Personal tools
You are here: Home Publications Publications

Publications

Publications from the Helms lab, sorted by year.

2016

Nazarieh, M., Wiese, A., Will, T., Hamed, M, and Helms, V. (2016, accepted) BMC Systems Biology. Identification of key player genes in gene regulatory networks.

Akulenko, R., Merl, M., Helms, V. (2016, accepted) PLOS ONE. BEclear: batch effect detection and adjustment in DNA methylation data.

Barghash, A., Golob-Schwarzl, N., Helms, V., Haybaeck, J., Kessler, S.M. (2016, accepted) Oncotarget. Elevated expression of the IGF2 mRNA binding protein 2 (IGF2BP2/IMP2) is linked to short survival and metastasis in esophageal adenocarcinoma.

Janocha, S., Carius, Y., Hutter, M., Lancaster, C.R.D., Bernhardt, R. (2016) ChemBioChem, Vol. 17, p. 852-860. Crystal structure of CYP106A2 in substrate-free and substrate-bound form. DOI: 10.1002/cbic.201500524

Ahmad, M., Helms, V., Kalinina, O., and Lengauer, T. (2016, accepted) Journal of Physical Chemistry Part B: Biophysical Chemistry, Biomaterials, Liquids, and Soft Matter, B: Biophysical Chemistry and Biomolecules. The role of conformational changes in molecular recognitions.

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.

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, abstract online) J. Clinic. Microbiology., doi: 10.1128/JCM.03022-15. Detecting staphylococcus aureus virulence and resistance genes - a comparison of whole genome sequencing and DNA microarray technology.

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.

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

Thomann, A., Zapp, J., Hutter, M., Empting, M, Hartmann, R.W. (2015) Org. Biomol. Chem., Vol. 13, p. 10620-10630. Steering the azido–tetrazole equilibrium of 4-azidopyrimidines via substituent variation – implications for drug design and azide–alkyne cycloadditions.

Mohamed, R., Degac, J., Helms, V. (2015, published online) PLoS ONE. Composition of overlapping protein-protein and protein-ligand interfaces.

Degac, J., Winter, U., Helms, V. (2015) J. Chem. Inf. Model., Vol. 55, p. 1944-1952, doi: 10.1021/acs.jcim.5b00045 Graph-based clustering of predicted ligand-binding pockets on protein surface.

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, online in advance of print) Infection, Genetics and Evolution, 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.

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.

Barghash, A., Helms, V., Kessler, S. (2015) Scand J Immunol, 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.

Ulucan, Ö, Helms, V. (2015) J. Phys. Chem. B, Vol. 119, p. 10524-10530, doi:10.1021/acs.jpcb.5b05831 How hydrophilic proteins form non-specific complexes.

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, e1894; doi:10.1038/cddis.2015.241 IMP2/p62 induces genomic instability and an aggressive hepatocellular carcinoma phenotype.

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.

Ahmad, M., Helms, V., Lengauer, T., Kalinina, O. (2015) J. Chem. Theory Comput. Vol. 11, 2945-2957, doi: 10.1021/acs.jctc.5b00235 How molecular conformational changes affect changes in free energy.

Hamed, M., Spaniol, C., Zapp, A., Helms, V. (2015) BMC Genomics, 16(Suppl 5):S2, doi: 10.1186/1471-2164-16-S5-S2 Integrative network-based approach identifies key genetic elements in breast invasive carcinoma.

Hamed, M., Spaniol, C., Nazarieh, M., Helms, V. (2015) Nucl. Acids Res. doi: 10.1093/nar/gkv418  TFmiR: A web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.

Zapp, A., Helms, V., and Hamed, M. (2015) Proc. of the Second Intl. Conf. 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.

Miederer, A.-M., Alansary, D., Schwaer, G., Lee, P.-H., Jung, M., Helms, V., and Niemeyer, B.A. (2015) Nat. Commun., Vol. 6, 6899, doi: 10.1038/ncomms7899 A STIM2 splice variant negatively regulates store operated calcium entry.

Ahmad, M., Helms, V., Lengauer, T., and Kalinina, O. (2015) J. Chem. Theor. Comp., Vol. ,11, p. 1410-1418, doi: 10.1021/ct501161t Enthalpy-entropy compensation upon molecular conformational changes.

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.

Dudek, J., Pfeffer, S., Lee, P.-H., Jung, M., Cavalié, A., Helms, V., Förster, F., Zimmermann, R. (2015) Journal of Molecular Biology, 427, 1159-1175, doi: 10.1016/j.jmb.2014.06.011. Protein transport into human endoplasmic reticulum.

