S., Carius, Y., Hutter, M., Lancaster, C.R.D., Bernhardt, R. (2016) ChemBioChem, vol. 17, p. 852-860, doi: 10.1002/cbic.201500524. Crystal structure of CYP106A2 in substrate-free and substrate-bound form.
  6. Ahmad, M., Helms, V., Kalinina, O., and Lengauer, T. (2016) Journal of Physical Chemistry Part B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter, B: Biophysical Chemistry and Biomolecules, vol. 120, p. 2138–2144, doi: 10.1021/acs.jpcb.5b11593. The role of conformational changes in molecular recognition.
  7. Barghash, A., Arslan, T., and Helms, V. (2016) Journal of Proteomics and Bioinformatics, vol. 9, p. 38-48, doi: 10.4172/jpb.1000387. Robust detection of outlier samples and genes in expression datasets.
  8. Strauss, L., Ruffing, U., Abdulla, S., Alabi, A., Akulenko, R., Garrine, M., Germann, A., Grobusch, M., Helms, V., Herrmann, M., Kazimoto, T., Kern, W., Mandomando, I., Peters, G., Schaumburg, F., von Müller, L., Mellmann, A. (2016) Journal of Clinical Microbiology, vol. 54, p. 1008-1016, doi: 10.1128/JCM.03022-15. Detecting staphylococcus aureus virulence and resistance genes – a comparison of whole genome sequencing and DNA microarray technology.
  9. Reuter, K., Steinbach, A., Helms, V. (2016) Perspectives in Medicinal Chemistry, vol. 2016:8, p. 1-15, doi: 10.4137/PMc.s13209. Interfering with bacterial quorum sensing.
  10. Will, T., Helms, V. (2016) Bioinformatics, vol. 32, p. 571-578, doi: 10.1093/bioinformatics/btv620. PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.

2015

  1. Thomann, A., Zapp, J., Hutter, M., Empting, M, Hartmann, R.W. (2015) Organic ] Biomolecular Chemistry, vol. 13, p. 10620-10630, doi: 10.1039/C5OB01006C. Steering the azido–tetrazole equilibrium of 4-azidopyrimidines via substituent variation – implications for drug design and azide–alkyne cycloadditions.
  2. Mohamed, R., Degac, J., Helms, V. (2015) PLOS ONE, vol. 10, no. e0140965, doi: 10.1371/journal.pone.0140965. Composition of overlapping protein-protein and protein-ligand interfaces.
  3. Degac, J., Winter, U., Helms, V. (2015) Journal of Chemical Information and Modeling, vol. 55, p. 1944-1952, doi: 10.1021/acs.jcim.5b00045. Graph-based clustering of predicted ligand-binding pockets on protein surface.
  4. Hamed, M., Nitsche-Schmitz D.P., Ruffing, U., Steglich, M., Dordel, J., Nguyen, D., Brink, J.-H., Singh Chhatwal, G., Herrmann, M., Nübel, U., Helms, V., von Müller, L. (2015) Infection, Genetics and Evolution, vol. 36, p. 475-482, doi: 10.1016/j.meegid.2015.08.020. Whole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant staphylococcus aureus isolates: Clues to phylogeny and invasiveness.
  5. Mosa, A., Hutter, M.C., Zapp, J., Bernhardt, R., Hannemann, F. (2015) ChemBioChem, vol. 16, p. 1670-1679, doi: 10.1002/cbic.201500125. Regioselective acetylation of C21 hydroxysteroids by the bacterial chloramphenicol acetyltransferase I.
  6. Barghash, A., Helms, V., Kessler, S. (2015) Scandinavian Journal of Immunology, vol. 82, p. 142-143, doi: 10.1111/sji.12307. Overexpression of IGF2 mRNA-Binding Protein 2 (IMP2/p62) as a feature of basal-like breast cancer correlates with short survival.
  7. Ulucan, Ö, Helms, V. (2015) Journal of Physical Chemistry B, vol. 119, p. 10524-10530, doi: 10.1021/acs.jpcb.5b05831. How hydrophilic proteins form non-specific complexes.
  8. Kiemer, A.K., Kessler, S., Laggai, S., Barghash, A., Schultheiss, C., Lederer, E., Artl, M., Helms, V., and Haybaeck, J. (2015) Cell Death and Disease, vol. 6, no. e1894, doi: 10.1038/cddis.2015.241. IMP2/p62 induces genomic instability and an aggressive hepatocellular carcinoma phenotype.
  9. Spaniol, C., Hamed, M., Trumm, J., and Helms, V. (2015) 7th International Conference on Bioinformatics and Computational Biology (BiCOB 2015), Honolulu, Hawaii, March 9-11, 2015. Mebitoo: an Extensible Software Framework for Bioinformatics Analysis Workflow Automatization.
  10. Ahmad, M., Helms, V., Lengauer, T., Kalinina, O. (2015) Journal of Chemical Theory and Computation, vol. 11, p. 2945-2957, doi: 10.1021/acs.jctc.5b00235. How molecular conformational changes affect changes in free energy.
  11. Hamed, M., Spaniol, C., Zapp, A., Helms, V. (2015) BMC Genomics, vol. 16 (Suppl 5), no. S2, doi: 10.1186/1471-2164-16-S5-S2. Integrative network-based approach identifies key genetic elements in breast invasive carcinoma.
  12. Hamed, M., Spaniol, C., Nazarieh, M., Helms, V. (2015) Nucleic Acids Research, vol. 43, p. W283-W288, doi: 10.1093/nar/gkv418.  TFmiR: A web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.
  13. Zapp, A., Helms, V., and Hamed, M. (2015) Proceedings of the Second International Conference on Advances in Bio-Informatics and Environmental Engineering – ICABEE 2015, doi: 10.15224/ 978-1-63248-043-9-127. SnvDMiR: Associating the genomic proximity of genetic variants with deregulated miRNAs and differentially methylated regions.
  14. Miederer, A.-M., Alansary, D., Schwaer, G., Lee, P.-H., Jung, M., Helms, V., and Niemeyer, B.A. (2015) Nature Communications, vol. 6, p. 6899, doi: 10.1038/ncomms7899. A STIM2 splice variant negatively regulates store operated calcium entry.
  15. Ahmad, M., Helms, V., Lengauer, T., and Kalinina, O. (2015) Journal of Chemical Theory and Computation, vol. 11, p. 1410-1418, doi: 10.1021/ct501161t. Enthalpy-entropy compensation upon molecular conformational changes.
  16. Hochscherf, J., Lindenblatt, D., Steinkrüger, M., Yoo, E., Ulucan, Ö., Herzig, S., Issinger, O.-G., Helms, V., Götz, C., Neundorf, I., Niefind, K., Pietsch, M. (2015) Analytical Biochemistry,  vol. 468., p. 4-14, doi: 10.1016/j.ab.2014.09.003. Development of a HTS-compatible assay to identify inhibitors of the CK2α/CK2β interaction.
  17. Dudek, J., Pfeffer, S., Lee, P.-H., Jung, M., Cavalié, A., Helms, V., Förster, F., Zimmermann, R. (2015) Journal of Molecular Biology, vol. 427, p. 1159-1175, doi: 10.1016/j.jmb.2014.06.011. Protein transport into human endoplasmic reticulum.
  18. Kessler, S.M., Barghash, A., Laggai, S., Helms, V., and Kiemer, A.K. (2015) Journal of  Hepatology, vol. 62, p. 977-979, doi: 10.1016/j.jhep.2014.10.046. Hepatic hepcidin expression is decreased in cirrhosis and HCC.
  19. Khatri, Y., Hannemann, F., Girhard, M., Hutter, M., Urlacher, V.B., and Bernhardt, R. (2015) FEBS Journal, vol. 282, p. 74-88, doi: 10.1111/febs.13104.  A natural heme-signature variant of CYP267A1 from Sorangium cellulosum So ce56 executes diverse ω-hydroxylation.

