Publications

2007

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

Eyrisch, S. and Helms, V. (2007, accepted) Journal of Medicinal Chemistry. 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, Dynamisches Protonierungsgleichgewicht der in Wasser gelösten Essigsäure, Vol. 46, p. 2939-2943, (German version); Dynamic Protonation Equilibrium of Solvated Acetic Acid, Vol. 119, p. 2997-3001 (English version).

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?

Helms, V. (2006) ChemPhysChem, Vol. 8, p. 23-33. Protein Dynamics Tightly Connected to the Dynamics of Surrounding and Internal Water Molecules.

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) Biophyical Journal, Vol. 90, p. 1913-1924. Diffusional Encounter of Barnase and Barstar.

2005

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.

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.