Kessler, S.M., Barghash, A., Laggai, S., Helms, V., and Kiemer, A.K. (2015) J Hepatol. Vol. 62, P. 977-979, doi: 10.1016/j.jhep.2014.10.046. Hepatic hepcidin expression is decreased in cirrhosis and HCC.


2014

Baowan, D. and Helms, V. (2014) J. Math. Chem., DOI 10.1007/s10910-014-0408-z. Quantitative study of BSA coating silica nanoparticle.

Khatri, Y., Hannemann, F., Girhard, M., Hutter, M., Urlacher, V.B., and Bernhardt, R. (2014, in press) FEBS J. A natural heme-signature variant of CYP267A1 from Sorangium cellulosum So ce56 executes diverse ω-hydroxylation.

Shanak, S. and Helms, V. (2014) J Chem Phys, Vol. 141, 22D512. 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.

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.

Chen, J., Lutsik, P., Akulenko, R., Walter, J., and Helms, V. (2014, accepted for GIW/ISCB) Journal of Bioinformatics and Computational Biology, V. 12, 1442005. AKSmooth: Human colon methylome profiling using low-coverage bisulfite sequencing data.

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. Mechanistic details for anthraniloyl transfer in PqsD: the initial step in HHQ biosynthesis.

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.

Ulucan, Ö., Tanushree, J., and Helms, V., (2014) Journal of Chemical Theory and Computation, Vol. 10., p. 3512-3524. Energetics of hydrophilic protein-protein association and the role of water.

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, 3, e02009. Transport of soluble proteins through the Golgi occurs by diffusion via continuities across cisternae.

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.

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.

Kessler, S.M., Laggai, S., Barghash, A., Helms, V., and Kiemer, A. (2014) Cancer Research, 74, p. 2903-2904, doi:10.1158/0008-5472.CAN-13-2852. Lipid metabolism signatures in NASH-associated HCC - letter.

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

Tretter, T., Pereira, F.P., Ulucan, Ö., Helms, V., Allan, S., Kalies, K.-U, and Römisch, K. (2013) BMC Cell Biology, 14, p. 56, doi:10.1186/1471-2121-14-56. ERAD and protein import defects in a sec61 mutant lacking ER-lumenal loop 7.

Barghash, A. and Helms, V. (2013) BMC Bioinformatics, 14:343. Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs.

Schaadt, N., Steinbach, A, Hartmann, R.W., and Helms, V. (2013) BMC Systems Biology, 7:81, doi:10.1186/1752-0509-7-81. Rule-based regulatory and metabolic model Quorum sensing in P. aeruginosa.

Will, T., Hutter, M., Jauch, J., and Helms, V. (2013). J. Comp. Chem., Vol. 34, p. 2485-2492. Batch tautomer Generation with MolTPC.

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). J. Biol. Chem., Vol. 288, p. 19471-19483. Conserved gating elements in TRPC4 and TRPC5 channels.

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.

Baowan, D., Peuschel, H., Kraegeloh, A.,  and Helms, V. (2013) J. Mol. Model., Vol. 19, p. 2459-2472. Energetics of liposomes encapsulating silica nanoparticles.

Walter, P., Metzger, J., Thiel, C., and Helms, V. (2013) PLoS One, Vol. 8, e58583 Predicting where small molecules bind at protein-protein interfaces.

Janocha, S., Zapp, J., Hutter, M., Kleser, M., Bohlmann, J., and Bernhardt, R. (2013) ChemBioChem, Vol. 14, p. 467-473. Resin acid conversion with CYP105A1: An enzyme with potential for the production of pharmaceutically relevant diterpenoids (Abstract).

Geyer, T.  (2013) Curr. Opin. Struct. Biol., Vol. 23, p. 218-223. Modeling metabolic processes between molecular and systems biology.

Zhukovsky, M.A., Lee, P.-H., Ott, A., and Helms, V. (2013) Proteins: Structure, Function, Bioinformatics, Vol. 81, p. 555-567. Putative cholesterol-binding sites in human immunodeficiency virus (HIV) coreceptors CXCR4 and CCR5.

2012

Ruffing, U., Akulenko, R., Bischoff, M., Helms, V., Herrmann, M., and von Müller, L. (2012) PLoS ONE. Matched-cohort DNA microarray diversity analysis of methicillin sensitive and methicillin resistant Staphylococcus aureus isolates from hospital admission patients.