2014

  1. Baowan, D. and Helms, V. (2014) Journal of Mathematical Chemistry, vol. 53. p. 29-40, doi: 10.1007/s10910-014-0408-z. Quantitative study of BSA coating silica nanoparticle.
  2. Shanak, S. and Helms, V. (2014) Journal of Chemical Phyics, vol. 141, no. 22D512, doi: 10.1063/1.4897525. Hydration properties of natural and synthetic DNA sequences with methylated adenine or cytosine bases in the R.DpnI target and BDNF promoter studied by molecular dynamics simulations.
  3. Ruffing, U., Abraham, A., Abdulla, S., Akulenko, R., …Helms, V., et. al. (2014) Tagungsband zur 4. Gemeinsamen Konferenz von DGHM und VAAM : VAAM-Jahrestagung 2014 ; 66. Jahrestagung der DGHM ; Dresden, 05.–08. Oktober 2014. – Heidelberg : Springer Spektrum, 2014. – (Biospektrum ; 2014, Sonderausg.), S. 121. Molecular genotyping of 1200 community acquired commensal and clinical Staphylococcus aureus isolates of the African-German StaphNet multicenter study.
  4. Chen, J., Lutsik, P., Akulenko, R., Walter, J., and Helms, V. (2014, accepted for GIW/ISCB) Journal of Bioinformatics and Computational Biology, vol. 12, no. 1442005, doi: 10.1142/S0219720014420050. AKSmooth: Human colon methylome profiling using low-coverage bisulfite sequencing data.
  5. Hutter, M.C., Brengel, C., Negri, M., Henn, C., Zimmer, C., Hartmann, R.W., Empting, M., Steinbach, A. (2014) Journal of Molecular Modeling, vol. 20, p. 2255-2264, doi: 10.1007%2Fs00894-014-2255-z. Mechanistic details for anthraniloyl transfer in PqsD: the initial step in HHQ biosynthesis.
  6. Will, T. and Helms, V. (2014) Bioinformatics, vol. 30 ECCB 2014, p. i415-i421, doi:10.1039/bioinformatics/btu448. Identifying transcription factor complexes and their roles.
  7. Ulucan, Ö., Jaitly, T., and Helms, V., (2014) Journal of Chemical Theory and Computation, vol. 10, p. 3512-3524, doi: 10.1021/ct5001796. Energetics of hydrophilic protein-protein association and the role of water.
  8. Beznoussenko, G., Parashuraman, S., Rizzo, R., Polishuk, R., Martella, O., Di Giandomenico, D., Fussella, A., Spaar, A., Sallese, M., Capestrano, M.G., Pavelka, M., Vos, M.R., Rikers, Y.G.M., Helms, V., Mironov, A.A., Luini, A. (2014) eLife, vol. 3, no. e02009, doi: 10.7554/eLife.02009.001. Transport of soluble proteins through the Golgi occurs by diffusion via continuities across cisternae.
  9. Ruffing, U., Akulenko, R., Kazimoto, T., …, Helms, V., et.al. (2014) 24th ECCMID 2014: European Congress of Clinical Microbiology and Infectious Diseases ; Barcelona, Spain, 10 – 13 May 2014; ESCMID online lecture library. DNA microarray-based genotyping of 1200 Staphylococcus aureus isolates of the African–German StaphNet multicentre study.
  10. Kessler, S.M., Simon, Y., Gemperlein, K., Gianmoena, K., Cadenas, C., Zimmer, V., Pokorny, J., Barghash, A., Helms, V., van Rooijen, N., Bohle, R.M., Lammert, F., Hengstler,  J.G., Müller, R., Haybaeck, J., Kiemer., A.K. (2014) International Journal of Molecular Sciences, vol. 15, p. 5762-5773, doi: 10.3390/ijms15045762. Fatty acid elongation in non-alcoholic steatohepatitis and hepatocellular carcinoma.
  11. Kessler, S.M., Laggai, S., Barghash, A., Helms, V., and Kiemer, A. (2014) Cancer Research, vol. 74, p. 2903-2904, doi: 10.1158/0008-5472.CAN-13-2852. Lipid metabolism signatures in NASH-associated HCC – letter.
  12. Nguyen, D., Helms, V., and Lee, P.-H. (2014) Proteins: Structure, Function, and Bioinformatics, vol. 82, p. 1503-1511, doi: 10.1002/prot.24520. PRIMSIPLR: Prediction of inner-membrane situated pore-lining residues for alpha-helical transmembrane proteins.

2013

  1. Tretter, T., Pereira, F.P., Ulucan, Ö., Helms, V., Allan, S., Kalies, K.-U, and Römisch, K. (2013) BMC Cell Biology, vol. 14, p. 56, doi: 10.1186/1471-2121-14-56. ERAD and protein import defects in a sec61 mutant lacking ER-lumenal loop 7.
  2. Barghash, A. and Helms, V. (2013) BMC Bioinformatics, vol. 14, no. 343, doi: 10.1186/1471-2105-14-343. Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs.
  3. Schaadt, N., Steinbach, A, Hartmann, R.W., and Helms, V. (2013) BMC Systems Biology, vol. 7, no. 81, doi:10.1186/1752-0509-7-81. Rule-based regulatory and metabolic model Quorum sensing in P. aeruginosa.
  4. Will, T., Hutter, M., Jauch, J., and Helms, V. (2013). Journal of Computational Chemistry, vol. 34, p. 2485-2492, doi:10.1002/jcc.23397. Batch tautomer Generation with MolTPC.
  5. Beck, A., Speicher, T., Stoerger, C., Sell, T., Dettmer, V., Jusoh, S.A., Abdulmughni, A., Cavalié, A., Philipp, S.E., Zhu, M.X., Helms, V., Wissenbach, U., and Flockerzi, V. (2013) Journal of Biological Chemistry, vol. 288, p. 19471-19483, doi: 10.1074/jbc.M113.478305. Conserved gating elements in TRPC4 and TRPC5 channels.
  6. Akulenko, R. and Helms, V. (2013) Human Molecular Genetics, vol. 22, p. 3016-3022, doi: 10.1093/hmg/ddt158. DNA co-methylation analysis suggests novel functional associations between gene pairs in breast cancer samples.
  7. Baowan, D., Peuschel, H., Kraegeloh, A.,  and Helms, V. (2013) Journal of Molecular Modeling, vol. 19, p. 2459-2472, doi: 10.1007/s00894-013-1784-1. Energetics of liposomes encapsulating silica nanoparticles.
  8. Walter, P., Metzger, J., Thiel, C., and Helms, V. (2013) PLOS One, vol. 8, no. e58583, doi: 10.1371/journal.pone.0058583. Predicting where small molecules bind at protein-protein interfaces.
  9. Janocha, S., Zapp, J., Hutter, M., Kleser, M., Bohlmann, J., and Bernhardt, R. (2013) ChemBioChem, vol. 14, p. 467-473, doi: 10.1002/cbic.201200729. Resin acid conversion with CYP105A1: An enzyme with potential for the production of pharmaceutically relevant diterpenoids.
  10. Geyer, T.  (2013) Current Opinion in Structural Biology, vol. 23, p. 218-223, doi: 10.1016/j.sbi.2012.12.001. Modeling metabolic processes between molecular and systems biology.
  11. Zhukovsky, M.A., Lee, P.-H., Ott, A., and Helms, V. (2013) Proteins: Structure, Function, Bioinformatics, vol. 81, p. 555-567, doi: 10.1002/prot.24211. Putative cholesterol-binding sites in human immunodeficiency virus (HIV) coreceptors CXCR4 and CCR5.

2012

  1. Ruffing, U., Akulenko, R., Bischoff, M., Helms, V., Herrmann, M., and von Müller, L. (2012) PLOS ONE, vol. 7, no. e52487, doi: 10.1371/journal.pone.0052487. Matched-cohort DNA microarray diversity analysis of methicillin sensitive and methicillin resistant Staphylococcus aureus isolates from hospital admission patients.
  2. Hamed, M., Ismael, S., Paulsen, M., and Helms, V. (2012) PLOS ONE, vol.7, no. e50285, doi: 10.1371/journal.pone.0050285. Cellular functions of genetically imprinted genes in human and mouse as annotated in the Gene Ontology.
  3. Lee, P-H, Helms, V, and Geyer, T. (2012) Journal of Chemical Physics., vol. 137, no. 145105, doi: 10.1063/1.4757265. Coarse-grained Brownian dynamics simulations of protein translocation through nanopores.
  4. Ulucan, Ö., Eyrisch, S., and Helms, V. (2012) Current Pharamceutical Design, vol. 18, p. 4599-4606, doi: 10.2174/138161212802651652. Druggability of dynamic protein-protein interfaces.
  5. Wagenmann, A. and Geyer, T. (2012) Journal of Chemical Theory and Computation, vol. 8, p. 4732–4745, doi: 10.1021/ct3005529. Coarse-grained simulations of protein backbone dynamics. I: Local sterics define the dihedral angles.
  6. Geyer, T. (2012) Journal of Chemical Physics, vol. 137, no. 115101, doi: 10.2174/138161212802651652. Mixing normal and anomalous diffusion.
  7. Geyer, T., Born, P., and Kraus, T. (2012) Physical Review Letters, vol. 109, no. 128302, doi: 10.1103/PhysRevLett.109.128302. Switching between crystallization and amorphous agglomeration of alkyl thiol-coated gold nanoparticles.
  8. Herzog, E., Gu, W., Juhnke, H.D., Haas, A.H., Mäntele, W., Simon, J., Helms, V., and Lancaster, C.R.D. (2012) Biophysical Journal, vol. 103, p. 1305-1314, doi: 10.1016/j.bpj.2012.07.037. Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol: Fumarate reductase.
  9. Schäuble, N., Lang, S., Jung, M., Cappel, S., Ulucan, O., Linxweiler, J., Dudek, J., Blum, R., Helms, V., Paton, A.W., Paton, J.C., Cavalié, A., Zimmermann, R. (2012) EMBO Journal, vol. 31, p. 3282-3296, doi: 10.1038/emboj.2012.189. BIP-mediated closing of the Sec61 channel limits Ca2+ leakage from ER.
  10. Walter, P., Ulucan, Ö., Metzger, J., and Helms, V. (2012) Current Bioinformatics, vol. 7, p. 159-172, doi: 10.2174/157489312800604444. Bioinformatics of protein-protein interfaces and small molecule effectors.
  11. Eyrisch, S., Medina-Franco, J.L., and Helms, V. (2012) Journal of Molecular Modeling, vol. 18, p. 2031-2042, doi: 10.1007/s00894-011-1217-y. Transient pockets on XIAP-BIR2: towards the characterization of putative binding sites of small-molecule XIAP inhibitors.
  12. Schaadt, N. and Helms, V. (2012) Biopolymers, vol. 97, p. 558-567, doi: 10.1002/bip.22043. Functional classification of membrane transporters and channels based on filtered TM/non-TM amino acid composition.
  13. Hobler, A., Kagawa, N., Hutter, M.C., Hartmann, M.F., Wudy, S.A., Hannemann, F., and Bernhardt, R. (2012) Journal of Steroid Biochemistry and Molecular Biology, vol. 132, 57-65, doi: 10.1016/j.jsbmb.2012.03.002. Human aldosterone synthase: Recombinant expression in E. coli and purification enables a detailed biochemical analysis of the protein on the molecular level.
  14. Zimmer, M.J. and Geyer, T. (2012) Journal of Physical Chemistry, vol. 136, p. 125102, doi: 10.1063/1.3698593. Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?
  15. Kieser, M., Hannemann, F., Hutter, M., Zapp, J., and Bernhardt, R. (2012) Journal of Biotechnology, vol. 157, p. 405-412, doi: 10.1016/j.jbiotec.2011.12.006. CYP105A1 mediated 3-hydroxylation of glimepiride and glibenclamide using a recombinant Bacillus megaterium whole-cell catalyst.
  16. Lee, P.-H. and Helms, V. (2012) Proteins: Structure, Function, and Bioinformatics, vol. 80, p. 421-432, doi: 10.1002/prot.23204. Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues.
  17. Ly, T.T.B., Khatri, Y., Zapp, J., Hutter, M.C. and Bernhardt, R. (2012) Applied Microbiology and Biotechnnology, vol. 95, p. 123-133, doi: 10.1007/s00253-011-3727-z. CYP264B1 from Sorangium cellulosum So ce56: a fascinating norisoprenoid and sesquiterpene hydroxylase.