Hamed, M., Ismael, S., Paulsen, M., and Helms, V. (2012) PLoS ONE, Vol.7, e50285. Cellular functions of genetically imprinted genes in human and mouse as annotated in the Gene Ontology.

Lee, P-H, Helms, V, and Geyer, T. (2012) J. Chem. Phys., Vol. 137, 145105. Coarse-grained Brownian dynamics simulations of protein translocation through nanopores.

Ulucan, Ö., Eyrisch, S., and Helms, V. (2012) Current Pharamceutical Design, Vol. 18, p. 4599-4606. Druggability of dynamic protein-protein interfaces. (Abstract)

Wagenmann, A. and Geyer, T. (2012) J. Chem. Theory Comput., Vol. 8, p. 4732–4745 Coarse-grained simulations of protein backbone dynamics. I: Local sterics define the dihedral angles.

Geyer, T. (2012) J. Chem. Phys., Vol. 137, 115101. Mixing normal and anomalous diffusion.

Geyer, T., Born, P., and Kraus, T. (2012) Phys. Rev. Lett., Vol. 109, 128302. Switching between crystallization and amorphous agglomeration of alkyl thiol-coated gold nanoparticles.

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. Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol: Fumarate reductase.

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. BIP-mediated closing of the Sec61 channel limits Ca2+ leakage from ER.

Walter, P., Ulucan, Ö., Metzger, J., and Helms, V. (2012) Current Bioinformatics, Vol. 7, p. 159-172. Bioinformatics of protein-protein interfaces and small molecule effectors. (Abstract)

Eyrisch, S., Medina-Franco, J.L., and Helms, V. (2012) Journal of Molecular Modeling, Vol. 18, p. 2031-2042. Transient pockets on XIAP-BIR2: towards the characterization of putative binding sites of small-molecule XIAP inhibitors.

Schaadt, N. and Helms, V. (2012) Biopolymers, Vol. 97, p. 558-567. Functional classification of membrane transporters and channels based on filtered TM/non-TM amino acid composition.

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. Human aldosterone synthase: Recombinant expression in E. coli and purification enables a detailed biochemical analysis of the protein on the molecular level.

Zimmer, M.J. and Geyer, T. (2012) J. Phys. Chem., Vol. 136, p. 125102. Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?

Kieser, M., Hannemann, F., Hutter, M., Zapp, J., and Bernhardt, R. (2012) Journal of Biotechnology, Vol. 157, p. 405-412. CYP105A1 mediated 3-hydroxylation of glimepiride and glibenclamide using a recombinant Bacillus megaterium whole-cell catalyst.

Lee, P.-H. and Helms, V. (2012) Proteins: Structure, Function, and Bioinformatics, Vol. 80, p. 421-432. Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues.

Ly, T.T.B., Khatri, Y., Zapp, J., Hutter, M.C. and Bernhardt, R. (2012) Applied Microbiology and Biotechnnology, Vol. 95, p. 123-133. CYP264B1 from Sorangium cellulosum So ce56: a fascinating norisoprenoid and sesquiterpene hydroxylase.

2011

Helms, V. and Gu, W. (2011). Proton travel in green fluorescent protein (Abstract). In: Jung, G. (Ed.) Fluorescent Proteins 1. Springer,  p. 171-181.

Hutter, M.C. (2011) Journal of Chemical Information and Modeling, Vol. 51, p. 3099-3104. Determining the degree of randomness of descriptors in linear regression equations with respect to the data size.

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.

Carbon-Mangels, M. and Hutter, M.C. (2011) Journal of Molecular Informatics, Vol. 30, p. 885-895. Selecting relevant descriptors for classification by Bayesian estimates: A comparison with decision trees and support vector machines approaches for disparate data sets.

Geyer, T. (2011) BMC Biophysics, Vol. 4:7. Many-particle Brownian and Langevin dynamics simulations with the Brownmove package.

Hutter, M.C. (2011) Future Medicinal Chemistry, Vol. 3, p. 485-501. Graph-based similarity concepts in virtual screening (Abstract).

Singh, N.K., Goodman, A., Walter, P., Helms, V., and Hayat, S. (2011) Biochimica et Biophysica Acta - Proteins and Proteomics, V. 1814, p. 664-670. TMBHMM: A frequency-profile based HMM for predicting the topology of transmembrane beta barrel proteins and the exposure status of transmembrane residues.