2011

  1. Helms, V. and Gu, W. (2011). Proton travel in green fluorescent protein (Abstract). In: Jung, G. (Ed.) Fluorescent Proteins 1. Springer,  p. 171-181.
  2. Hutter, M.C. (2011) Journal of Chemical Information and Modeling, vol. 51, p. 3099-3104, doi: 10.1021/ci200403j. Determining the degree of randomness of descriptors in linear regression equations with respect to the data size.
  3. Metzger, J., Schaadt, N., Hayat; S., and Helms, V. (2011) Annual Reports in Computational Chemistry, vol. 7, p. 39-64. Ed. Wheeler, R.A. Predicting structural and functional properties of membrane proteins from protein sequence.
  4. Carbon-Mangels, M. and Hutter, M.C. (2011) Journal of Molecular Informatics, vol. 30, p. 885-895, doi: 10.1002/minf.201100069. Selecting relevant descriptors for classification by Bayesian estimates: A comparison with decision trees and support vector machines approaches for disparate data sets.
  5. Geyer, T. (2011) BMC Biophysics, vol. 4, no. 7, doi: 10.1186/2046-1682-4-7. Many-particle Brownian and Langevin dynamics simulations with the Brownmove package.
  6. Hutter, M.C. (2011) Future Medicinal Chemistry, vol. 3, p. 485-501, doi: 10.4155/fmc.11.3. Graph-based similarity concepts in virtual screening.
  7. Singh, N.K., Goodman, A., Walter, P., Helms, V., and Hayat, S. (2011) Biochimica et Biophysica Acta – Proteins and Proteomics, vol. 1814, p. 664-670, doi: 10.1016/j.bbapap.2011.03.004. TMBHMM: A frequency-profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues.
  8. Ahmad, M., Gu, W., Geyer, T., and Helms, V. (2011) Nature Communications, vol. 2, no. 261, doi: 10.1038/ncomms1258. Adhesive water networks facilitate binding of protein interfaces.
  9. Hayat, S., Park, Y., and Helms, V. (2011). Computational Biology and Chemistry, vol. 35, p. 96-107, doi: 10.1016/j.compbiolchem.2011.03.002. Statistical analysis and exposure status classification of transmembrane beta barrel residues.
  10. Zimmermann, R., Eyrisch, S., Ahmad, M., and Helms, V. (2011) BBA – Biomembranes, vol. 1808, p. 912-924, 10.1016/j.bbamem.2010.06.015. Protein translocation across the ER membrane.
  11. Hayat, S., Walter, P., Park, Y., and Helms, V. (2011) Journal of Bioinformatics and Computational Biology, vol. 9, p. 43-65, doi: 10.1142/S0219720011005240. Prediction of the exposure status of transmembrane beta barrel residues from protein sequence.
  12. Erdmann, F., Schäuble, N., Lang, S., Jung, M., Honigmann, A., Ahmad, M., Dudek, J., Benedix, J., Harsmann, A., Kopp, A., Helms, V., Cavalié, A., Wagner, R., and Zimmermann, R. (2011) EMBO Journal, vol. 30, p. 17-31, doi: 10.1038/emboj.2010.284. Interaction of calmodulin with Sec61 limits Ca2+ leakage from the endoplasmic reticulum.
  13. Gu, W., Zhou, B., Geyer, T., Hutter, M., Fang, H., and Helms, V. (2011) Angewandte Chemie (DE) vol. 123, p. 794-797, doi: 10.1002/ange.201002564. Design eines steuerbaren molekularen Protonenkanals. Angewandte Chemie International Edition (EN) vol. 50, p. 768-771, doi: 10.1002/anie.201002564. Design of a gated molecular proton channel.
  14. Jusoh, S.A. and Helms, V. (2011) BBA Biomembranes, vol. 1808, p. 1040-1049, doi: 10.1016/j.bbamem.2011.01.004. Helical integrity and microsolvation of transmembrane domains from Flaviviridae envelope glycoproteins.