Ahmad, M., Gu, W., Geyer, T., and Helms, V. (2011) Nature Communications, Vol. 2, Article no. 261. Adhesive water networks facilitate binding of protein interfaces (Abstract).

Hayat, S., Park, Y., and Helms, V. (2011). Computational Biology and Chemistry, Vol. 35, p. 96-107. Statistical analysis and exposure status classification of transmembrane beta barrel residues.

Zimmermann, R., Eyrisch, S., Ahmad, M., and Helms, V. (2011) BBA - Biomembranes, Vol. 1808, p. 912-924. Protein translocation across the ER membrane.

Hayat, S., Walter, P., Park, Y., and Helms, V. (2011) Journal of Bioinformatics and Computational Biology Vol. 9, p. 43-65. Prediction of the exposure status of transmembrane beta barrel residues from protein sequence (Abstract).

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. Interaction of calmodulin with Sec61 limits Ca2+ leakage from the endoplasmic reticulum.

Gu, W., Zhou, B., Geyer, T., Hutter, M., Fang, H., and Helms, V. (2011) Angewandte Chemie (DE) Vol. 123, p. 794-797. Design eines steuerbaren molekularen Protonenkanals. Angewandte Chemie International Edition (EN) Vol. 50, p. 768-771. Design of a gated molecular proton channel.

Jusoh, S.A. and Helms, V. (2011) BBA Biomembranes,Vol. 1808, p. 1040-1049. Helical integrity and microsolvation of transmembrane domains from Flaviviridae envelope glycoproteins.

2010

Hutter, B., Bieg, M., Helms, V., and Paulsen, M. (2010) BMC Genomics, 11:649. Imprinted genes show unique patterns of sequence conservation.

Geyer, T., Mol, X., Blaß, S., and Helms, V. (2010) PLoS ONE 5(11): e14070. Bridging the gap: Linking molecular simulations and systemic descriptions of cellular compartments.

Kathri, Y., Girhard, A., Romankiewicz, A., Ringle, M., Hannemann, F., Urlacher, V.B., Hutter, M., and Bernhardt, R. (2010). Appl. Microbiol. Biotechnol., Vol. 88, p. 485-495. Regioselective Hydroxylation of Norisoprenoids by CYP109D1 from Sorangium cellulosum So ce56.

Hutter, M. (2010) ChemMedChem, Vol. 5, p. 306-307. Book review: Molecular Descriptors for Chemoinformatics (2nd. Ed.).

Schaadt, N., Christoph, J., and Helms, V. (2010) Journal of Chemical Information and Modeling, Vol. 50, p. 1899-1905. Classifying substrate specifities of membrane transporters from arabidopsis thaliana.

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. Atomistic simulation of water percolation and proton hopping in nafion fuel cell membrane.

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.

Wang, L., Siu, S., Gu, W., and Helms, V. (2010) Biopolymers, Vol. 93, p. 977-985. Downhill binding energy surface of the barnase-barstar complex.

Hutter, B., Bieg, M. Helms, V., and Paulsen, M. (2010) BMC Evolutionary Biology, 10:116. Divergence of imprinted genes during mammalian evolution.

Jusoh, S.A., Welsch, C., Siu, S.W.I., Böckmann, R.A., and Helms, V. (2010) Journal of Molecular Modelling, Vol. 16, p. 1625-1637. Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus.

Berwanger, A., Eyrisch, S., Schuster, I., Helms, V., and Bernhardt, R. (2010) Journal of Inorganic Biochemistry, Vol. 104, 118-125. Polyamines: Naturally occurring small molecule modulators of electrostatic protein-protein interactions.

2009

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.

Winter, U. and Geyer, T. (2009) Journal of Chemical Physics, 131, 104102. Coarse grained simulations of a small peptide: Effects of finite damping and hydrodynamic interactions.

Erdmann, F., Jung, M., Eyrisch, S., Lang, S., Helms, V., Wagner, R., and Zimmermann, R. (2009) FEBS Letters, Vol. 583, p. 2359-2364. Lanthanum ions inhibit the mammalian Sec61 complex in its channel dynamics and protein transport activity. (Abstract)

Wang, L., Stumm, B., and Helms, V. (2009) Journal of Computational Chemistry, Vol. 31, p. 847-854. Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.

Krier, M. and Hutter, M. C. (2009) Journal of Chemical Information and Modeling, Vol. 49, p. 1280-1297. Bioisosteric similarity of molecules based on structural alignment and observed chemical replacements in drugs.

Geyer, T. and Winter, U. (2009) Journal of Chemical Physics, Vol. 130, 114905. An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations.

Lauck, F., Helms; V., and Geyer, T. (2009) Journal of Chemical Theory and Computation, Vol. 5, p. 641-648. Graph measures reveal fine structure of complexes forming in multiparticle simulations.

Gu, W. and Helms, V. (2009) Journal of the American Chemical Society, Vol. 131, p. 2080-2081. Tightly connected water wires facilitate fast proton uptake at the proton entrance of proton pumping proteins.

Eyrisch, S. and Helms, V. (2009) Journal of Computer-Aided Molecular Design, Vol. 23, p. 73-86. What induces pocket openings on protein surface patches involved in protein-protein interactions?

Hutter, M. C. (2009) Current Medicinical Chemistry, Vol. 16, p. 189-202. In Silico Prediction of Drug Properties.

Spaar, A., Flöck, D., and Helms, V. (2009) Biophysical Journal, Vol. 96, p. 1721-1732. Association of cytochrome c with membrane-bound cytochrome c oxidase proceeds parallel to the membrane rather than in bulk solution.

2008

Schluttig, J., Alamanova, D., Helms, V., and Schwarz, U. S. (2008) Journal of Chemical Physics, Vol. 129, 155106. Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches.

Hutter, B., Paulsen, M., and Helms, V. (2008) OMICS: A Journal of Integrative Biology. Identifying CpG islands by different computational techniques (Abstract).

Eyrisch, S. and Helms, V. (2008) GCB 2008. Designing Binding Pockets on Protein Surfaces using the A* Algorithm.

Helms, V. (2008) Principles of Computational Cell Biology - From Protein Complexes to Cellular Networks. Wiley-VCH.

Ahmad, M., Gu, W., and Helms, V. (2008), Angewandte Chemie, Vol. 120, p. 7738-7742. Mechanismus der schnellen Peptiderkennung durch SH3-Domänen (DE). Angewandte Chemie International Edition, Vol. 47, p. 7626-7630. Mechanism of Fast Peptide Recognition by SH3 Domains (EN).

Park, Y. and Helms, V. (2008) Bioinformatics, Vol. 24, p. 1819-1820. MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon.

Park, Y. and Helms, V. (2008) Bioinformatics, Vol. 24, p. 1271-1277. Prediction of the translocon-mediated membrane insertion free energies of protein sequences.

Schneider, N., Jäckels, C., Andres, C., and Hutter, M. (2008) Journal of Chemical Information and Modeling, Vol. 48, p. 613-628. Gradual in Silico Filtering for Druglike Substances.

2007

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.

Gu, W. and Helms, V. (2007) ChemPhysChem, Vol. 8, p. 2445-2451. Different Protonation Equilibria of 4-Methylimidazole and Acetic Acid.

Geyer, T. (2007) Biophysical Journal, Vol. 93, p. 4374-4381. On the effects of PufX on the absorption properties of the light-harvesting complexes of Rhodobacter sphaeroides.

Park, Y., Hayat, S., and Helms, V. (2007) BMC Bioinformatics, 8:302. Prediction of the Burial Status of Transmembrane Residues of Helical Membrane Proteins.

Eyrisch, S. and Helms, V. (2007) Journal of Medicinal Chemistry, Vol. 50, p. 3457-3464. Transient Pockets on Protein Surfaces Involved in Protein-Protein Interaction.

Walter, P., Ansari, S., and Helms, V. (2007) Journal of Integrative Bioinformatics, 4(1):50. The ABC (Analysing Biomolecular Contacts) Database.

Geyer, T., Lauck, F., and Helms, V. (2007) Journal of Biotechnology, Vol. 129, p. 212-228. Molecular Stochastic Simulations of Chromatophore Vesicles from Rhodobacter Sphaeroides.

Park, Y. and Helms, V. (2007) Bioinformatics, Vol. 23, p. 701-708. On the Derivation of Propensity Scales for Predicting Exposed Transmembrane Residues of Helical Membrane Proteins.

Hutter, M.C.. (2007) Journal of Chemical Information and Modeling, Vol. 47, p. 186-104. Separating Drugs from Non-Drugs: A Statistical Approach Using Atom Pair Distributions.

Gu, W., Frigato, T., Straatsma, T.P., and Helms, V. (2007) Angewandte Chemie, Vol. 119, p. 2997-3001 Dynamisches Protonengleichgewicht der in Wasser gelösten Essigsäure (DE). Angewandte Chemie International Edition, Vol. 46, p. 2939-2943 Dynamic Protonation Equilibrium of Solvated Acetic Acid (EN).