2010

  1. Hutter, B., Bieg, M., Helms, V., and Paulsen, M. (2010) BMC Genomics, vol. 11, no. 649, doi: 10.1186/1471-2164-11-649. Imprinted genes show unique patterns of sequence conservation.
  2. Geyer, T., Mol, X., Blaß, S., and Helms, V. (2010) PLOS ONE, vol. 5, no. e14070, doi: 10.1371/journal.pone.0014070. Bridging the gap: Linking molecular simulations and systemic descriptions of cellular compartments.
  3. Kathri, Y., Girhard, A., Romankiewicz, A., Ringle, M., Hannemann, F., Urlacher, V.B., Hutter, M., and Bernhardt, R. (2010) Applied Microbiology and Biotechnology, vol. 88, p. 485-495, doi: 10.1007/s00253-010-2756-3. Regioselective Hydroxylation of Norisoprenoids by CYP109D1 from Sorangium cellulosum So ce56.
  4. Hutter, M. (2010) ChemMedChem, vol. 5, p. 306-307. Book review: Molecular Descriptors for Chemoinformatics (2nd. Ed.).
  5. Schaadt, N., Christoph, J., and Helms, V. (2010) Journal of Chemical Information and Modeling, vol. 50, p. 1899-1905, vol. 10.1021/ci100243m. Classifying substrate specifities of membrane transporters from arabidopsis thaliana.
  6. Devanathan, R., Venkatnathan, A., Rousseau, R., Dupuis, M., Frigato, T., Gu, W., Helms, V. (2010) Journal of Physical Chemistry B, vol. 114, p. 13681-13690, doi: 10.1021/jp103398b. Atomistic simulation of water percolation and proton hopping in nafion fuel cell membrane.
  7. Helms, V., Hayat, S., and Metzger, J. (2010) Predicting the burial/exposure status of transmembrane residues in helical membrane proteins. In: Structural Bioinformatics of Membrane Proteins, Ed. D. Frishman, Springer.
  8. Wang, L., Siu, S., Gu, W., and Helms, V. (2010) Biopolymers, vol. 93, p. 977-985, doi: 10.1002/bip.21507. Downhill binding energy surface of the barnase-barstar complex.
  9. Hutter, B., Bieg, M. Helms, V., and Paulsen, M. (2010) BMC Evolutionary Biology, vol. 10, no. 116, doi: 10.1186/1471-2148-10-116. Divergence of imprinted genes during mammalian evolution.
  10. Jusoh, S.A., Welsch, C., Siu, S.W.I., Böckmann, R.A., and Helms, V. (2010) Journal of Molecular Modeling, vol. 16, p. 1625-1637, doi: 10.1007/2Fs00894-010-0672-1. Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus.
  11. Berwanger, A., Eyrisch, S., Schuster, I., Helms, V., and Bernhardt, R. (2010) Journal of Inorganic Biochemistry, vol. 104, p. 118-125, doi: 10.1016/j.jinorgbio.2009.10.007. Polyamines: Naturally occurring small molecule modulators of electrostatic protein-protein interactions.

2009

  1. Hutter, M.C. (2009) Chemical Modelling: Applications and Theory, vol. 6, p. 112-130. QSAR – Old And New Directions, in Ed. M.Springborg, RSC Publishing, Cambridge UK, 2009.
  2. Winter, U. and Geyer, T. (2009) Journal of Chemical Physics, vol. 131, no. 104102, doi: 10.1063/1.3216573. Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions.
  3. Erdmann, F., Jung, M., Eyrisch, S., Lang, S., Helms, V., Wagner, R., and Zimmermann, R. (2009) FEBS Letters, vol. 583, p. 2359-2364, doi: 10.1016/j.febslet.2009.06.032. Lanthanum ions inhibit the mammalian Sec61 complex in its channel dynamics and protein transport activity. 
  4. Wang, L., Stumm, B., and Helms, V. (2009) Journal of Computational Chemistry, vol. 31, p. 847-854, doi: 10.1002/jcc.21368. Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.
  5. Krier, M. and Hutter, M. C. (2009) Journal of Chemical Information and Modeling, vol. 49, p. 1280-1297, doi: 10.1021/ci8003418. Bioisosteric similarity of molecules based on structural alignment and observed chemical replacements in drugs.
  6. Geyer, T. and Winter, U. (2009) Journal of Chemical Physics, vol. 130, no. 114905, doi: 10.1063/1.3089668. An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations.
  7. Lauck, F., Helms; V., and Geyer, T. (2009) Journal of Chemical Theory and Computation, vol. 5, p. 641-648, doi: 10.1021/ct800396v. Graph measures reveal fine structure of complexes forming in multiparticle simulations.
  8. Gu, W. and Helms, V. (2009) Journal of the American Chemical Society, vol. 131, p. 2080-2081, doi: 10.1021/ja809301w. Tightly connected water wires facilitate fast proton uptake at the proton entrance of proton pumping proteins.
  9. Eyrisch, S. and Helms, V. (2009) Journal of Computer-Aided Molecular Design, vol. 23, p. 73-86, doi: 10.1007/s10822-008-9239-y. What induces pocket openings on protein surface patches involved in protein-protein interactions?
  10. Hutter, M. C. (2009) Current Medicinical Chemistry, vol. 16, p. 189-202, doi: 10.2174/092986709787002736. In silico prediction of drug properties.
  11. Spaar, A., Flöck, D., and Helms, V. (2009) Biophysical Journal, vol. 96, p. 1721-1732, doi: 10.1016/j.bpj.2008.11.052. Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution.

2008

  1. Schluttig, J., Alamanova, D., Helms, V., and Schwarz, U. S. (2008) Journal of Chemical Physics, vol. 129, no. 155106, doi: 10.1063/1.2996082. Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches.
  2. Hutter, B., Paulsen, M., and Helms, V. (2008) OMICS: A Journal of Integrative Biology, vol. 13, no. 2, doi: 10.1089/omi.2008.0046. Identifying CpG islands by different computational techniques (Abstract).
  3. Eyrisch, S. and Helms, V. (2008) Proceedings of the German Conference on Bioinformatics 2008. Designing binding pockets on protein surfaces using the A* algorithm.
  4. Helms, V. (2008) Principles of Computational Cell Biology – From Protein Complexes to Cellular Networks. Wiley-VCH.
  5. Ahmad, M., Gu, W., and Helms, V. (2008), Angewandte Chemie, vol. 120, p. 7738-7742, doi: 10.1002/ange.200801856.Mechanismus der schnellen Peptiderkennung durch SH3-Domänen (DE). Angewandte Chemie International Edition, vol. 47, p. 7626-7630, doi:10.1002/anie.200801856. Mechanism of fast peptide recognition by SH3 domains(EN).
  6. Park, Y. and Helms, V. (2008) Bioinformatics, vol. 24, p. 1819-1820, doi: 10.1093/bioinformatics/btn255. MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon.
  7. Park, Y. and Helms, V. (2008) Bioinformatics, vol. 24, p. 1271-1277, doi: 10.1093/bioinformatics/btn114. Prediction of the translocon-mediated membrane insertion free energies of protein sequences.
  8. Schneider, N., Jäckels, C., Andres, C., and Hutter, M. (2008) Journal of Chemical Information and Modeling, vol. 48, p. 613-628, doi: 10.1021/ci700351y. Gradual in silico filtering for druglike substances.