Helms, V. (2007) ChemPhysChem, Vol. 8, p. 23-33. Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules.

2006

Park, Y. and Helms, V. (2006) Biopolymers, Vol. 83, 389-399. How Strongly do Sequence Conservation Patterns and Empirical Scales Correlate with Exposure Patterns of Transmembrane Helices of Membrane Proteins?

Geyer, T. and Helms, V. (2006) Biophysical Journal, Vol. 91, p. 927-937. Reconstruction of a Kinetic Model of the Chromatophore Vesicles from Rhodobacter Sphaeroides.

Geyer, T. and Helms, V. (2006) Biophysical Journal, Vol. 91, p. 921-926. A Spatial Model of the Chromatophore Vesicles of Rhodobacter Sphaeroides and the Position of the Cytochrome bc1 Complex.

Hutter, B., Helms, V., and Paulsen, M. (2006) Genomics, Vol. 88, p. 323-332. Tandem Repeats in the CpG Islands of Imprinted Genes.

Spaar, A. and Helms, V. (2006) Journal of Non-Crystalline Solids, Vol. 352, p. 4437-4444. Ionic Strength Effects on the Association Funnel of Barnase and Barstar Investigated by Brownian Dynamics Simulations.

Gepp, M. and Hutter, M.C. (2006) Bioorganic & Medicinal Chemistry, Vol. 14, p. 5325-5332. Determination of hERG Channel Blockers Using a Decision Tree.

Park, Y. and Helms, V. (2006) Proteins: Structure, Function, and Bioinformatics, Vol. 64, p. 895-905. Assembly of Transmembrane Helices of Simple Polytopic Membrane Proteins from Sequence Conservation Patterns.

Hutter, M.C. (2006) Chemical Physics, Vol. 326, p. 240-245. Stability of the Guanine-Cytosine Radical Cation in DNA Base Pairs Triplets (Abstract).

Andres, C. and Hutter, M.C. (2006) QSAR & Combinatorial Science, Vol.25, p. 305-309. CNS Permeability of Drugs Predicted by a Decision Tree.

Herzog, E., Frigato, T., Helms, V., and Lancaster, C.R.D. (2006) Journal of Computational Chemistry, Vol. 27, p. 1534-1547. Energy Barriers of Proton Transfer Reactions between Amino Acid Side Chain Analogs and Water from ab initio Calculations.

Spaar, A., Dammer, C., Gabdoulline, R.R., Wade, R.C., and Helms, V. (2006) Biophysical Journal, Vol. 90, p. 1913-1924. Diffusional Encounter of Barnase and Barstar.

2005

Helms, V., Hutter, M, and Gu, W. (2005) Magazin Forschung, p. 28-32. Was hat das Eiweiß in einem Computer zu suchen?

Geyer, T. and Tannor, D.J. (2005) Journal of Physics B: Atomic, Molecular, and Optical Physics, Vol. 38, p. 3423-2446. A Mapping Approach to Synchronization in the "Zaifman Trap": II. The observed Bunch

Staritzbichler, R., Gu, W. and Helms, V. (2005) Journal of Physical Chemistry B, Vol. 109 (140), p. 19000-19007. Are Solvation Free Energies of Homogeneous Helical Peptides Additive?

Gu, W. and Helms, V. (2005) Biochimica and Biophysica Acta (Proteins and Proteomics), Vol. 1754, p. 232-238. Dynamical Binding of Proline-rich Peptides to their Recognition Domains (Abstract).

Olkhova, E., Helms, V., and Michel, H. (2005) Biophysical Journal, Vol. 89, p. 2324 - 2331. Titration Behaviour of Residues at the Entrance of the D-pathway of Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Continuum Electrostatic Calculations.

Piotukh, K., Gu, W., Kofler, M., Helms, V., and Freund, C. (2005) Journal of Biological Chemistry, Vol. 280 (25), p. 23668-23674. Cyclophilin A Binds to Linear Peptide Motifs Containing a Consensus that is Present in many Human Proteins.

Spaar, A. and Helms, V. (2005) Journal of Chemical Theory and Computation, Vol. 1 (4), p. 723-736. Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase: Barstar

Gu, W., Kofler, W., Antes, I., Freund, C., and Helms, V. (2005) Biochemistry, Vol. 44, p. 6404-6415. Alternative Binding Modes of Proline-rich Peptides Binding to the GYF-Domain.