2007

  1. Kunz, K. and Helms, V. (2007) GI-Edition – Lecture Notes in Informatics (LNI) – Proceedings, vol. 115. QVADIS: A Package to Compute Proton Transfer Pathways in Proteins. (Eds.) Falter, C., Schliep, A., Selbig, J., Vingron, M., and Walther, D.
  2. Gu, W. and Helms, V. (2007) ChemPhysChem, vol. 8, p. 2445-2451, doi:10.1002/cphc.200700442. Different protonation equilibria of 4-methylimidazole and acetic acid.
  3. Geyer, T. (2007) Biophysical Journal, vol. 93, p. 4374-4381, doi: 10.1529/biophysj.107.106377. On the effects of PufX on the absorption properties of the light-harvesting complexes of Rhodobacter sphaeroides.
  4. Park, Y., Hayat, S., and Helms, V. (2007) BMC Bioinformatics, vol. 8, no. 302, doi: 10.1186/2F1471-2105-8-302. Prediction of the burial status of transmembrane residues of helical membrane proteins.
  5. Eyrisch, S. and Helms, V. (2007) Journal of Medicinal Chemistry, vol. 50, p. 3457-3464, doi:10.1021/jm070095g. Transient pockets on protein surfaces involved in protein-protein interaction.
  6. Walter, P., Ansari, S., and Helms, V. (2007) Journal of Integrative Bioinformatics, vol. 4, no. 50., doi: 10.2390/biecoll-jib-2007-50. The ABC (Analysing Biomolecular Contacts) database.
  7. Geyer, T., Lauck, F., and Helms, V. (2007) Journal of Biotechnology, vol. 129, p. 212-228, doi: 10.1016/j.jbiotec.2006.12.018. Molecular stochastic simulations of chromatophore vesicles from Rhodobacter sphaeroides.
  8. Park, Y. and Helms, V. (2007) Bioinformatics, vol. 23, p. 701-708, doi: 10.1093/bioinformatics/btl653. On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins.
  9. Hutter, M.C.. (2007) Journal of Chemical Information and Modeling, vol. 47, p. 186-104, doi: 10.1021/ci600329u. Separating drugs from non-drugs: A statistical approach using atom pair distributions.
  10. Gu, W., Frigato, T., Straatsma, T.P., and Helms, V. (2007) Angewandte Chemie, vol. 119, p. 2997-3001, doi: 10.1002/ange.200603583. Dynamisches Protonierungsgleichgewicht der in Wasser gelösten Essigsäure (DE). Angewandte Chemie International Edition, vol. 46, p. 2939-2943, doi: 10.1002/anie.200603583. Dynamic protonation equilibrium of solvated acetic acid (EN).
  11. Helms, V. (2007) ChemPhysChem, vol. 8, p. 23-33, doi: 10.1002/cphc.200600298. Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules.

2006

  1. Park, Y. and Helms, V. (2006) Biopolymers, vol. 83, p. 389-399, doi: 10.1002/bip.20569. How strongly do sequence conservation patterns and empirical scales correlate with exposure patterns of transmembrane helices of membrane proteins?
  2. Geyer, T. and Helms, V. (2006) Biophysical Journal, vol. 91, p. 927-937, doi: 10.1529/biophysj.105.067561. Reconstruction of a kinetic model of the chromatophore vesicles from Rhodobacter sphaeroides.
  3. Geyer, T. and Helms, V. (2006) Biophysical Journal, vol. 91, p. 921-926, doi: 10.1529/2Fbiophysj.105.078501. A spatial model of the chromatophore vesicles of Rhodobacter sphaeroides and the position of the cytochrome bc1 complex.
  4. Hutter, B., Helms, V., and Paulsen, M. (2006) Genomics, vol. 88, p. 323-332, doi: 10.1016/j.ygeno.2006.03.019. Tandem repeats in the CpG islands of imprinted genes.
  5. Spaar, A. and Helms, V. (2006) Journal of Non-Crystalline Solids, vol. 352, p. 4437-4444, doi: 10.1016/j.jnoncrysol.2006.03.117. Ionic strength effects on the association funnel of barnase and barstar investigated by Brownian dynamics simulations.
  6. Gepp, M. and Hutter, M.C. (2006) Bioorganic & Medicinal Chemistry, vol. 14, p. 5325-5332, doi: 10.1016/j.bmc.2006.03.043. Determination of hERG channel blockers using a decision tree.
  7. Park, Y. and Helms, V. (2006) Proteins: Structure, Function, and Bioinformatics, vol. 64, p. 895-905, doi: 10.1002/prot.21025. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.
  8. Hutter, M.C. (2006) Chemical Physics, vol. 326, p. 240-245, doi: 10.1016/j.chemphys.2006.01.007. Stability of the guanine-cytosine radical cation in DNA base pairs triplets.
  9. Andres, C. and Hutter, M.C. (2006) QSAR & Combinatorial Science, vol.25, p. 305-309, doi:10.1002/qsar.200510200. . CNS permeability of drugs predicted by a decision tree.
  10. Herzog, E., Frigato, T., Helms, V., and Lancaster, C.R.D. (2006) Journal of Computational Chemistry, vol. 27, p. 1534-1547, doi: 10.1002/jcc.20442. Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations.
  11. Spaar, A., Dammer, C., Gabdoulline, R.R., Wade, R.C., and Helms, V. (2006) Biophysical Journal, vol. 90, p. 1913-1924, doi: 10.1529/biophysj.105.075507. Diffusional encounter of barnase and barstar.