Ansari, S. and Helms, V. (2005) Proteins: Structure, Function, and Bioinformatics, Vol. 61 (2), p. 344 - 355. Statistical Analysis of Predominantly Transient Protein-Protein Interfaces

Shakya, S.K., Gu, W., and Helms, V. (2005) Biopolymers, Vol. 78 (1), p. 9-20. Molecular Dynamics Simulation of Truncated Bovine Adrenodoxin.

2004

Hutter, M.C. and Hartmann, R.W., (2004) QSAR & Combinatorial Science, Vol. 23 (6), p. 406-415. QSAR of Human Steroid 5α-Reductase Inhibitors: Where are the differences between Isoenzyme Type 1 and 2?.

Park, Y., Elsner, M., Staritzbichler, R., and Helms, V., (2004) Proteins: Structure, Function, and Bioinformatics, Vol. 57 (3), p. 577-585. Novel Scoring Function for Modeling Structures of Oligomers of Transmembrane alpha-helices.

Gorba, C., Geyer, T., and Helms, V., (2004) Journal of Chemical Physics, Vol. 121, p. 457-464. Brownian Dynamics Simulations of Simplified Cytochrome c Molecules in the Presence of a Charged Surface.

Geyer, T., (2004) Journal of Physics B, Vol. 37 (6), p. 1215-1235. Electron Impact Double Ionization of Helium from Classical Trajectory Calculations.

Flöck, D. and Helms, V., (2004) Biophysical Journal, Vol. 87, p. 65-74. A Brownian Dynamics Study: The Effect of a Membrane Environment on an Electron Transfer System. Corrigendum 2008.

Olkhova, E., Hutter, M.C., Lill, M.A., Helms, V., and Michel, H., (2004) Biophysical Journal, Vol. 86, p. 1873-1889. Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus Denitrificans Investigated by Molecular Dynamics Simulations.

Gu, W., Rahi, S.J., and Helms, V., (2004) Journal of Physical Chemistry B, Vol. 108, p. 5806-5814. Solvation Free Energies and Transfer Free Energies for Amino Acids from Hydrophobic Solution to Water Solution from a Very Simple Residue Model.

Geyer, T., Gorba, C., and Helms, V., (2004) Journal of Chemical Physics, Vol. 120, p. 4573-4580. Interfacing Brownian Dynamics Simulations.

Geyer, T. and Tannor, D.J., (2004) Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 37 (1), p. 73-92. A Mapping Approach to Synchronization in the "Zajfman Trap": Stability Conditions and the Synchronization Mechanism.

2003

Gorba, C., and Helms, V., (2003) Soft Materials, Vol. 1, p. 187-204. Diffusional Dynamics of Cytochrome c Molecules in the Presence of a Charged Surface.

Zachariae, U., Helms, V., and Engelhardt, H., (2003) Biophysical Journal, Vol. 85, p. 954-962. Multistep Mechanism of Chloride Translocation in a Strongly Anion-Selective Porin Channel.

Hutter, M.C., and Helms, V., (2003) International Journal of Quantum Chemistry, Vol. 95, p. 479-486. Mechanism of Phosphoryl Transfer in Kinases Investigated by Semiempirical Calculations.

Hutter, M.C., (2003) Journal of Computer-Aided Molecular Design, Vol. 17 (7), p. 415-433. Prediction of Blood-Brain Barrier Permeation Using Quantum Chemically Derived Information

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 (28), p. 8546-8554. 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

de Groot, Bert L., Frigato,T., Helms, V., and Grubmüller, H., (2003) Journal of Molecular Biology, Vol. 333, p. 279-293. The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

Geyer, T., and Rost, J.M., (2003) Journal of Physics B: Atomic, Molecular and Optical Physics, Vol. 36, L107-L112. Dynamical Stabilization of Classical Multi-Electron Targets against Autoionization

Krebs, J., Helms, V., Griesinger, C. und Carafoli, E., (2003) Helv. Chim. Acta, Vol. 86, p. 3875-3888. The Regulation of the Calcium Signal by Membrane Pumps


2002

Helms, V., (2002) EMBO Reports, Vol. 3, p. 1133-1138. Attraction within the Membrane - Forces behind transmembrane protein folding and supramolecular compley assembly

Hutter, M.C., Krebs, J., Meiler, J., Griesinger, C., Carafoli, E., and Helms, V., (2002), ChemBioChem., Vol. 3 (12), p. 1200-1208 A Structural Model of the Complex between Phospholamban and the Calcium Pump of Sarcoplasmic Reticulum obtained by Molecular Mechanics

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. Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytochromes P450cam and P450lin

Hutter, M.C. and Helms, V., (2002) ChemBioChem, Vol. 3 (7),p. 643-651. The Mechanism of Phosphorylation of Natural Nucleosides and Anti-HIV Analogs by Nucleoside Diphosphate Kinase is Independent of their Sugar Substituents.