2005

  1. Helms, V., Hutter, M, and Gu, W. (2005) Magazin Forschung, p. 28-32. Was hat das Eiweiß in einem Computer zu suchen?
  2. Geyer, T. and Tannor, D.J. (2005) Journal of Physics B: Atomic, Molecular, and Optical Physics, vol. 38, p. 3423-2446, doi: 10.1088/0953-4075/38/18/012. A mapping approach to synchronization in the “Zaifman trap”: II. The observed bunch
  3. Staritzbichler, R., Gu, W. and Helms, V. (2005) Journal of Physical Chemistry B, vol. 109, p. 19000-19007, doi: 10.1021/jp052403x. Are solvation free energies of homogeneous helical peptides additive?
  4. Gu, W. and Helms, V. (2005) Biochimica and Biophysica Acta (Proteins and Proteomics), vol. 1754, p. 232-238, doi: 10.1016/j.bbapap.2005.07.033 Dynamical binding of proline-rich peptides to their recognition domains (Abstract).
  5. Olkhova, E., Helms, V., and Michel, H. (2005) Biophysical Journal, vol. 89, p. 2324 – 2331, doi: 10.1529/2Fbiophysj.105.062091. Titration behaviour of residues at the entrance of the D-pathway of cytochrome c oxidase from paracoccus denitrificans investigated by continuum electrostatic calculations.
  6. Piotukh, K., Gu, W., Kofler, M., Helms, V., and Freund, C. (2005) Journal of Biological Chemistry, vol. 280, p. 23668-23674, doi:10.1074/jbc.M503405200. Cyclophilin A binds to linear peptide motifs containing a consensus that is present in many human proteins.
  7. Spaar, A. and Helms, V. (2005) Journal of Chemical Theory and Computation, vol. 1, p. 723-736, doi:10.1021/ct050036n. Free energy landscape of protein-protein encounter resulting from Brownian dynamics simulations of barnase: barstar
  8. Gu, W., Kofler, W., Antes, I., Freund, C., and Helms, V. (2005) Biochemistry, vol. 44, p. 6404-6415, doi: 10.1021/bi0479914. Alternative binding modes of proline-rich peptides binding to the GYF-domain.
  9. Ansari, S. and Helms, V. (2005) Proteins: Structure, Function, and Bioinformatics, vol. 61, p. 344 – 355, doi: 10.1002/prot.20593. Statistical analysis of predominantly transient protein-protein interfaces.
  10. Shakya, S.K., Gu, W., and Helms, V. (2005) Biopolymers, vol. 78, p. 9-20, doi:10.1002/bip.20242. Molecular dynamics simulation of truncated bovine adrenodoxin.

2004

  1. Hutter, M.C. and Hartmann, R.W., (2004) QSAR & Combinatorial Science, vol. 23, p. 406-415, doi: 10.1002/qsar.200430876. QSAR of human steroid 5α-reductase inhibitors: where are the differences between isoenzyme Type 1 and 2?
  2. Park, Y., Elsner, M., Staritzbichler, R., and Helms, V., (2004) Proteins: Structure, Function, and Bioinformatics, vol. 57, p. 577-585, doi: 10.1002/prot.20229. Novel scoring function for modeling structures of oligomers of transmembrane alpha-helices.
  3. Gorba, C., Geyer, T., and Helms, V., (2004) Journal of Chemical Physics, vol. 121, p. 457-464, doi: 10.1063/1.1755668. Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged surface.
  4. Geyer, T., (2004) Journal of Physics B, vol. 37, p. 1215-1235, doi: 10.1088/0953-4075/37/6/007. Electron impact double ionization of helium from classical trajectory calculations.
  5. Flöck, D. and Helms, V., (2004) Biophysical Journal, vol. 87, p. 65-74, doi: 10.1529/biophysj.103.035261. A Brownian dynamics study: the effect of a membrane environment on an electron transfer system. doi:  10.1529/2Fbiophysj.108.0900183. Corrigendum 2008.
  6. Olkhova, E., Hutter, M.C., Lill, M.A., Helms, V., and Michel, H., (2004) Biophysical Journal, vol. 86, p. 1873-1889 doi:10.1016/S0006-3495(04)74254-X . Dynamic water networks in cytochrome c oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations.
  7. Gu, W., Rahi, S.J., and Helms, V., (2004) Journal of Physical Chemistry B, vol. 108, p. 5806-5814, doi: 10.1021/jp0376424. Solvation free energies and transfer free energies for amino acids from hydrophobic solution to water solution from a very simple residue model.
  8. Geyer, T., Gorba, C., and Helms, V., (2004) Journal of Chemical Physics, vol. 120, p. 4573-4580, doi: 10.1063/1.1647522. Interfacing Brownian dynamics simulations.
  9. Geyer, T. and Tannor, D.J., (2004) Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 37, p. 73-92, doi: 10.1088/0953-4075/37/1/005. A mapping approach to synchronization in the “Zajfman trap”: stability conditions and the synchronization mechanism.

2003

  1. Gorba, C., and Helms, V., (2003) Soft Materials, vol. 1, p. 185-20s, doi: 10.1081/SMTS-120021736. Diffusional dynamics of cytochrome c molecules in the presence of a charged surface.
  2. Zachariae, U., Helms, V., and Engelhardt, H., (2003) Biophysical Journal, vol. 85, p. 954-962, doi: 10.1016%2FS0006-3495(03)74534-2. Multistep mechanism of chloride translocation in a strongly anion-selective porin channel.
  3. Hutter, M.C., and Helms, V., (2003) International Journal of Quantum Chemistry, vol. 95, p. 479-486, doi: 10.1002/qua.10651. Mechanism of phosphoryl transfer in kinases investigated by semiempirical calculations.
  4. Hutter, M.C., (2003) Journal of Computer-Aided Molecular Design, vol. 17, p. 415-433, doi: 10.1023/A:1027359714663. Prediction of blood-brain barrier permeation using quantum chemically derived information
  5. Corrie, John E.T., Barth, A., Munasinghe, V. Ranjit N., Trentham, David R., Hutter, M.C., (2003) Journal of the American Chemical Society, vol. 125, p. 8546-8554, doi: 10.1021/ja034354c. Photolytic cleavage of 1-(2-nitrophenyl)ethyl ethers involves two parallel pathways and product release is rate-limited by decomposition of a common hemiacetal intermediate.
  6. de Groot, Bert L., Frigato,T., Helms, V., and Grubmüller, H., (2003) Journal of Molecular Biology, vol. 333, p. 279-293, doi: 10.1016/j.jmb.2003.08.003. The mechanism of proton exclusion in the aquaporin-1 water channel
  7. Geyer, T., and Rost, J.M., (2003) Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 36, L107-L112, doi: 10.1088/0953-4075/36/4/105/fulltext/. Dynamical stabilization of classical multi-electron targets against autoionization
  8. Krebs, J., Helms, V., Griesinger, C. und Carafoli, E., (2003) Helvetica Chimica Acta, vol. 86, p. 3875-3888, doi: 10.1002/hlca.200390325. The regulation of the calcium signal by membrane pumps.