Helms, V., (2002) Current Opinion in Structural Biology, Vol. 12, p. 169-175. Electronic Excitations of Biocmolecules Studied by Quantum Chemistry

Lill, M. and Helms, V., (2002) The Proceedings of the National Academy of Sciences, USA, Vol. 99 (5), p. 2778-2781. Proton Shuttle in Green Fluorescent Protein Studied by Dynamic Simulations

Floeck, D. and Helms, V. (2002) Proteins: Structure, Function, and Genetics, Vol. 47 (1), p. 75-85. Protein-Protein Docking of Electron Transfer Complexes - Cytochrome c Oxidase and Cytochrome c


2001

Kamberaj, H. and Helms, V., (2001) Computer Physics Communications, Vol. 141 (3), p.375-402. Monte Carlo simulation of biomolecular systems with BIOMCSIM

Lill, M.A. and Helms, V., (2001) Journal of Chemical Physics, Vol. 115, p. 7993-8005. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)

Lill, M.A. and Helms, V., (2001) Journal of Chemical Physics, Vol. 115, p. 7985-7992 Reaction rates for proton transfer over small barriers and connection to transition state theory

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. Re-face stereospecificity of methylenetetrahydromethanopterin dehydrogenases and methylenetertrahydrofolate dehydrogenases is predetermined by instrinsic properties of the sustrate.

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. 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.

Lill, M.A. and Helms, V., (2001) Journal of Chemical Physics, Vol. 114, p.1125-1132 Compact parameter set for fast estimation of proton rates


2000

Hutter, M. C. and Helms, V., (2000) Protein Science, Vol. 9,p. 2225-2231, Phosporyl transfer by a concerted reaction mechanism in UMP/CMP-kinase.

Lill, M. A., Hutter, M. C., and Helms V., (2000) Journal of Physical Chemistry A, Vol. 104, p. 8283-8289Accounting for Environmental Effects in Ab Initio Calculations of Proton Transfer Barriers.

Das, B., Helms, V., Lounnas, V., and Wade R.C. (2000) Journal of Inorganic Biochemistry Vol. 81,p. 121-131.Multicopy Molecular Dynamics Simulations Suggest How to Reconcile Crystallographic and Product Formation for Camphor Enantiomers Bound to Cytochrome P-450cam

Helms, V., Winstead, C., and Langhoff, P.W. (2000) Journal of Molecular Structure (Theochem), Vol. 506, p. 179-189. Low-lying electronic excitations of the Green Fluorescent Protein chromosphore.

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. The Molecular Dynamics Module of NWChem - Design and Application in Protein Simulations


1999

Hutter, M. C. and Helms, V. (1999) Protein Science, Vol. 8, p. 2728-2733, Influence of key residues on the reaction mechanism of the cAMP-dependent protein kinase.

Weber, W., Helms, V., McCammon, J. A., and Langhoff, P. W. (1999) Proc. Natl. Acad. Sci. USA, Vol 96, p. 6177-6182. Shedding light on the dark and weakly fluorescent states of green fluorescent proteins

Baker, N. A., Helms, V., and McCammon, J. A. (1999) Proteins: Str. Fn. Gen., Vol. 36, p. 447-453.Dynamical Properties of Fasciculin-2

Tara, S., Helms V., Straatsma, T.P., and McCammon, J. A., (1999) Biopolymers, Vol. 50, p. 347-359.Molecular Dynamics of Mouse Acetylcholinesterase Complexed with Huperzine A.

Helms, V., Straatsma, T.P., and McCammon J. A.(1999) Journal of Physical Chemistry B, Vol. 103, p. 3263-3269. Internal dynamics of green fluorescent proteins.

Huenenberger P., Helms, V., Narayana N., Taylor, S. S., and McCammon J. A. (1999) Biochemistry, Vol. 38, p. 2358-2366 Determinants of Ligand Binding to cAMP-dependent Proteins Kinase.

Document Actions
« September 2017 »
September
MoTuWeThFrSaSu
123
45678910
11121314151617
18192021222324
252627282930