2002

  1. Helms, V., (2002) EMBO Reports, vol. 3, p. 1133-1138, doi: 10.1093/embo-reports/kvf245. Attraction within the membrane – forces behind transmembrane protein folding and supramolecular compley assembly
  2. Hutter, M.C., Krebs, J., Meiler, J., Griesinger, C., Carafoli, E., and Helms, V., (2002), ChemBioChem, vol. 3, p. 1200-1208, doi: 10.1002/1439-7633(20021202)3:12%3C1200::AID-CBIC1200%3E3.0.CO;2-H. A structural model of the complex between phospholamban and the calcium pump of sarcoplasmic reticulum obtained by molecular mechanics.
  3. Deprez, E., Gill, E., Helms, V., Wade, R.C., and Hoa, G.H.H. (2002) The Journal of Inorganic Chemistry, vol. 91, p. 597-606, doi: 10.1016/S0162-0134(02)00467-1. Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin.
  4. Hutter, M.C. and Helms, V., (2002) ChemBioChem, vol. 3, p. 643-651, doi: 10.1002/1439-7633(20020703)3:7%3C643::AID-CBIC643%3E3.0.CO;2-L. The mechanism of phosphorylation of natural nucleosides and anti-HIV analogs by nucleoside diphosphate kinase is independent of their sugar substituents.
  5. Helms, V., (2002) Current Opinion in Structural Biology, vol. 12, p. 169-175, doi: .10.1016/S0959-440X(02)00305-6. Electronic excitations of biocmolecules studied by quantum chemistry
  6. Lill, M. and Helms, V., (2002) The Proceedings of the National Academy of Sciences, USA, vol. 99, p. 2778-2781, doi: 10.1073/pnas.052520799. Proton shuttle in green fluorescent protein studied by dynamic simulations.
  7. Floeck, D. and Helms, V. (2002) Proteins: Structure, Function, and Genetics, vol. 47, p. 75-85, doi: 10.1002/prot.10066. Protein-protein docking of electron transfer complexes – cytochrome c oxidase and cytochrome c

2001

  1. Kamberaj, H. and Helms, V., (2001) Computer Physics Communications, vol. 141, p.375-402, doi: 10.1016/S0010-4655(01)00434-9. Monte Carlo simulation of biomolecular systems with BIOMCSIM.
  2. Lill, M.A. and Helms, V., (2001) Journal of Chemical Physics, vol. 115, p. 7993-8005, doi: 10.1063/1.1407293. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)
  3. Lill, M.A. and Helms, V., (2001) Journal of Chemical Physics, vol. 115, p. 7985-7992, doi: 10.1063/1.1407292. Reaction rates for proton transfer over small barriers and connection to transition state theory
  4. Bartoschek, S., Burrman, G., Thauer, R.K., Geierstanger, B.H., Weyraus, J.P., Griesinger, C., Nilges, M., Hutter, M.C, and Helms, V., (2001) ChemBioChem, vol. 2, p. 530-541, doi: 10.1002/1439-7633(20010803)2:7/8%3C530::AID-CBIC530%3E3.0.CO;2-0. Re-face stereospecificity of methylenetetrahydromethanopterin dehydrogenases and methylenetertrahydrofolate dehydrogenases is predetermined by instrinsic properties of the sustrate.
  5. Yoo, H. Y., Boatz, J.A., Helms, V., McCannon, J.A., and Langhoff, P.W. (2001) Journal of Physical Chemistry B, vol. 105, p. 2850-2857, doi: 10.1021/jp003683d. Chromophore protonation states and the proton shuttle mechanism in green flourescent protein: inferences drawn from ab-initio theoretical studies of chemical structures and vibrational spectra.
  6. Lill, M.A. and Helms, V., (2001) Journal of Chemical Physics, vol. 114, p.1125-1132, doi: 10.1063/1.1332993. Compact parameter set for fast estimation of proton rates.

2000

  1. Hutter, M. C. and Helms, V., (2000) Protein Science, vol. 9, p. 2225-2231, doi: 10.1110/ps.9.11.2225. Phosporyl transfer by a concerted reaction mechanism in UMP/CMP-kinase.
  2. Lill, M. A., Hutter, M. C., and Helms V., (2000) Journal of Physical Chemistry A, vol. 104, p. 8283-8289, doi: 10.1021/jp001550m.  Accounting for environmental effects in ab initio calculations of proton transfer barriers.
  3. Das, B., Helms, V., Lounnas, V., and Wade R.C. (2000) Journal of Inorganic Biochemistry, vol. 81, p. 121-131, doi: 10.1016/S0162-0134(00)00095-7. Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation for camphor enantiomers bound to cytochrome P-450cam.
  4. Helms, V., Winstead, C., and Langhoff, P.W. (2000) Journal of Molecular Structure (Theochem), vol. 506, p. 179-189, doi: 10.1016/S0166-1280(00)00411-5. Low-lying electronic excitations of the green fluorescent protein chromosphore.
  5. Straatsma, T. P. and Helms, V. (2000) Molecular Dynamics on Parallel Computers, Proceedings of workshop in Juelich Feb. 8 – 10, 1999, World Scientific. p. 70-82. R. Esser, Grassberger, P., Grotendorst, J., and Lewerenz, M., editors, doi: 10.1142/9789812793768_0004.  The molecular dynamics module of NWChem – design and application in protein simulations.

1999

  1. Hutter, M. C. and Helms, V. (1999) Protein Science, vol. 8, p. 2728-2733, doi: 10.1110/ps.8.12.2728.  Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase.
  2. Weber, W., Helms, V., McCammon, J. A., and Langhoff, P. W. (1999) Proceedings of the National Academy of Sciences USA, vol 96, p. 6177-6182, doi: 10.1073/pnas.96.11.6177. Shedding light on the dark and weakly fluorescent states of green fluorescent proteins
  3. Baker, N. A., Helms, V., and McCammon, J. A. (1999) Proteins: Structure Function Bioinformatics, vol. 36, p. 447-453, doi: 10.1002/(SICI)1097-0134(19990901)36:4%3C447::AID-PROT8%3E3.0.CO;2-E. Dynamical properties of fasciculin-2.
  4. Tara, S., Helms V., Straatsma, T.P., and McCammon, J. A., (1999) Biopolymers, vol. 50, p. 347-359, doi: 10.1002/(SICI)1097-0282(19991005)50:4%3C347::AID-BIP1%3E3.0.CO;2-R. Molecular dynamics of mouse acetylcholinesterase complexed with huperzine A.
  5. Helms, V., Straatsma, T.P., and McCammon J. A.(1999) Journal of Physical Chemistry B, vol. 103, p. 3263-3269, doi: 10.1021/jp983120q. Internal dynamics of green fluorescent proteins.
  6. Huenenberger P., Helms, V., Narayana N., Taylor, S. S., and McCammon J. A. (1999) Biochemistry, vol. 38, p. 2358-2366, doi: 10.1021/bi982064g. Determinants of ligand binding to cAMP-dependent proteins kinase.